From c6b072ae1c4fda8819506c8032f3698320e1773e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 15 Sep 2024 13:59:26 +0000 Subject: [PATCH] Add changes --- data.js | 4758 ++++++++++++++++++++++++++-------------------------- skips.json | 312 ++-- 2 files changed, 2535 insertions(+), 2535 deletions(-) diff --git a/data.js b/data.js index a78b818..022230a 100644 --- a/data.js +++ b/data.js @@ -3,11 +3,11 @@ var data = { "config_readme": null, "data_format": 2, - "description": "Code to generate the data and website for Rat TWAS Hub", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbtujbe3p/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "daniel-munro/rat-twas-hub", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbtujbe3p/Snakefile\", line 9, in \u003cmodule\u003e\n traits_df = pd.read_csv(\"data/traits.par\", sep=\"\\t\", index_col=1)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027data/traits.par\u0027\n\n", + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\": Keyword \"output\" at line 50 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\": Keyword \"input\" at line 71 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "radio1988/ccount", + "latest_release": "v0.2", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n\n File \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/scripts/ccount/snake/get_samples.py\", line 42, in get_samples\n SAMPLES=os.listdir(DATA_DIR)\n ^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027data/\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -15,37 +15,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725419933.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure the workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to yout needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eAssembly units sheet\u003c/h1\u003e\u003ca id=\"user-content-assembly-units-sheet\" class=\"anchor\" aria-label=\"Permalink: Assembly units sheet\" href=\"#assembly-units-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd assemblies to file \u003ccode\u003econfig/assembly_units.txt\u003c/code\u003e. This file is tab-separated file with two columns: \u003ccode\u003eassembly_id\u003c/code\u003e and \u003ccode\u003epath\u003c/code\u003e. The former is the alias of the assembly and the latter the path of .fasta assembly file. Both columns are mandatory and cannot be duplicated.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eTarget variants sheet\u003c/h1\u003e\u003ca id=\"user-content-target-variants-sheet\" class=\"anchor\" aria-label=\"Permalink: Target variants sheet\" href=\"#target-variants-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd target variants where you want to design the Tm-shit primers in the file \u003ccode\u003econfig/target_variants.txt\u003c/code\u003e. This file is tab-sepparated. In the column \u003ccode\u003evariant_id\u003c/code\u003e specify a unique name to identify the variant. The \u003ccode\u003eassembly_id\u003c/code\u003e uses the \u003ccode\u003eassembly_id\u003c/code\u003e specified in \u003ccode\u003econfig/assembly_units.txt\u003c/code\u003e and the columns \u003ccode\u003echrom\u003c/code\u003e and \u003ccode\u003epos\u003c/code\u003e define the physical position on the given assembly. In columns \u003ccode\u003eref\u003c/code\u003e and \u003ccode\u003ealt\u003c/code\u003e is stored the reference and alternative allele that the primers going to genotype.\u003c/p\u003e\n", - "data_format": 2, - "description": "A workflow intended to perform the design of tm-shift primers for genotype SNPs ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/sequence_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_selection.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Bioinflows-Bioversity-CIAT/tm-shift_designer", - "latest_release": "v0.1.0", - "linting": "Lints for snakefile /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/common.smk:\n * Absolute path \"/*.txt\" in line 148:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk:\n * Absolute path \"/{variant_id}_{allele}_{primer_id}.txt\" in line 76:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 11:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 11:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule extract_roi (line 1, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/sequence_processing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_alternative_roi (line 37, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/sequence_processing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_primer3_input (line 1, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule build_primer3_input_primercheck (line 50, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule primer3_search_alt (line 114, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule primer3_search (line 164, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule select_primers (line 1, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_selection.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": null, - "report": false, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1725397842.0 + "updated_at": 1725552375.0 }, { "config_readme": null, "data_format": 2, - "description": "In this repository all the codes to run the master\u0027s thesis is hosted", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpc0upxkk0/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Jerkur123/MA", + "description": "Snakemake workflow for Whole Genome analysis with minION", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\#\u0027\n[DEBUG] In file \"/tmp/tmp_mylcuqi/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "lisosome/minION_snakemake", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpc0upxkk0/Snakefile\", line 6, in \u003cmodule\u003e\n from tqdm import tqdm\n\nModuleNotFoundError: No module named \u0027tqdm\u0027\n\n", + "linting": "/tmp/tmp_mylcuqi/Snakefile:70: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n \"ont-guppy-gpu/6.5.7\",\n/tmp/tmp_mylcuqi/Snakefile:86: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n export CUDA_VISIBLE_DEVICES=0\n/tmp/tmp_mylcuqi/Snakefile:203: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n resources:\n/tmp/tmp_mylcuqi/Snakefile:241: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n/tmp/tmp_mylcuqi/Snakefile:294: SyntaxWarning: invalid escape sequence \u0027\\#\u0027\n/tmp/tmp_mylcuqi/Snakefile:303: SyntaxWarning: invalid escape sequence \u0027\\#\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp_mylcuqi/Snakefile\", line 4, in \u003cmodule\u003e\n raw_data = config[\"paths\"][\"rawdata\"] # path of the folder containing the data transferred from the minION\n ^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027paths\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -53,16 +32,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725390671.0 + "updated_at": 1724849960.0 }, { "config_readme": null, "data_format": 2, - "description": "My PhD thesis at the University of Zurich. It contains the three papers making up the thesis, as well as the dissertation itself.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6t8034lz/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "stanmart/phd-thesis", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6t8034lz/Snakefile\", line 2, in \u003cmodule\u003e\n from src.util.makeutils import find_input_files\n\n File \"/tmp/tmp6t8034lz/src/util/makeutils.py\", line 7, in \u003cmodule\u003e\n import typer\n\nModuleNotFoundError: No module named \u0027typer\u0027\n\n", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/0.0_angsd_pipeline.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/2.0_downsampling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/1.0_landscape_modeling.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "zjnolen/polyommatini-landcover-diversity", + "latest_release": "v1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/Snakefile\", line 10, in \u003cmodule\u003e\n include: \"rules/0.0_angsd_pipeline.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/0.0_angsd_pipeline.smk\", line 15, in \u003cmodule\u003e\n use rule all from angsd as angsd_all\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 2147, in decorate\n module.use_rules(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/modules.py\", line 104, in use_rules\n self.workflow.include(snakefile, overwrite_default_target=True)\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"https://:ghs_00HNn0swOh4G4RhVL3lARFbuHBWzOJ0b5Fl6@raw.githubusercontent.com/zjnolen/PopGLen/v0.2.0/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n from dataclasses import dataclass, field\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"https://:ghs_00HNn0swOh4G4RhVL3lARFbuHBWzOJ0b5Fl6@raw.githubusercontent.com/zjnolen/PopGLen/v0.2.0/workflow/rules/common.smk\", line 95, in \u003cmodule\u003e\n from snakemake.wrapper import wrapper\n ^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027reference\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -70,16 +49,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725389641.0 + "updated_at": 1724838425.0 }, { "config_readme": null, "data_format": 2, - "description": "Cleaning transcriptome annotations with ab initio assemblers", - "formatting": null, - "full_name": "isaacvock/AnnotationCleaner", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpvy6e55xv/workflow/rules/common.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 102:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\n", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 64 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 144 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"input\" at line 180 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 194 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/variables.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/input.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile\": \n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/read_orientation.smk\": Keyword \"shell\" at line 80 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/read_orientation.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/alleles.smk\": Keyword \"shell\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/alleles.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "kilpert/FAME3_analyses", + "latest_release": "v0.2", + "linting": "/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile:189: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n \n/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile:190: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n \nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n from Bio.Seq import Seq\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -87,76 +66,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725388992.0 + "updated_at": 1724832178.0 }, { "config_readme": null, "data_format": 2, - "description": "A pipeline to gather snoRNA and RBP interactions to perform a snoRNA-RBP interaction network analysis.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/rules/interactions.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[ERROR] In file \"/tmp/tmp_mamoktv/workflow/rules/filter.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 39)\n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/rules/filter.smk\": \n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/rules/cytoscape.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "scottgroup/snoFlake", + "description": "Workflow for massive analysis of internet images", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[WARNING] In file \"/tmp/tmp63i3npu6/Snakefile\": Keyword \"input\" at line 46 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp63i3npu6/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "eamonnbell-dur/maoii-workflow", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp_mamoktv/workflow/Snakefile\", line 17, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027resources/filtered_genes/sig_exp_CD_snoRNAs.tsv\u0027\n\n", + "linting": "/tmp/tmp63i3npu6/Snakefile:6: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n regionid=\"\\d+\"\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp63i3npu6/Snakefile\", line 3, in \u003cmodule\u003e\n HTTP = HTTPRemoteProvider()\n ^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/remote/__init__.py\", line 8, in __init__\n raise NotImplementedError(\n\nNotImplementedError: Remote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1725371775.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eUnit sheet\u003c/h1\u003e\u003ca id=\"user-content-unit-sheet\" class=\"anchor\" aria-label=\"Permalink: Unit sheet\" href=\"#unit-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd samples to \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003eunit_name\u003c/code\u003e. This can be a running number, or an actual run, lane or replicate id (for now this is not functional as we want to make this workflow to comply with the dna-seq-varlociraptor-workflow because we will import this wokrflow as a module there. For that reason, it\u0027s not called \u003ccode\u003esamples.tsv\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003esample_name\u003c/code\u003e, which associates it with the biological sample it comes from. This information is used to merged all the units of a sample before read mapping and duplicate marking.\u003c/li\u003e\n\u003cli\u003eFor each unit, you need to specify:\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e for paired end reads. These can point to any FASTQ files on your system.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n", - "data_format": 2, - "description": "A Snakemake workflow for typing and quantifying HLAs using Orthanq.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/rules/orthanq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/rules/preparation.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "orthanq/orthanq-hla-quantification", - "latest_release": null, - "linting": "Workflow defines that rule get_genome is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule genome_faidx is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this).\nLints for rule get_hla_genes_and_xml (line 65, /tmp/tmpr3qlotoe/workflow/rules/preparation.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule unzip_xml (line 94, /tmp/tmpr3qlotoe/workflow/rules/preparation.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_pangenome (line 156, /tmp/tmpr3qlotoe/workflow/rules/preparation.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": null, - "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1725355823.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": "ABComp : Assembly Polishing and Bacterial Whole-genome Comparison Pipeline for Multi-group Clinical Isolates", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3mur9azr/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "young5454/ABComp", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp3mur9azr/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 82:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule polypolish (line 375, /tmp/tmp3mur9azr/workflow/Snakefile):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule busco (line 458, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule quast (line 529, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prokka_ref (line 577, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule prokka_strain (line 653, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule roary_strain_ref_pairwise (line 732, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule move_gff_files (line 827, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param workspace is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param tmp_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule roary_within_group (line 889, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule gene_list_maker (line 952, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule move_faa_files (line 1002, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param workspace is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param group_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fasta_curation (line 1064, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cog_analysis_core (line 1120, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cog_analysis_shells (line 1190, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cog_visualization (line 1260, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule roary_visualization (line 1343, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule abricate_strain (line 1404, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule abricate_ref (line 1516, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1725328424.0 + "updated_at": 1724827560.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpok9x7dt3/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "edbennett/unify_lmh_2016", + "description": "Dataprocessing project for converting the FAST-GBS pipeline to a snakemake pipeline.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpngi0u1el/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Kyreria/Dataprocessing_FAST-GBS", "latest_release": null, - "linting": "Lints for rule get_gaugegravity_csvs (line 14, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_su2_code (line 37, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule unzip_su2_code (line 59, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule unify_gaugegravity_data (line 86, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule unify_su2_data (line 115, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpngi0u1el/workflow/Snakefile\", line 38, in \u003cmodule\u003e\n include: \"Rules/Trimming.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpngi0u1el/workflow/Rules/Fasta.smk\", line 26, in \u003cmodule\u003e\n message:\n \n\n File \"/tmp/tmpngi0u1el/workflow/Rules/Fasta.smk\", line 14, in get_new_demultiplex_file_names\n return [f\"{data_dir}/demultiplexed/{sample}_R{read}.fastq\" for read in [1,2] for sample in get_sample_names_from_barcodes()]\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/tmp/tmpngi0u1el/workflow/Snakefile\", line 30, in get_sample_names_from_barcodes\n split_line = line.strip().split(\" \")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/students/2023-2024/Thema11/dhaandrikman_snakemake/data/barcodes/barcodes.txt\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -164,52 +100,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725307570.0 + "updated_at": 1724810573.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake pipeline for detection limit test", - "formatting": null, - "full_name": "3d-omics/mg_quant", - "latest_release": "v1.2.0", - "linting": "Workflow defines that rule helpers__samtools__index_fa_gz__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__host__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__mags__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule preprocess__index__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule quantify__index__ is eligible for caching between workflows (use the --cache argument to enable this).\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/preprocess/index.smk:\n * Absolute path \"/{genome}\" in line 11:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/preprocess/bowtie2.smk:\n * Absolute path \"/{genome}\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/quantify/index.smk:\n * Absolute path \"/{mag_catalogue}\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/quantify/bowtie2.smk:\n * Absolute path \"/{mag_catalogue}\" in line 49:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\n", + "description": "Materials for organization data dictionary", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpks5nstct/CT-Data-Haven-dictionary-build-5905514/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 10:6: conda:\n```\n\n[INFO] In file \"/tmp/tmpks5nstct/CT-Data-Haven-dictionary-build-5905514/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "CT-Data-Haven/dictionary-build", + "latest_release": "v0.2.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpks5nstct/CT-Data-Haven-dictionary-build-5905514/Snakefile\", line 1, in \u003cmodule\u003e\n from dotenv import load_dotenv\n\nModuleNotFoundError: No module named \u0027dotenv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "pipeline" - ], - "updated_at": 1725294290.0 + "subscribers_count": 3, + "topics": [], + "updated_at": 1724802397.0 }, { "config_readme": null, "data_format": 2, - "description": "A Snakemake pipeline to assemble Nanopore WGS data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5i5_ucjw/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MortenEneberg/Nanopore_WGS", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9xzo805v/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "DariaKIL/Glioblastoma_mutations", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5i5_ucjw/Snakefile\", line 48, in \u003cmodule\u003e\n METADATA_FOLDER = config[\"metadata_folder\"]\n ~~~~~~^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027metadata_folder\u0027\n\n", + "linting": "Lints for rule split_vcf (line 33, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fix_GERP_notation (line 58, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule to_tsv_main (line 83, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule to_vcf_VEP (line 108, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule header_to_main (line 133, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule header_to_VEP (line 158, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_tsv (line 182, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1725269237.0 + "updated_at": 1724798308.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3cv2tngk/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "sagieb/pMPBA", + "description": "Pipeline to analyze DNA sequencing data with legacy compatibility for the Pool lab\u0027s Drosophila Genome Nexus data.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/fas1k.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpnvu0aj6j/Snakefile\": EmptyContextError: L364: rule has no keywords attached to it.\n[DEBUG] In file \"/tmp/tmpnvu0aj6j/Snakefile\": \n[ERROR] In file \"/tmp/tmpnvu0aj6j/rules/genome_indexing.smk\": EmptyContextError: L2: rule has no keywords attached to it.\n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/genome_indexing.smk\": \n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/qc.smk\": Formatted content is different from original\n[INFO] 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "JamieCFreeman/DGN_compatible", "latest_release": null, - "linting": "Lints for rule cutadapt (line 9, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bowtie_map (line 35, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort (line 61, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all (line 82, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpnvu0aj6j/Snakefile:\n * Absolute path \"/round1/alt_ref/\u0027, wildcards.sample, \" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/round1/alt_ref/\u0027, wildcards.sample, \" in line 49:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/opt/bioscript/stampy/stampy.py\" in line 191:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpnvu0aj6j/rules/genome_indexing.smk:\n * Absolute path \"/opt/bioscript/stampy/stampy.py\" in line 59:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpnvu0aj6j/rules/fas1k.smk:\n * Absolute path \"/home/jamie/FAS1K_utils\" in line 75:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule calc_fas1k_het (line 1, /tmp/tmpnvu0aj6j/rules/stats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule multiqc (line 33, /tmp/tmpnvu0aj6j/rules/qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule round1_index_ok (line 2, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule round2_index_ok (line 28, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all_round2_index_ok (line 54, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_index (line 76, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ref_fai (line 97, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prep_indel_shift (line 1, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_indel_shift (line 28, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fas (line 66, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule indel_mask_bed (line 106, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule add_fas_header (line 143, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule mask_around_indels (line 167, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule wrap_fas1k (line 196, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mv_fas1k (line 223, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule test (line 163, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_aln_1 (line 187, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_aln_2 (line 218, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_sampe (line 249, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule aln_flagstat (line 278, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_mem (line 298, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule flagstat (line 333, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sam2bam (line 390, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule stampy_flagstat (line 411, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule qfilter_bam (line 432, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_bam (line 454, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mark_dups (line 479, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule add_RG (line 516, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dup_bam_bai (line 541, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gz_vcf (line 715, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_vcf (line 785, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tgz_alt_ref (line 941, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -217,16 +151,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725262513.0 + "updated_at": 1724797409.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/08_seq_depth.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/06_primary_alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/01_basecall_dorado.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/05_minimap2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/09_isoform_bambu.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "guillermoscb/ont-dRNA-isoforms", + "description": "Repository for my Advanced dataprocessing school project. A pipeline made with snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/reference_files.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/fasta.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/feature_counts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/visualization.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/alignment.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "SibrenReekers/Snakemake", "latest_release": null, - "linting": "WorkflowError in file /tmp/tmpq6md6upg/workflow/Snakefile, line 6:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmpq6md6upg/config/config.yaml).\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpsatfeeb4/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n include: \"rules/alignment.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpsatfeeb4/workflow/rules/fasta.smk\", line 56, in \u003cmodule\u003e\n\nKeyError: \u0027mem_mb\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -234,33 +168,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725210100.0 + "updated_at": 1724790650.0 }, { "config_readme": null, "data_format": 2, - "description": "Workflow module for mapping", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpic7_f4te/cuspuk-workflow_mapping-eec105e/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpic7_f4te/cuspuk-workflow_mapping-eec105e/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 3 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "cuspuk/workflow_mapping", - "latest_release": "v3.1.10", - "linting": "WorkflowError:\nError validating config file.\nValidationError: Additional properties are not allowed (\u0027exclude_ancestors\u0027, \u0027exclude_children\u0027, \u0027exclude_taxa_ids\u0027 were unexpected)\n\nFailed validating \u0027additionalProperties\u0027 in schema[\u0027allOf\u0027][0][\u0027then\u0027][\u0027properties\u0027][\u0027reads__decontamination__kraken\u0027]:\n {\u0027type\u0027: \u0027object\u0027,\n \u0027additionalProperties\u0027: False,\n \u0027properties\u0027: {\u0027kraken_dir\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027description\u0027: \u0027Directory with the \u0027\n \u0027kraken DB files. If \u0027\n \u0027does not exist, the \u0027\n \u0027workflow tries to \u0027\n \u0027download DB by using \u0027\n \u0027the basename. See \u0027\n \u0027https://benlangmead.github.io/aws-indexes/k2.\u0027,\n \u0027pattern\u0027: \u0027.*k2_.*_\\\\d{8}\\\\/?$\u0027,\n \u0027examples\u0027: [\u0027/data/genome/metagenome/kraken/k2_pluspf_20240112\u0027]},\n \u0027taxa_ids\u0027: {\u0027type\u0027: \u0027array\u0027,\n \u0027description\u0027: \u0027List of taxonomy IDs for \u0027\n \u0027filter logic. Example: \u0027\n \u00279606 - Homo Sapiens of \u0027\n \u0027rank=species.\u0027,\n \u0027minItems\u0027: 1,\n \u0027items\u0027: {\u0027type\u0027: \u0027integer\u0027},\n \u0027default\u0027: [9606]},\n \u0027filter_mode\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027enum\u0027: [\u0027exclude\u0027, \u0027include\u0027],\n \u0027description\u0027: \u0027Reads with specified \u0027\n \u0027taxa ids are either \u0027\n \u0027excluded or included.\u0027,\n \u0027default\u0027: \u0027exclude\u0027},\n \u0027filter_children\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027default\u0027: False,\n \u0027description\u0027: \u0027Whether to filter \u0027\n \u0027reads classified \u0027\n \u0027at more specific \u0027\n \u0027levels than \u0027\n \u0027specified taxonomy \u0027\n \u0027ID levels.\u0027},\n \u0027filter_ancestors\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027default\u0027: False,\n \u0027description\u0027: \u0027Whether to filter \u0027\n \u0027reads classified \u0027\n \u0027at all taxonomy \u0027\n \u0027levels between \u0027\n \u0027root and the \u0027\n \u0027specified \u0027\n \u0027taxonomy ID \u0027\n \u0027levels.\u0027},\n \u0027save_memory\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027description\u0027: \u0027If true, kraken limits \u0027\n \u0027RAM memory usage but \u0027\n \u0027sacrifices speed.\u0027,\n \u0027default\u0027: True},\n \u0027generate_krona\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027description\u0027: \u0027If true, krona is \u0027\n \u0027generated from \u0027\n \u0027kraken report.\u0027,\n \u0027default\u0027: False},\n \u0027krona_dir\u0027: {\u0027type\u0027: [\u0027string\u0027, \u0027null\u0027],\n \u0027description\u0027: \u0027Directory where krona \u0027\n \u0027dataset is located, or \u0027\n \u0027where will be \u0027\n \u0027downloaded.\u0027,\n \u0027examples\u0027: [\u0027/data/genome/taxonomy/krona/2023-12-03/\u0027]}},\n \u0027required\u0027: [\u0027taxa_ids\u0027,\n \u0027kraken_dir\u0027,\n \u0027filter_mode\u0027,\n \u0027filter_children\u0027,\n \u0027filter_ancestors\u0027,\n \u0027save_memory\u0027,\n \u0027generate_krona\u0027,\n \u0027krona_dir\u0027],\n \u0027title\u0027: \u0027ReadsDecontaminationKraken\u0027,\n \u0027if\u0027: {\u0027properties\u0027: {\u0027generate_krona\u0027: {\u0027const\u0027: True}}},\n \u0027then\u0027: {\u0027properties\u0027: {\u0027krona_dir\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027pattern\u0027: \u0027.*/\\\\d{4}-\\\\d{2}-\\\\d{2}\\\\/?$\u0027}},\n \u0027message\u0027: \u0027reads__decontamination__kraken-\u003ekrona_dir must \u0027\n \u0027be valid if generate_krona is True.\u0027}}\n\nOn instance[\u0027reads__decontamination__kraken\u0027]:\n {\u0027kraken_dir\u0027: \u0027/data/genome/metagenome/kraken/k2_pluspf_20240112\u0027,\n \u0027exclude_taxa_ids\u0027: [9606],\n \u0027exclude_children\u0027: False,\n \u0027exclude_ancestors\u0027: False,\n \u0027save_memory\u0027: True,\n \u0027generate_krona\u0027: False,\n \u0027krona_dir\u0027: \u0027/data/genome/taxonomy/krona/2023-12-03/\u0027}\n File \"https://:ghs_IeDJpmWTuQlQw4bViKzOm0InikjEi62zmraA@raw.githubusercontent.com/cuspuk/workflow_reads/v3.6.1/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n File \"https://:ghs_IeDJpmWTuQlQw4bViKzOm0InikjEi62zmraA@raw.githubusercontent.com/cuspuk/workflow_reads/v3.6.1/workflow/rules/common.smk\", line 9, in \u003cmodule\u003e\n", + "description": null, + "formatting": null, + "full_name": "tauqeerrumaney/RSE_2", + "latest_release": null, + "linting": "WorkflowError:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmp3p9pjll8/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1725197236.0 + "updated_at": 1724776328.0 }, { "config_readme": null, "data_format": 2, - "description": "Workflow module for read processing", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpu2gkglmx/cuspuk-workflow_reads-44925a2/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpu2gkglmx/cuspuk-workflow_reads-44925a2/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "cuspuk/workflow_reads", - "latest_release": "v3.6.7", - "linting": null, + "description": "Lecture on Advertising Attribution Models for Digital and Social Media Strategies at Tilburg U", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpu7x0jbic/rules/renv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpu7x0jbic/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "deer-marketing-lab/dsms-lecture-ad-attribution", + "latest_release": null, + "linting": "Lints for rule build_html (line 16, /tmp/tmpu7x0jbic/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 46, /tmp/tmpu7x0jbic/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 89, /tmp/tmpu7x0jbic/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 22, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 34, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 46, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 58, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -268,16 +202,16 @@ var data = "stargazers_count": 0, "subscribers_count": 0, "topics": [], - "updated_at": 1725197223.0 + "updated_at": 1724775155.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpck2p5egj/workflow/rules/download.smk\": NoParametersError: L22: In input definition.\n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/rules/download.smk\": \n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/rules/train_pop_gen_cnn.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "xin-huang/prml", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk\": Keyword \"output\" at line 6 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpr17ecgo_/workflow/Snakefile\": SyntaxError: L26: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/4_sequence_level.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zeyak/barkhanus", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpck2p5egj/workflow/rules/download.smk:\n * Absolute path \"/print \\\\(.*\\\\)/print(\\\\1)/\u0027 | sed s\" in line 50:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule download_training_data (line 20, /tmp/tmpck2p5egj/workflow/rules/download.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_test_data (line 47, /tmp/tmpck2p5egj/workflow/rules/download.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule training (line 20, /tmp/tmpck2p5egj/workflow/rules/train_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule original_model_performance (line 20, /tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule reproduced_model_performance (line 57, /tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot (line 90, /tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw\" in line 3:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/{process}/nanopore.fastq.gz\" in line 16:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases/{db}\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 74:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 101:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 133:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc_before_trimming (line 1, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule setup_nr_db (line 66, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule blastn (line 87, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule makeblastdb (line 122, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outname is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule blastn_EST (line 160, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule meryl (line 224, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 257, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 293, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 324, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 355, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 1, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule glimmerhmm_ (line 29, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule augustus (line 85, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule V3_busco_geneset (line 118, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_transcriptome (line 152, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_plot (line 187, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 214, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 259, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eggnogmapper (line 294, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule interproscan (line 328, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -285,67 +219,73 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725184830.0 + "updated_at": 1724769923.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppgts66o_/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "bluegenes/2024-nsurp", + "description": "Simulation of long-read sequencing data with structural variations in human genomes", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpauhlru5d/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "villena-francis/visor-simulations", "latest_release": null, - "linting": "Lints for rule branchwater_fastmultigather (line 75, /tmp/tmppgts66o_/Snakefile):\n * Param outd is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sourmash_taxonomy (line 123, /tmp/tmppgts66o_/Snakefile):\n * Param output_base is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "Lints for snakefile /tmp/tmpauhlru5d/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule generate_bed (line 102, /tmp/tmpauhlru5d/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable GENOME_FILE from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule visor_laser_tumour (line 153, /tmp/tmpauhlru5d/workflow/Snakefile):\n * Shell command directly uses variable COVERAGE from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule visor_laser_normal (line 228, /tmp/tmpauhlru5d/workflow/Snakefile):\n * Shell command directly uses variable COVERAGE from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1725068190.0 + "updated_at": 1724765812.0 }, { "config_readme": null, "data_format": 2, - "description": "Codebase exploring figure-ground segregation in texture stimuli through neural synchrony mechanisms. Contains simulations based on the theory of weakly coupled oscillators, psychophysics experiments, and statistical analyses.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpizzb9992/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ccnmaastricht/NeuralSynchrony-FigureGround", + "description": "\ud83e\uddec\ud83d\udd0dCNV analysis and outcome prediction in Ultra-High-Risk and First Episode Psychosis individuals \ud83e\ude7a\ud83e\udde0", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiod6la1s/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zhukovanadezhda/cnv-psychosis", "latest_release": null, - "linting": "Lints for rule download_data (line 28, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_system_info (line 44, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_gee_accuracy (line 60, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_behavioral_arnold_tongue (line 81, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_transfer_session_model_comparison (line 105, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_parameter_exploration (line 126, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_crossval_estimation (line 147, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_crossval_prediction (line 168, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_high_resolution_simulations (line 190, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule test_model_predictions (line 211, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_figure_two (line 234, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_figure_three (line 260, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_figure_four (line 281, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_figure_five (line 305, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for rule all (line 5, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule produce_pathogenic_file (line 13, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule execute_notebooks (line 25, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_classifycnv (line 42, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_cnv_database (line 55, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_brain_database (line 66, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_cytobands (line 75, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule annotate_vcf (line 86, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_to_cytobands (line 97, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule define_brain_genes (line 109, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule identify_rare_cnv (line 121, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_cnv (line 133, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_initial_stat_per_individual (line 144, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_genetic_and_clinical (line 154, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule exclude_pathogenic (line 167, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_updated_stat_per_individual (line 178, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule final_merge_with_clinical (line 188, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1725028128.0 + "topics": [ + "cnv", + "cnv-analysis", + "outcome-prediction", + "psychosis", + "wgs" + ], + "updated_at": 1725813013.0 }, { "config_readme": null, "data_format": 2, - "description": "A tool designed specifically for analyzing RNA-seq data using Snakemake workflows", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/hisat2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/fastp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/salmon.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/DESeqFromFeatureCounts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/BigWig.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/featureCounts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/DESeqFromHTSeqCount.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/fastqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/arriba.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/htseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/STAR.smk\": Formatted content is different from original\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "littleisland8/Transcriptomestic", + "description": "A workflow to train a convolutional neural network with SLiM outputs", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/sweep_stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/extract_log_data.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/stratified_sampling.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp1re72tuf/workflow/rules/create_image.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 4)\n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/create_image.smk\": \n[WARNING] In file \"/tmp/tmp1re72tuf/workflow/rules/slim.smk\": Keyword \"output\" at line 102 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/slim.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp1re72tuf/workflow/Snakefile\": Keyword \"input\" at line 14 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/fit_cnn.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "milesroberts-123/selection-demography-cnn", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpi4vzwe2l/workflow/Snakefile\", line 5, in \u003cmodule\u003e\n include: \"rules/STAR.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpi4vzwe2l/workflow/rules/fastqc.smk\", line 4, in \u003cmodule\u003e\n output:\n\nTypeError: unsupported operand type(s) for +: \u0027NoneType\u0027 and \u0027str\u0027\n\n", + "linting": "WorkflowError:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1725015928.0 + "updated_at": 1724702227.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[WARNING] In file \"/tmp/tmpgnn_t2gx/Snakefile\": Keyword \"output\" at line 178 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpgnn_t2gx/Snakefile\": Keyword \"output\" at line 1000 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpgnn_t2gx/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "LukasFrankenQ/pypsa-earth-sec", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpt_50h4ge/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 14)\n[INFO] In file \"/tmp/tmpt_50h4ge/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "cjfiscus/Kmer-it", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpgnn_t2gx/Snakefile, line 61:\nKeyword subworkflow is deprecated. Use module directive instead :\nNone\n", + "linting": "TabError in file \u003cstring\u003e, line 14:\ninconsistent use of tabs and spaces in indentation:\n\t expand(\"results/cn_ests/{id}.txt\", id=all_ids)\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -353,50 +293,54 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725005433.0 + "updated_at": 1724697796.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003einput_dir\u003c/code\u003e: The input folder is expected to contain a subfolder for each sampleID/barcode, then all fastq files in each subfolder are concatenated and the folder name is used as sample ID downstream. This is usually the \"fastq_pass\" folder from nanopore sequencing and basecalling output\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eoutput_dir\u003c/code\u003e: Output directory with the final results\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003etmp_dir\u003c/code\u003e: Directory for temporary files\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003elog_dir\u003c/code\u003e: Directory for log files for all rules\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003edb_fasta\u003c/code\u003e: Database for minimap2 in fasta file format. Each sequence header must only contain an ID matching the taxonomy file below, nothing else.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003edb_tax\u003c/code\u003e: 2-column TSV file with corresponding taxonomy for each sequence in the above fasta file. The first column is for the sequence IDs, the second a semi-colon separated taxonomy string.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eminalignlen\u003c/code\u003e: Minimum alignment length for the mapping. Any alignments shorter than this threshold will be filtered\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eminIDfrac\u003c/code\u003e: Minimum identity threshold of each mapping (value must be between \u003ccode\u003e0.0-1.0\u003c/code\u003e). Any alignments with an identity lower than this threshold will be filtered.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003efiltlong_args\u003c/code\u003e: Arguments passed on to the \u003ccode\u003efiltlong\u003c/code\u003e command for pre-filtering reads\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003emax_threads\u003c/code\u003e: Max number of threads for any rule\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eHave a look in the \u003ccode\u003e.test\u003c/code\u003e directory for example files.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eDatabase files\u003c/h2\u003e\u003ca id=\"user-content-database-files\" class=\"anchor\" aria-label=\"Permalink: Database files\" href=\"#database-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIf you want to use the SILVA database, you can use \u003ca href=\"https://github.com/KasperSkytte/bioscripts/blob/main/extract_qiimetax.R\"\u003ethis R script\u003c/a\u003e to create the two requires database files. For the MiDAS database the files can be downloaded directly from \u003ca href=\"https://midasfieldguide.org/guide/downloads\" rel=\"nofollow\"\u003edownload section\u003c/a\u003e on the website.\u003c/p\u003e\n", "data_format": 2, - "description": "Lightweight snakemake pipeline for preprocessing, alignmen, and QC of PROseq/ChROseq data", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpf3ix66yp/rules/1b_rule.smk\": InvalidParameterSyntax: 3\"file1.extension\"\nINPUT_2=\"file2.extension\"\n\n[DEBUG] In file \"/tmp/tmpf3ix66yp/rules/1b_rule.smk\": \n[ERROR] In file \"/tmp/tmpf3ix66yp/rules/0_rule.smk\": InvalidParameterSyntax: 3\"file1.extension\"\nINPUT_2=\"file2.extension\"\n\n[DEBUG] In file \"/tmp/tmpf3ix66yp/rules/0_rule.smk\": \n[ERROR] In file \"/tmp/tmpf3ix66yp/rules/1a_rule.smk\": InvalidParameterSyntax: 3\"file1.extension\"\nINPUT_2=\"file2.extension\"\n\n[DEBUG] In file \"/tmp/tmpf3ix66yp/rules/1a_rule.smk\": \n[ERROR] In file \"/tmp/tmpf3ix66yp/Snakefile\": NoParametersError: L52: In input definition.\n[INFO] In file \"/tmp/tmpf3ix66yp/Snakefile\": 4 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "mckellardw/runon_snake", - "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpf3ix66yp/config.yaml).\n", - "mandatory_flags": [], + "description": "Snakemake workflow to process 16S nanopore amplicon sequences (of any length) and produce an abundance table including taxonomy", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/05-mapping_overview.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/04-map2db.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/03-checksum_fq_headers.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/02-qfilter.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/01-cat_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/06-abund_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/Snakefile\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "cmc-aau/nanopore_16Samp", + "latest_release": "v2.0.5", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/Snakefile\", line 17, in \u003cmodule\u003e\n ]\n \n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027nanopore_run_xyz123/fastq_pass\u0027\n\n", + "mandatory_flags": null, "report": false, - "software_stack_deployment": null, - "standardized": false, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 3, "topics": [], - "updated_at": 1724953436.0 + "updated_at": 1724682622.0 }, { "config_readme": null, "data_format": 2, - "description": "Media Mix Modelling: Lecture 3 of Digital and Social Media Strategies (DSMS) at Tilburg U", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpcswibnm_/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcswibnm_/rules/renv.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "deer-marketing-lab/dsms-lecture-mediamix", + "description": "This pipeline uses repeatmasker, repeatmodeler, and the TREP database (https://trep-db.uzh.ch/) to annotate and mask transposable elements (TEs) in a wheat genome assembly.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj65z628m/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mattrwillman/wheat-te-annotation", "latest_release": null, - "linting": "Lints for rule build_html (line 16, /tmp/tmpcswibnm_/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 46, /tmp/tmpcswibnm_/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 89, /tmp/tmpcswibnm_/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 22, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 34, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 46, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 58, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpj65z628m/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n GENOTYPE = config[\u0027GENOTYPE\u0027]\n ~~~~~~^^^^^^^^^^^^^\n\nKeyError: \u0027GENOTYPE\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1724950425.0 + "updated_at": 1724681984.0 }, { "config_readme": null, "data_format": 2, - "description": "Basic RNA-seq snakemake workflow. Use as a module for larger workflows.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/SplicingAnalysis.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpxp575kpp/rules/IndexGenome.smk\": NoParametersError: L107: In params definition.\n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/IndexGenome.smk\": \n[ERROR] In file \"/tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk\": NoParametersError: L47: In params definition.\n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk\": \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/ExpressionAnalysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/QC.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/MakeBigwigs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxp575kpp/Snakefile\": Keyword \"input\" at line 37 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxp575kpp/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "bfairkun/snakemake-workflow_rna-seq", + "description": "The repository contains scripts for wheat genome assembly of PacBio CCS reads.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpb_m2zqad/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mattrwillman/wheat-assembly", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk:\n * Absolute path \"/STARIndex\" in line 86:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpxp575kpp/rules/IndexGenome.smk:\n * Absolute path \"/^#/ || /tag \"basic\"/ || /transcript_biotype \"mRNA\"/ || /transcript_biotype \"protein_coding\"/ || $3==\"gene\" || /transcript_id \"[XN]M/\u0027 {input.gtf} | sed -e \" in line 28:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk:\n * Absolute path \"/Reference.basic.gtf\" in line 169:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 93:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpxp575kpp/rules/MakeBigwigs.smk:\n * Absolute path \"/project2/yangili1/bjf79/ChromatinSplicingQTLs/code/ReferenceGenome/Fasta/GRCh38.primary_assembly.genome.fa.fai\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule CopyFastq (line 1, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule CopyFastq_SE (line 39, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule STAR_Align (line 185, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule indexBam (line 238, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule idxstats (line 269, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule DownloadFastaAndGtf (line 1, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule GetBasicGtf (line 30, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule faidxGenome (line 71, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gtf_to_bed12 (line 96, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_colored_bed12 (line 174, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule STAR_make_index (line 202, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ConcatJuncFilesAndKeepUniq (line 92, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_leafcutter_juncfile (line 168, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule leafcutter_cluster (line 199, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bgzip_PSI_bed (line 288, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule Get5ssSeqs (line 331, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ConvertLeacfutterJuncNames_To_True_Bed_Coords (line 419, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule MultiQC (line 53, /tmp/tmpxp575kpp/rules/QC.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule CountReadsPerSample (line 88, /tmp/tmpxp575kpp/rules/QC.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule MakeBigwigs_NormalizedToGenomewideCoverage (line 2, /tmp/tmpxp575kpp/rules/MakeBigwigs.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpb_m2zqad/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n GENOTYPE = config[\u0027GENOTYPE\u0027]\n ~~~~~~^^^^^^^^^^^^^\n\nKeyError: \u0027GENOTYPE\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -404,16 +348,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724948624.0 + "updated_at": 1724681636.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile\": Keyword \"output\" at line 37 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile\": Keyword \"shell\" at line 48 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "jiapeng-CP/Snakemake_MTG", - "latest_release": "v1.0.0", - "linting": "RuleException in rule catFq in file /tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile, line 90:\nNot all output, log and benchmark files of rule catFq contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.\n", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Keyword \"input\" at line 34 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Keyword \"input\" at line 166 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Keyword \"output\" at line 424 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "imallona/rhapsodist", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp2zf9x_5g/Snakefile\", line 32, in \u003cmodule\u003e\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 225, in makedirs\n\nPermissionError: [Errno 13] Permission denied: \u0027/home/imallona\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -421,67 +365,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724944578.0 + "updated_at": 1724677895.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptjcq7m2e/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "daisybio/DysRegNet_workflow", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmph1ig95i3/workflow/rules/qc.smk\": Keyword \"params\" at line 39 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmph1ig95i3/workflow/rules/qc.smk\": Keyword \"shell\" at line 48 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmph1ig95i3/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmph1ig95i3/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 19:0: \u003cline number missing in source\u003e\n```\n\n[INFO] In file \"/tmp/tmph1ig95i3/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmph1ig95i3/workflow/Snakefile\": 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "kilpert/minion_basecalling", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmptjcq7m2e/workflow/Snakefile:\n * Absolute path \"/nfs/data/patients_networks/data\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule prepare_HTRIdb (line 115, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_string (line 142, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_pancan_tpm (line 173, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sample_infos (line 217, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscoring (line 251, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3 (line 284, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_shared (line 324, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_top (line 357, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet (line 392, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet_no_direction (line 428, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ssn (line 465, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compute_overlap_shared (line 500, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_shared (line 538, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_benchmark_shared (line 579, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_tests (line 614, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_tests (line 650, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_plots (line 686, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_plots (line 728, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mutation_plots (line 813, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule model_stats_plots (line 859, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats (line 896, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats_plots (line 925, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_tests (line 964, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_plots (line 998, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_dysregnet (line 1037, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_ssn (line 1078, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_plots (line 1117, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_meta (line 1151, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_dysregnet (line 1180, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_plots (line 1216, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule provide_db (line 1256, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule load_db (line 1295, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Shell command directly uses variable DB_PW from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "linting": "Lints for snakefile /tmp/tmph1ig95i3/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmph1ig95i3/workflow/rules/qc.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule folder_nanoplot (line 54, /tmp/tmph1ig95i3/workflow/rules/qc.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule run_multiqc (line 109, /tmp/tmph1ig95i3/workflow/rules/qc.smk):\n * Param indir_pycoqc is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param indir_nanoplot is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule guppy_basecaller_available_workflows (line 255, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule guppy_basecaller (line 280, /tmp/tmph1ig95i3/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule guppy_basecaller_fastq (line 339, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastq_sequencing_summary (line 393, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastq (line 430, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastq_md5 (line 458, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastq_overview (line 492, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastq_flowcell_stats_figures (line 532, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastq_fastqc (line 566, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1724916589.0 + "updated_at": 1724676010.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpgsdtaw6f/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "JohannesKersting/DysRegNet_workflow", + "formatting": null, + "full_name": "fneum/import-benefits", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpgsdtaw6f/workflow/Snakefile:\n * Absolute path \"/nfs/data/patients_networks/data\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule prepare_HTRIdb (line 115, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_string (line 142, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_pancan_tpm (line 173, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sample_infos (line 217, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscoring (line 251, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3 (line 284, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_shared (line 324, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_top (line 357, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet (line 392, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet_no_direction (line 428, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ssn (line 465, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compute_overlap_shared (line 500, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_shared (line 538, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_benchmark_shared (line 579, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_tests (line 614, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_tests (line 650, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_plots (line 686, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_plots (line 728, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mutation_plots (line 813, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule model_stats_plots (line 859, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats (line 896, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats_plots (line 925, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_tests (line 964, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_plots (line 998, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_dysregnet (line 1037, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_ssn (line 1078, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_plots (line 1117, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_meta (line 1151, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_dysregnet (line 1180, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_plots (line 1216, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule provide_db (line 1256, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule load_db (line 1295, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Shell command directly uses variable DB_PW from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724916566.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Clinical Genomics Uppsala inheritance disease pipeline for WGS", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/add_ref_to_vcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/extract_str_bed.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/concat_vcfs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/coverage.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/fix_sv_header.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/bcftools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/peddy.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/vcf_to_aed.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "clinical-genomics-uppsala/poirot_rd_wgs", - "latest_release": "v0.6.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/common.smk\", line 10, in \u003cmodule\u003e\n from hydra_genetics.utils.misc import get_module_snakefile\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp40w9k1ic/workflow/Snakefile\", line 5, in \u003cmodule\u003e\n shell:\n \n\nKeyError: \u0027remote\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 2, "topics": [], - "updated_at": 1724916636.0 + "updated_at": 1724665636.0 }, { - "config_readme": "\u003cp\u003eUser needs to change the simulation parameters in the config file without changing the format.\u003c/p\u003e\n", + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": null, - "full_name": "bethanyyk/DENV_simulations", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpyxqaszb4/workflow/Snakefile\": SyntaxError: \u003cfunction line_nb at 0x7fb2d3744b80\u003eNewline expected after keyword \u0027onstart\u0027\n[DEBUG] In file \"/tmp/tmpyxqaszb4/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpyxqaszb4/workflow/rules/setup.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mdondrup/admixture_workflow", "latest_release": null, - "linting": null, + "linting": "SyntaxError in file /tmp/tmpyxqaszb4/workflow/Snakefile, line 24:\ninvalid syntax:\n print (\"The workflow will re-try these jobs up to 5 times\")\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -496,16 +423,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725495840.0 + "updated_at": 1724596081.0 }, { "config_readme": null, "data_format": 2, - "description": "Performs analysis of mass spectrometry data for John Belisle\u0027s lab.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmprw7gf7pd/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ryanjob42/mass-spec-analysis", + "description": null, + "formatting": null, + "full_name": "Pierre-Alexandre35/weather_pipeline", "latest_release": null, - "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\nusage: snakemake [-h] [--dry-run] [--profile PROFILE]\n [--workflow-profile WORKFLOW_PROFILE] [--cache [RULE ...]]\n [--snakefile FILE] [--cores N] [--jobs N] [--local-cores N]\n [--resources NAME=INT [NAME=INT ...]]\n [--set-threads RULE=THREADS [RULE=THREADS ...]]\n [--max-threads MAX_THREADS]\n [--set-resources RULE:RESOURCE=VALUE [RULE:RESOURCE=VALUE ...]]\n [--set-scatter NAME=SCATTERITEMS [NAME=SCATTERITEMS ...]]\n [--set-resource-scopes RESOURCE=[global|local]\n [RESOURCE=[global|local] ...]]\n [--default-resources [NAME=INT ...]]\n [--preemptible-rules [PREEMPTIBLE_RULES ...]]\n [--preemptible-retries PREEMPTIBLE_RETRIES]\n [--configfile FILE [FILE ...]] [--config [KEY=VALUE ...]]\n [--envvars VARNAME [VARNAME ...]] [--directory DIR] [--touch]\n [--keep-going]\n [--rerun-triggers {code,input,mtime,params,software-env} [{code,input,mtime,params,software-env} ...]]\n [--force] [--executor {local,dryrun,touch}] [--forceall]\n [--forcerun [TARGET ...]] [--prioritize TARGET [TARGET ...]]\n [--batch RULE=BATCH/BATCHES] [--until TARGET [TARGET ...]]\n [--omit-from TARGET [TARGET ...]] [--rerun-incomplete]\n [--shadow-prefix DIR] [--scheduler [{ilp,greedy}]]\n [--wms-monitor [WMS_MONITOR]]\n [--wms-monitor-arg [NAME=VALUE ...]]\n [--scheduler-ilp-solver {PULP_CBC_CMD,COIN_CMD}]\n [--conda-base-path CONDA_BASE_PATH] [--no-subworkflows]\n [--precommand PRECOMMAND] [--groups GROUPS [GROUPS ...]]\n [--group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]]\n [--report [FILE]] [--report-stylesheet CSSFILE]\n [--reporter PLUGIN] [--draft-notebook TARGET]\n [--edit-notebook TARGET] [--notebook-listen IP:PORT]\n [--lint [{text,json}]] [--generate-unit-tests [TESTPATH]]\n [--containerize] [--export-cwl FILE] [--list-rules]\n [--list-target-rules] [--dag] [--rulegraph] [--filegraph]\n [--d3dag] [--summary] [--detailed-summary] [--archive FILE]\n [--cleanup-metadata FILE [FILE ...]] [--cleanup-shadow]\n [--skip-script-cleanup] [--unlock]\n [--list-changes {input,params,code}] [--list-input-changes]\n [--list-params-changes] [--list-untracked]\n [--delete-all-output | --delete-temp-output]\n [--keep-incomplete] [--drop-metadata] [--version]\n [--printshellcmds] [--debug-dag] [--nocolor]\n [--quiet [{all,progress,rules} ...]] [--print-compilation]\n [--verbose] [--force-use-threads] [--allow-ambiguity]\n [--nolock] [--ignore-incomplete]\n [--max-inventory-time SECONDS] [--latency-wait SECONDS]\n [--wait-for-files [FILE ...]] [--wait-for-files-file FILE]\n [--queue-input-wait-time SECONDS] [--notemp] [--all-temp]\n [--unneeded-temp-files FILE [FILE ...]]\n [--keep-storage-local-copies]\n [--target-files-omit-workdir-adjustment]\n [--allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]]\n [--max-jobs-per-timespan MAX_JOBS_PER_TIMESPAN]\n [--max-jobs-per-second MAX_JOBS_PER_SECOND]\n [--max-status-checks-per-second MAX_STATUS_CHECKS_PER_SECOND]\n [--seconds-between-status-checks SECONDS_BETWEEN_STATUS_CHECKS]\n [--retries RETRIES] [--wrapper-prefix WRAPPER_PREFIX]\n [--default-storage-provider DEFAULT_STORAGE_PROVIDER]\n [--default-storage-prefix DEFAULT_STORAGE_PREFIX]\n [--local-storage-prefix LOCAL_STORAGE_PREFIX]\n [--remote-job-local-storage-prefix REMOTE_JOB_LOCAL_STORAGE_PREFIX]\n [--shared-fs-usage {input-output,persistence,software-deployment,source-cache,sources,storage-local-copies,none} [{input-output,persistence,software-deployment,source-cache,sources,storage-local-copies,none} ...]]\n [--scheduler-greediness SCHEDULER_GREEDINESS] [--no-hooks]\n [--debug] [--runtime-profile FILE]\n [--local-groupid LOCAL_GROUPID] [--attempt ATTEMPT]\n [--show-failed-logs] [--log-handler-script FILE]\n [--log-service {none,slack,wms}] [--job-deploy-sources]\n [--benchmark-extended] [--container-image IMAGE]\n [--immediate-submit] [--jobscript SCRIPT] [--jobname NAME]\n [--flux]\n [--software-deployment-method {apptainer,conda,env-modules} [{apptainer,conda,env-modules} ...]]\n [--container-cleanup-images] [--use-conda]\n [--conda-not-block-search-path-envvars] [--list-conda-envs]\n [--conda-prefix DIR] [--conda-cleanup-envs]\n [--conda-cleanup-pkgs [{tarballs,cache}]]\n [--conda-create-envs-only] [--conda-frontend {conda,mamba}]\n [--use-apptainer] [--apptainer-prefix DIR]\n [--apptainer-args ARGS] [--use-envmodules]\n [--scheduler-solver-path SCHEDULER_SOLVER_PATH]\n [--deploy-sources QUERY CHECKSUM]\n [--target-jobs TARGET_JOBS [TARGET_JOBS ...]]\n [--mode {remote,subprocess,default}]\n [--report-html-path VALUE]\n [--report-html-stylesheet-path VALUE]\n [targets ...]\nsnakemake: error: argument --executor/-e: invalid choice: \u0027slurm\u0027 (choose from \u0027local\u0027, \u0027dryrun\u0027, \u0027touch\u0027)\n", + "linting": "Lints for rule get_weather (line 1, /tmp/tmpm_lavqm5/workflow/rules/get_weather.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -513,16 +440,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724882363.0 + "updated_at": 1724528043.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpt52y0ckk/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "IMCBioinformatics/dada2_ITS_workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5ju0r58g/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_short-read-assembly", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpt52y0ckk/Snakefile\", line 10, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027samples/samples.tsv\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5ju0r58g/workflow/Snakefile\", line 14, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \"short-read-assembly\")\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -530,16 +457,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724878213.0 + "updated_at": 1724522800.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "Could not parse .gitignore: Invalid git pattern: \u0027.Ruserdata\\\\\\n\u0027\nValueError: Escape character found with no next character to escape: \u0027.Ruserdata\\\\\u0027\n\nThe above exception was the direct cause of the following exception:\n\npathspec.patterns.gitwildmatch.GitWildMatchPatternError: Invalid git pattern: \u0027.Ruserdata\\\\\\n\u0027\n\nsnakefmt version: 0.10.2", - "full_name": "krferrier/EWAS", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpfuhf1bjf/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_gene-catalog", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpexugv3hd/rules/annotate.smk, line 58:\ninvalid syntax:\n\tshell ( , bench_record=bench_record, bench_iteration=bench_iteration\n\n", + "linting": "/tmp/tmpfuhf1bjf/workflow/Snakefile:339: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n/tmp/tmpfuhf1bjf/workflow/Snakefile:349: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpfuhf1bjf/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027gene_catalog\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 2, + "topics": [], + "updated_at": 1724521396.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "example snakemake workflow for the 2024 SAGC workflow workshop", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/rules/report.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/rules/preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/Snakefile\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "beardymcjohnface/snakemake-example-workflow-2024", + "latest_release": null, + "linting": "Lints for rule minimap (line 3, /tmp/tmpddufb8g3/workflow/rules/mapping.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_alignment (line 51, /tmp/tmpddufb8g3/workflow/rules/mapping.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fastp (line 3, /tmp/tmpddufb8g3/workflow/rules/preprocessing.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule flagstat (line 3, /tmp/tmpddufb8g3/workflow/rules/report.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule multiqc (line 30, /tmp/tmpddufb8g3/workflow/rules/report.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param qcdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -547,16 +491,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724874419.0 + "updated_at": 1724480463.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppulecl4m/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Fotowatikha/sc-sn-RNA-seq-Pre-Processing-Pipeline", + "description": "Snakemake port of https://github.com/fedorrik/HumAS-HMMER_for_AnVIL/tree/main.", + "formatting": null, + "full_name": "logsdon-lab/Snakemake-HumAS-HMMER", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/tmp/tmppulecl4m/Snakefile\", line 21, in \u003cmodule\u003e\n name_of_configfile = args[args.index(\"--configfiles\") + 1] # hpc\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nValueError: \u0027--configfiles\u0027 is not in list\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmppulecl4m/Snakefile\", line 23, in \u003cmodule\u003e\n name_of_configfile = args[args.index(\"--configfile\") + 1] # one config\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nValueError: \u0027--configfile\u0027 is not in list\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5hgnrheo/workflow/Snakefile\", line 27, in \u003cmodule\u003e\n hmm=config[\"model\"],\n ^\n\nKeyError: \u0027input_dir\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -564,16 +508,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724872193.0 + "updated_at": 1724473258.0 }, { "config_readme": null, "data_format": 2, - "description": "Seabreeze: an automated pipeline for structrual variant analysis of bacterial resequencing experiments", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpuws_dkki/Snakefile\": Keyword \"output\" at line 86 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpuws_dkki/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ira-zibbu/seabreeze-ltee-analysis", + "description": "Pipeline for Somatic Variant Calling with WES and WGS data", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmppkvj6rza/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 10)\n[DEBUG] In file \"/tmp/tmppkvj6rza/Snakefile\": \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/pon.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/preprocessing.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "JeBinLEE/ngs-pipeline", "latest_release": null, - "linting": "Lints for rule rename_contigs (line 53, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule compute_genome_stats (line 85, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_ISEScan_summary (line 171, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param input_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule align_genomes_nucmer (line 212, /tmp/tmpuws_dkki/Snakefile):\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule call_variants_syri (line 279, /tmp/tmpuws_dkki/Snakefile):\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_synteny_plot (line 345, /tmp/tmpuws_dkki/Snakefile):\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule clean_syri_output (line 407, /tmp/tmpuws_dkki/Snakefile):\n * Param isescan_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_synteny_plot_clean (line 463, /tmp/tmpuws_dkki/Snakefile):\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule reindex_contigs_oric (line 515, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_ori_dif_locations (line 543, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule analyse_replichore_arms (line 588, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule annotate_SV_boundaries_IS (line 667, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_SV_mechanism (line 709, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule classify_inversion_replichore (line 756, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_genome_diffs_tables (line 812, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param gd_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param html_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "TabError in file \u003cstring\u003e, line 10:\ninconsistent use of tabs and spaces in indentation:\n\t\"qc/depths.csv\",\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -581,16 +525,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724869348.0 + "updated_at": 1724431394.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake pipeline for parsing simulation outputs across scaling factors", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpkpgy83jb/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "SchriderLab/simscale-snakemake", + "description": "A snakemake workflow to produce mode-resolved INS intensities in incoherent approximation", + "formatting": null, + "full_name": "ajjackson/abins-mode-intensities", "latest_release": null, - "linting": "TypeError in file /tmp/tmpkpgy83jb/workflow/Snakefile, line 11:\n\u0027NoneType\u0027 object is not subscriptable\n File \"/tmp/tmpkpgy83jb/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n", + "linting": "Lints for rule get_all_intensities (line 21, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_reference (line 61, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule write_modes (line 101, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule write_highlights (line 135, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bin_and_broaden (line 169, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_modes (line 204, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_reference (line 238, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -598,16 +542,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725894756.0 + "updated_at": 1724427780.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/rules/ncbi_blast.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 8 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "vdclab/sORTholog", + "latest_release": "0.6.2", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/Snakefile\", line 85, in \u003cmodule\u003e\n include: \"rules/hmmer.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/rules/common.smk\", line 245, in \u003cmodule\u003e\n seed_table = pd.read_table(seed_file, dtype=seed_dtypes)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027path/to/seeds.tsv\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 3, + "topics": [], + "updated_at": 1724425769.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/rules/toblow5.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/rules/fetch_data.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "loganylchen/prep_public_nanoporeDRS_data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpcysasrw2/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "alzel/refseq_pipeline", "latest_release": null, - "linting": "/tmp/tmpiobvfk4r/workflow/Snakefile:9: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n sample=\"[\\da-zA-Z]+\"\nFileNotFoundError in file /tmp/tmpiobvfk4r/workflow/rules/common.smk, line 6:\n[Errno 2] No such file or directory: \u0027config/samples.tsv\u0027\n File \"/tmp/tmpiobvfk4r/workflow/rules/common.smk\", line 6, in \u003cmodule\u003e\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n", + "linting": "Lints for snakefile /tmp/tmpcysasrw2/workflow/Snakefile:\n * Absolute path \"/\" + genome + f\" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data\" in line 109:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data\" in line 129:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Deprecated singularity directive used for container definition in line 110.:\n Use the container directive instead (it is agnostic of the underlying\n container runtime).\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_genomic (line 78, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_gff (line 105, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gunzip (line 131, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_parts (line 199, /tmp/tmpcysasrw2/workflow/Snakefile):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule filter_fasta (line 247, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -622,50 +583,57 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725894100.0 + "updated_at": 1724422964.0 }, { - "config_readme": null, + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpy9boas6k/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "daiuc/splice-pub", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp9cqhnd78/workflow/Snakefile\": Keyword \"output\" at line 137 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp9cqhnd78/workflow/Snakefile\": Keyword \"shell\" at line 151 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp9cqhnd78/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mdondrup/admixture_simulation", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpy9boas6k/Snakefile:\n * Absolute path \"/project/yangili1/cdai/SpliFi\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/smk-plots/gtex-sqtl-enrichment-v4\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/data/WGS_Feature_overlap_collapsed_VEP_short_4torus.MAF01.txt.gz\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/SpliFi\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/smk-plots/gtex-sqtl-enrichment-v4-C\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/data/WGS_Feature_overlap_collapsed_VEP_short_4torus.MAF01.txt.gz\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 15:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule plotGTExsQTLEnrichment (line 33, /tmp/tmpy9boas6k/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plotGTExsQTLEnrichment_test (line 76, /tmp/tmpy9boas6k/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepTorusInputData (line 63, /tmp/tmpy9boas6k/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outprefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule RunTorusEnrich (line 85, /tmp/tmpy9boas6k/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, + "linting": "Lints for rule setup (line 49, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_model (line 77, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule subsample_recode (line 107, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule make_new_clusterfile (line 180, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule treemix_input (line 230, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule TreeMix_bootstrap_{wildcards.model}_{wildcards.migrations}_{wildcards.replicate} (line 262, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule merge_replicates_{wildcards.model}_{wildcards.migrations} (line 344, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule OptM (line 384, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule plot_trees (line 444, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule consensus (line 529, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule final_tree_from_consensus (line 597, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725892780.0 + "updated_at": 1724420390.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpl4vsaazr/Snakefile\": SyntaxError: L107: Unrecognised keyword \u0027savedir\u0027 in rule definition\n[INFO] In file \"/tmp/tmpl4vsaazr/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "ML4GW/gwak", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6wwq7z5b/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "kenji-yt/snake-GENESPACE", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpl4vsaazr/Snakefile:\n * Absolute path \"/home/katya.govorkova/gwak/{version}/data/{dataclass}.npz\" in line 87:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule find_valid_segments (line 31, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_omicron (line 40, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fetch_site_data (line 52, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_data (line 64, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PERIOD from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule upload_data (line 81, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule validate_data (line 92, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable VERSION from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule train_quak (line 101, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_timeslides_for_far (line 113, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule evaluate_signals (line 137, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_timeslides_for_fm (line 150, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule train_final_metric (line 173, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule recreation_and_quak_plots (line 192, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compute_far (line 208, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_far_hist (line 232, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule quak_plotting_prediction_and_recreation (line 242, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_results (line 257, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param evaluation_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule make_pipeline_plot (line 272, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Make sure there is a config.yaml file in /tmp/tmp6wwq7z5b or specify one with the --configfile commandline parameter.\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 1, "topics": [], - "updated_at": 1725890954.0 + "updated_at": 1724411185.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpijdr3wdn/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "iedun/XDEM-Project", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk\": Keyword \"output\" at line 6 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp7dl9bldo/workflow/Snakefile\": SyntaxError: L22: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmp7dl9bldo/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zeyak/GenoDiplo", "latest_release": null, - "linting": "RuleException in file /tmp/tmpijdr3wdn/Snakefile, line 32:\nOnly input files can be specified as functions\n", + "linting": "Lints for snakefile /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw\" in line 3:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/{process}/nanopore.fastq.gz\" in line 16:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases/{db}\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 74:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 101:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 133:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc_before_trimming (line 1, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule setup_nr_db (line 66, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule blastn (line 87, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule makeblastdb (line 122, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outname is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule blastn_EST (line 160, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule meryl (line 224, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 257, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 293, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 324, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 355, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 1, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule glimmerhmm_ (line 29, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule augustus (line 85, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule V3_busco_geneset (line 118, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_transcriptome (line 152, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_plot (line 187, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 214, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp_ (line 259, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eggnogmapper (line 294, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule interproscan (line 328, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -673,67 +641,84 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725890597.0 + "updated_at": 1724406283.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmplmj6xu4a/workflow/Snakefile\": Keyword \"input\" at line 71 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmplmj6xu4a/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "caballero/snakemake-pairtools-phased", - "latest_release": null, - "linting": "KeyError in file /tmp/tmplmj6xu4a/workflow/Snakefile, line 12:\n\u0027fastq_dir\u0027\n File \"/tmp/tmplmj6xu4a/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n", + "description": "A snakemake workflow for amplicon sequencing ", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/rules/qc-notebooks.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/rules/analysis.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 6 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "sanjaynagi/AmpSeeker", + "latest_release": "v0.3.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/Snakefile\", line 17, in \u003cmodule\u003e\n metadata = pd.read_csv(config[\"metadata\"], sep=\",\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027config/metadata.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1725870943.0 + "subscribers_count": 4, + "topics": [ + "amplicon-sequencing", + "gene-drive", + "genomic-surveillance", + "illumina", + "insecticide-resistance", + "snakemake-workflow" + ], + "updated_at": 1724405875.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": null, - "full_name": "rababerladuseladim/megadudes-evaluation", - "latest_release": null, - "linting": "Lints for rule mmseqs2_top_10 (line 116, /tmp/tmptk_adkyi/workflow/rules/run_mmseqs2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\n", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/convert_pdf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/summary_report.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/results.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/dotnet.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/create_background_file.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/sample_order_for_multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/bcftools.smk\": Formatted content is different from original\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "clinical-genomics-uppsala/pickett_bcr_abl_pipeline", + "latest_release": "v0.2.2", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/common.smk\", line 16, in \u003cmodule\u003e\n from hydra_genetics.utils.misc import replace_dict_variables\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1725821035.0 + "updated_at": 1724400847.0 }, { "config_readme": null, "data_format": 2, - "description": "A self contained snakemake workflow to test new features", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp13a3ojow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ETH-NEXUS/basic_snakemake_workflow", + "description": "A repository for efficient population genomic analysis using Snakemake workflow.", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp58ll2v5d/Snakefile\": SyntaxError: L125: Unrecognised keyword \u0027expand\u0027 in rule definition\n[INFO] In file \"/tmp/tmp58ll2v5d/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "meeranhussain/Population_genomic_analysis", "latest_release": null, - "linting": "Lints for rule generate_data (line 27, /tmp/tmp13a3ojow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_data (line 53, /tmp/tmp13a3ojow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule aggregate_data (line 79, /tmp/tmp13a3ojow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp58ll2v5d/Snakefile\", line 13, in \u003cmodule\u003e\n fasta_path = config[\"fasta_path\"]\n ~~~~~~^^^^^^^^^^^^^^^\n\nKeyError: \u0027fasta_path\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1725772983.0 + "subscribers_count": 1, + "topics": [ + "genome-analysis", + "ngs", + "ngs-analysis", + "population", + "population-genomics", + "snakemake-workflow", + "variant-calling", + "whole", + "rprogramming" + ], + "updated_at": 1724388998.0 }, { "config_readme": null, "data_format": 2, - "description": "Dockerized RNA-seq analysis pipeline built with Snakemake through steps like quality control, trimming, alignment, and quantification, ultimately generating a count matrix for downstream analysis. ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpwgq__i7v/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "irishevia/RNAseq-box", - "latest_release": null, - "linting": "Lints for rule fastqc (line 41, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule trim_galore (line 71, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule hisat2_index (line 109, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable REFERENCE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule hisat2_align (line 142, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable REFERENCE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule samtools_sort (line 169, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule featurecounts (line 191, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "description": "Align almost any kind of RNA-seq data", + "formatting": null, + "full_name": "isaacvock/THE_Aligner", + "latest_release": "v1.0.0", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -741,54 +726,54 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725723184.0 + "updated_at": 1724360758.0 }, { "config_readme": null, "data_format": 2, - "description": "A snakemake workflow that assemble diploid genome using HiFi and HiC sequencing reads", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/03.yahs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/02.arima_hic_mapping.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ZexuanZhao/HiFi-HiC-genome-assembly", + "description": "Code to generate the data and website for Rat TWAS Hub", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbtujbe3p/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "daniel-munro/rat-twas-hub", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp8zh91gwq/Snakefile:\n * Environment variable PATH used but not asserted with envvars directive in line 9.:\n Asserting existence of environment variables with the envvars directive\n ensures proper error messages if the user fails to invoke a workflow with\n all required environment variables defined. Further, it allows snakemake\n to pass them on in case of distributed execution.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#environment-variables\n * Environment variable PATH used but not asserted with envvars directive in line 10.:\n Asserting existence of environment variables with the envvars directive\n ensures proper error messages if the user fails to invoke a workflow with\n all required environment variables defined. Further, it allows snakemake\n to pass them on in case of distributed execution.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#environment-variables\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 9:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk:\n * Absolute path \"/^S/{{print \"\u003e\"$2;print $3}}\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc_hic_before_trimming (line 2, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastp_hic (line 42, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule fastqc_hic_after_trimming (line 93, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc_hifi_before_trimming (line 134, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule hifiAdapterFilt (line 173, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc_hifi_after_trimming (line 232, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule hifiasm (line 1, /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule gfa2fasta (line 61, /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule hifi_assembly_stats (line 91, /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbtujbe3p/Snakefile\", line 9, in \u003cmodule\u003e\n traits_df = pd.read_csv(\"data/traits.par\", sep=\"\\t\", index_col=1)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027data/traits.par\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1725720694.0 + "updated_at": 1725419933.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure the workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to yout needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eAssembly units sheet\u003c/h1\u003e\u003ca id=\"user-content-assembly-units-sheet\" class=\"anchor\" aria-label=\"Permalink: Assembly units sheet\" href=\"#assembly-units-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd assemblies to file \u003ccode\u003econfig/assembly_units.txt\u003c/code\u003e. This file is tab-separated file with two columns: \u003ccode\u003eassembly_id\u003c/code\u003e and \u003ccode\u003epath\u003c/code\u003e. The former is the alias of the assembly and the latter the path of .fasta assembly file. Both columns are mandatory and cannot be duplicated.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eTarget variants sheet\u003c/h1\u003e\u003ca id=\"user-content-target-variants-sheet\" class=\"anchor\" aria-label=\"Permalink: Target variants sheet\" href=\"#target-variants-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd target variants where you want to design the Tm-shit primers in the file \u003ccode\u003econfig/target_variants.txt\u003c/code\u003e. This file is tab-sepparated. In the column \u003ccode\u003evariant_id\u003c/code\u003e specify a unique name to identify the variant. The \u003ccode\u003eassembly_id\u003c/code\u003e uses the \u003ccode\u003eassembly_id\u003c/code\u003e specified in \u003ccode\u003econfig/assembly_units.txt\u003c/code\u003e and the columns \u003ccode\u003echrom\u003c/code\u003e and \u003ccode\u003epos\u003c/code\u003e define the physical position on the given assembly. In columns \u003ccode\u003eref\u003c/code\u003e and \u003ccode\u003ealt\u003c/code\u003e is stored the reference and alternative allele that the primers going to genotype.\u003c/p\u003e\n", "data_format": 2, - "description": "A Snakemake workflow for using SLEAP and NAPS", - "formatting": null, - "full_name": "Wolfffff/snakemake-sleap-naps", + "description": "A workflow intended to perform the design of tm-shift primers for genotype SNPs ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/sequence_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_selection.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Bioinflows-Bioversity-CIAT/tm-shift_designer", "latest_release": "v0.1.0", - "linting": "Lints for rule compute_metrics (line 1, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/sleap_model_qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_sleap (line 2, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/sleap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_naps (line 1, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/naps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule copy_config (line 1, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/copy_config.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], + "linting": "Lints for snakefile /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/common.smk:\n * Absolute path \"/*.txt\" in line 148:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk:\n * Absolute path \"/{variant_id}_{allele}_{primer_id}.txt\" in line 76:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 11:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 11:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule extract_roi (line 1, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/sequence_processing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_alternative_roi (line 37, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/sequence_processing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_primer3_input (line 1, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule build_primer3_input_primercheck (line 50, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule primer3_search_alt (line 114, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule primer3_search (line 164, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_search.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule select_primers (line 1, /tmp/tmp9e8rtunx/Bioinflows-Bioversity-CIAT-tm-shift_designer-fba6131/workflow/rules/primer_selection.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": null, "report": false, - "software_stack_deployment": null, - "standardized": false, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "behavior", - "pose", - "snakemake" - ], - "updated_at": 1725719913.0 + "subscribers_count": 0, + "topics": [], + "updated_at": 1725397842.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpd7qc3qgo/workflow/rules/gsea.smk\": SyntaxError: L16: Colon (not \u0027gsea\u0027) expected after \u0027checkpoint rule\u0027\n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/gsea.smk\": \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/delivery.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpd7qc3qgo/workflow/rules/rseqc.smk\": Keyword \"input\" at line 210 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/rseqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/star.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/fastp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/deseq.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "jprnz/rnaseq-deseq2-star", + "description": "In this repository all the codes to run the master\u0027s thesis is hosted", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpc0upxkk0/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Jerkur123/MA", "latest_release": null, - "linting": "Using workflow specific profile workflow/profiles/default for setting default command line arguments.\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/Snakefile:\n * Absolute path \"/{species}/{release}-{build}/star-index\" in line 52:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 52:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/reference.smk:\n * Absolute path \"/dev/null\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/dev/null\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-dna-fasta.log\" in line 93:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-gtf.log\" in line 102:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-gtf-genes.log\" in line 113:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-dna-fai.log\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 93:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 102:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 113:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 124:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 138:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/fastp.smk:\n * Absolute path \"/fastqs/{sample}_{pair}.fastq.gz\" in line 13:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/combine-{sample}_{pair}.log\" in line 15:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqs/{sample}_R1.fastq.gz\" in line 29:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqs/{sample}_R2.fastq.gz\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R1.fastq.gz\" in line 32:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R2.fastq.gz\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/json_reports/{sample}.json\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/html_reports/{sample}.html\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}.log\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqs/{sample}_{pair}.fastq.gz\" in line 57:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/json_reports/{sample}.json\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 15:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 61:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/star.smk:\n * Absolute path \"/{sample}_R1.fastq.gz\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R2.fastq.gz\" in line 20:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_Aligned.sortedByCoord.out.bam\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_ReadsPerGene.out.tab\" in line 25:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}.log\" in line 27:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_\" in line 29:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_Aligned.sortedByCoord.out.bam\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}_link.log\" in line 66:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 75:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam.bai\" in line 77:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}_index.log\" in line 79:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_ReadsPerGene.out.tab\" in line 90:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 92:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/count-matrix.log\" in line 94:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 104:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam.bai\" in line 108:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 109:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 25:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 27:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 60:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 66:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 75:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 79:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 90:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 92:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 104:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/rseqc.smk:\n * Absolute path \"/annotation.bed\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.db\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/rseqc_gtf2bed.log\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 20:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.junction.bed\" in line 22:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/junction_annotation/{sample}.log\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 27:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.junctionSaturation_plot.pdf\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/junction_saturation/{sample}.log\" in line 48:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 67:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 68:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.stats.txt\" in line 70:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/bam_stats/{sample}.log\" in line 72:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 83:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 84:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.infer_experiment.txt\" in line 86:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/infer_experiment/{sample}.log\" in line 88:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 99:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 100:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.inner_distance.txt\" in line 102:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/inner_distance/{sample}.log\" in line 104:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 107:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 123:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.readdistribution.txt\" in line 126:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/read_distribution/{sample}.log\" in line 128:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 131:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 145:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.pos.DupRate.xls\" in line 147:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/read_duplication/{sample}.log\" in line 149:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 152:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 167:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.GC.xls\" in line 169:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/read_gc/{sample}.log\" in line 171:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 173:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 184:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 185:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.geneBodyCoverage.txt\" in line 187:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/genebody_coverage/{sample}.log\" in line 188:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/gene_body_coverage/{sample}.log\" in line 190:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 193:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.stats.txt\" in line 209:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.readdistribution.txt\" in line 210:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.junctionSaturation_plot.pdf\" in line 211:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.pos.DupRate.xls\" in line 212:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.geneBodyCoverage.txt\" in line 213:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 8:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 22:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 27:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 46:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 48:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 51:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 67:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 70:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 83:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 86:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 88:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 99:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 102:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 104:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 107:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 123:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 126:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 128:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 131:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 145:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 149:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 152:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 167:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 171:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 173:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 184:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 187:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 188:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 190:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 193:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 209:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 210:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 211:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 212:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 213:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/multiqc.smk:\n * Absolute path \"/QC.html\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/multiqc.log\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/deseq.smk:\n * Absolute path \"/counts.csv\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.RData\" in line 12:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.xlsx\" in line 13:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/counts.csv\" in line 14:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/normalized-counts.csv\" in line 15:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{analysis}.log\" in line 17:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.xlsx\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 9:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 14:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 15:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 17:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/gsea.smk:\n * Absolute path \"/{wc.analysis}/rnk-files/*.rnk\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.xlsx\" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/GSEA-{geneset}.xlsx\" in line 23:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{analysis}/{geneset}.log\" in line 25:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/GSEA-{set}.xlsx\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 21:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 23:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 25:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk:\n * Absolute path \"/{v}/analysis.xlsx\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{v}/GSEA-{s}.xlsx\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/analysis.xlsx\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/GSEA/GSEA-{s}.xlsx\" in line 40:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/{v}/analysis.xlsx\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/{v}/GSEA/GSEA-{s}.xlsx\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Methods.docx\" in line 53:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/QC.html\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 84:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 103:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 53:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 71:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule star_link (line 87, /tmp/tmpd7qc3qgo/workflow/rules/star.smk):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule multiqc (line 1, /tmp/tmpd7qc3qgo/workflow/rules/multiqc.smk):\n * Param output_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule deliver_methods (line 49, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_qc (line 66, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_bamfiles (line 83, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_counts (line 104, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_analysis (line 126, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpc0upxkk0/Snakefile\", line 6, in \u003cmodule\u003e\n from tqdm import tqdm\n\nModuleNotFoundError: No module named \u0027tqdm\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -796,16 +781,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725656443.0 + "updated_at": 1725390671.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/extra_env.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpau0wp52n/workflow/rules/cellranger_arc.smk\": Keyword \"input\" at line 26 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/cellranger_arc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/main_seurat.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpau0wp52n/workflow/Snakefile\": Keyword \"input\" at line 18 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/integration.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "yzeng-lol/iSHARC", + "description": "My PhD thesis at the University of Zurich. It contains the three papers making up the thesis, as well as the dissertation itself.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6t8034lz/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "stanmart/phd-thesis", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpau0wp52n/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n include: \"rules/main_seurat.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpau0wp52n/workflow/rules/common.smk\", line 1, in \u003cmodule\u003e\n workdir: config[\u0027work_dir\u0027]\n ^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6t8034lz/Snakefile\", line 2, in \u003cmodule\u003e\n from src.util.makeutils import find_input_files\n\n File \"/tmp/tmp6t8034lz/src/util/makeutils.py\", line 7, in \u003cmodule\u003e\n import typer\n\nModuleNotFoundError: No module named \u0027typer\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -813,16 +798,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725644105.0 + "updated_at": 1725389641.0 }, { "config_readme": null, "data_format": 2, - "description": "Repository containing all code used for dataset construction, analysis and figure generation for Tubbs et al. 2024", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/04_Annotate-SNVs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/05_Final-Matrix.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/03_Annotate-Bases.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp9jy4ezwi/workflow/rules/01_Annotate-rDHS.smk\": Keyword \"input\" at line 29 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/01_Annotate-rDHS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/02_Process-Motifs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/00_Setup.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "RuderferLab/CBS_FunctionalAnnotation", + "description": "Cleaning transcriptome annotations with ab initio assemblers", + "formatting": null, + "full_name": "isaacvock/AnnotationCleaner", "latest_release": null, - "linting": null, + "linting": "Lints for snakefile /tmp/tmpvy6e55xv/workflow/rules/common.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 102:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -830,50 +815,52 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725626810.0 + "updated_at": 1725388992.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp6ykksmrt/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 288:0: EOF in multi-line statement\n```\n\n[INFO] In file \"/tmp/tmp6ykksmrt/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "JavedMS/highRES-model", + "description": "A pipeline to gather snoRNA and RBP interactions to perform a snoRNA-RBP interaction network analysis.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/rules/interactions.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[ERROR] In file \"/tmp/tmp_mamoktv/workflow/rules/filter.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 39)\n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/rules/filter.smk\": \n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp_mamoktv/workflow/rules/cytoscape.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "scottgroup/snoFlake", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85/cluster/EFF/results\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85/cluster/EFF\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85/cluster\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6ykksmrt/workflow/Snakefile\", line 219, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n self.parent.mkdir(parents=True, exist_ok=True)\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n self.parent.mkdir(parents=True, exist_ok=True)\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n self.parent.mkdir(parents=True, exist_ok=True)\n\n [Previous line repeated 4 more times]\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nPermissionError: [Errno 13] Permission denied: \u0027/fp\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp_mamoktv/workflow/Snakefile\", line 17, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027resources/filtered_genes/sig_exp_CD_snoRNAs.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1725626201.0 + "updated_at": 1725371775.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eUnit sheet\u003c/h1\u003e\u003ca id=\"user-content-unit-sheet\" class=\"anchor\" aria-label=\"Permalink: Unit sheet\" href=\"#unit-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd samples to \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003eunit_name\u003c/code\u003e. This can be a running number, or an actual run, lane or replicate id (for now this is not functional as we want to make this workflow to comply with the dna-seq-varlociraptor-workflow because we will import this wokrflow as a module there. For that reason, it\u0027s not called \u003ccode\u003esamples.tsv\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003esample_name\u003c/code\u003e, which associates it with the biological sample it comes from. This information is used to merged all the units of a sample before read mapping and duplicate marking.\u003c/li\u003e\n\u003cli\u003eFor each unit, you need to specify:\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e for paired end reads. These can point to any FASTQ files on your system.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n", "data_format": 2, - "description": "Snakemake workflow for mTags extraction and classification", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4ebanfcv/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "aleixop/mtags_snakemake", + "description": "A Snakemake workflow for typing and quantifying HLAs using Orthanq.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/rules/orthanq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr3qlotoe/workflow/rules/preparation.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "orthanq/orthanq-hla-quantification", "latest_release": null, - "linting": "Lints for rule format_input (line 18, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule blast_search (line 48, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_blast_hits (line 82, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_mtags (line 103, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_mtags (line 127, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_consensus_taxonomy (line 163, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_otu_table (line 190, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], + "linting": "Workflow defines that rule get_genome is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule genome_faidx is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this).\nLints for rule get_hla_genes_and_xml (line 65, /tmp/tmpr3qlotoe/workflow/rules/preparation.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule unzip_xml (line 94, /tmp/tmpr3qlotoe/workflow/rules/preparation.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_pangenome (line 156, /tmp/tmpr3qlotoe/workflow/rules/preparation.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": null, "report": false, - "software_stack_deployment": null, - "standardized": false, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1725616248.0 + "updated_at": 1725355823.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "Snakemake workflow for RNA-Seq differential transcript analysis using STAR/Deseq2", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/deseq2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/plotting.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/deeptools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/resources.smk\": Keyword \"shell\" at line 170 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/resources.smk\": Keyword \"shell\" at line 199 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/resources.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/fastqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/Snakefile\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "niekwit/rna-seq-star-deseq2", - "latest_release": "v0.5.0", - "linting": "Workflow version: v0.5.0\nWrapper version: v4.2.0\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/Snakefile\", line 32, in \u003cmodule\u003e\n include: \"rules/trim.smk\"\n ^^^^^^^^^^^^^\n\n File \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/scripts/general_functions.smk\", line 90, in paired_end\n assert len(reads) != 0, \"No fastq files found...\"\n ^^^^^^^^^^^^^^^^^^\n\nAssertionError: No fastq files found...\n\n", + "description": "ABComp : Assembly Polishing and Bacterial Whole-genome Comparison Pipeline for Multi-group Clinical Isolates", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3mur9azr/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "young5454/ABComp", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmp3mur9azr/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 82:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule polypolish (line 375, /tmp/tmp3mur9azr/workflow/Snakefile):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule busco (line 458, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule quast (line 529, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prokka_ref (line 577, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule prokka_strain (line 653, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule roary_strain_ref_pairwise (line 732, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule move_gff_files (line 827, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param workspace is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param tmp_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule roary_within_group (line 889, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule gene_list_maker (line 952, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule move_faa_files (line 1002, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param workspace is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param group_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fasta_curation (line 1064, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cog_analysis_core (line 1120, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cog_analysis_shells (line 1190, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cog_visualization (line 1260, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule roary_visualization (line 1343, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule abricate_strain (line 1404, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule abricate_ref (line 1516, /tmp/tmp3mur9azr/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -888,91 +875,86 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725611083.0 + "updated_at": 1725328424.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/bgzip.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/imagemagick.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/bedtools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/tabix.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/samtools.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "hydra-genetics/misc", - "latest_release": "v0.2.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/common.smk\", line 12, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpok9x7dt3/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "edbennett/unify_lmh_2016", + "latest_release": null, + "linting": "Lints for rule get_gaugegravity_csvs (line 14, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_su2_code (line 37, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule unzip_su2_code (line 59, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule unify_gaugegravity_data (line 86, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule unify_su2_data (line 115, /tmp/tmpok9x7dt3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 1, "topics": [], - "updated_at": 1725608822.0 + "updated_at": 1725307570.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpfwso929l/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfwso929l/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "yjkimmdphd/asthma_bal", - "latest_release": null, - "linting": null, + "description": "Snakemake pipeline for detection limit test", + "formatting": null, + "full_name": "3d-omics/mg_quant", + "latest_release": "v1.2.0", + "linting": "Workflow defines that rule helpers__samtools__index_fa_gz__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__host__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__mags__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule preprocess__index__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule quantify__index__ is eligible for caching between workflows (use the --cache argument to enable this).\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/preprocess/index.smk:\n * Absolute path \"/{genome}\" in line 11:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/preprocess/bowtie2.smk:\n * Absolute path \"/{genome}\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/quantify/index.smk:\n * Absolute path \"/{mag_catalogue}\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp4jvhc17a/3d-omics-mg_quant-f6960e8/workflow/rules/quantify/bowtie2.smk:\n * Absolute path \"/{mag_catalogue}\" in line 49:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1725555964.0 + "topics": [ + "pipeline" + ], + "updated_at": 1725294290.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "The aim of this repository is to practice on how to create a workflow that allows automatic creation of a global map.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp8dx357ai/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "gonzarizzo/globe_map", + "description": "A Snakemake pipeline to assemble Nanopore WGS data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5i5_ucjw/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MortenEneberg/Nanopore_WGS", "latest_release": null, - "linting": null, - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5i5_ucjw/Snakefile\", line 48, in \u003cmodule\u003e\n METADATA_FOLDER = config[\"metadata_folder\"]\n ~~~~~~^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027metadata_folder\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1725546879.0 + "updated_at": 1725269237.0 }, { "config_readme": null, "data_format": 2, - "description": "Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpout79y2u/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 22:6: conda:\n```\n\n[INFO] In file \"/tmp/tmpout79y2u/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "jbloomlab/Flu-HA-H5-2.3.4.4-DMS-informed-surveillance", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3cv2tngk/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "sagieb/pMPBA", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpout79y2u/Snakefile\", line 6, in \u003cmodule\u003e\n import ruamel.yaml as yaml\n\nModuleNotFoundError: No module named \u0027ruamel\u0027\n\n", + "linting": "Lints for rule cutadapt (line 9, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bowtie_map (line 35, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort (line 61, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all (line 82, /tmp/tmp3cv2tngk/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1725538932.0 + "updated_at": 1725262513.0 }, { "config_readme": null, "data_format": 2, - "description": "Variant effect prediction using Kipoi", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmplswqabat/workflow/rules/benchmark.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmplswqabat/workflow/Snakefile\": SyntaxError: L14: \u0027use rule benchmark, evaluation, comparison from benchmark_workflow\u0027 not of form \u0027\"use\" \"rule\" (identifier | \"*\") \"from\" identifier [\"exclude\" identifier {\",\" identifier}] [\"as\" identifier] [\"with\" \":\"]\u0027\n[DEBUG] In file \"/tmp/tmplswqabat/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmplswqabat/workflow/rules/enformer.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmplswqabat/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "gtsitsiridis/kipoi_veff_analysis", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/08_seq_depth.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/06_primary_alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/01_basecall_dorado.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/05_minimap2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/rules/09_isoform_bambu.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6md6upg/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "guillermoscb/ont-dRNA-isoforms", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplswqabat/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n assert len(config) \u003e 0, \"The config file has not been defined or is empty\"\n ^^^^^^^^^^^^^^^^^^\n\nAssertionError: The config file has not been defined or is empty\n\n", + "linting": "WorkflowError in file /tmp/tmpq6md6upg/workflow/Snakefile, line 6:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmpq6md6upg/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -980,50 +962,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725525923.0 + "updated_at": 1725210100.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpixwe1_8l/workflow/rules/00_modules.smk\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "core-unit-bioinformatics/workflow-smk-vcf-annotation", - "latest_release": null, - "linting": "/tmp/tmpixwe1_8l/workflow/rules/commons/30_settings.smk:205: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n RUN_SUFFIX = RUN_SUFFIX.replace(\".\", \"-\").replace(\"_\", \"-\")\n/tmp/tmpixwe1_8l/workflow/rules/commons/30_settings.smk:208: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n # consecutive hyphens, replace with single one\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpixwe1_8l/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n include: \"rules/commons/00_commons.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpixwe1_8l/workflow/rules/commons/00_commons.smk\", line 17, in \u003cmodule\u003e\n # Module containing generic\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpixwe1_8l/workflow/rules/commons/30_settings.smk\", line 55, in \u003cmodule\u003e\n VERBOSE = workflow.verbose\n ^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027verbose\u0027\n\n", + "description": "Workflow module for mapping", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpic7_f4te/cuspuk-workflow_mapping-eec105e/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpic7_f4te/cuspuk-workflow_mapping-eec105e/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 3 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "cuspuk/workflow_mapping", + "latest_release": "v3.1.10", + "linting": "WorkflowError:\nError validating config file.\nValidationError: Additional properties are not allowed (\u0027exclude_ancestors\u0027, \u0027exclude_children\u0027, \u0027exclude_taxa_ids\u0027 were unexpected)\n\nFailed validating \u0027additionalProperties\u0027 in schema[\u0027allOf\u0027][0][\u0027then\u0027][\u0027properties\u0027][\u0027reads__decontamination__kraken\u0027]:\n {\u0027type\u0027: \u0027object\u0027,\n \u0027additionalProperties\u0027: False,\n \u0027properties\u0027: {\u0027kraken_dir\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027description\u0027: \u0027Directory with the \u0027\n \u0027kraken DB files. If \u0027\n \u0027does not exist, the \u0027\n \u0027workflow tries to \u0027\n \u0027download DB by using \u0027\n \u0027the basename. See \u0027\n \u0027https://benlangmead.github.io/aws-indexes/k2.\u0027,\n \u0027pattern\u0027: \u0027.*k2_.*_\\\\d{8}\\\\/?$\u0027,\n \u0027examples\u0027: [\u0027/data/genome/metagenome/kraken/k2_pluspf_20240112\u0027]},\n \u0027taxa_ids\u0027: {\u0027type\u0027: \u0027array\u0027,\n \u0027description\u0027: \u0027List of taxonomy IDs for \u0027\n \u0027filter logic. Example: \u0027\n \u00279606 - Homo Sapiens of \u0027\n \u0027rank=species.\u0027,\n \u0027minItems\u0027: 1,\n \u0027items\u0027: {\u0027type\u0027: \u0027integer\u0027},\n \u0027default\u0027: [9606]},\n \u0027filter_mode\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027enum\u0027: [\u0027exclude\u0027, \u0027include\u0027],\n \u0027description\u0027: \u0027Reads with specified \u0027\n \u0027taxa ids are either \u0027\n \u0027excluded or included.\u0027,\n \u0027default\u0027: \u0027exclude\u0027},\n \u0027filter_children\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027default\u0027: False,\n \u0027description\u0027: \u0027Whether to filter \u0027\n \u0027reads classified \u0027\n \u0027at more specific \u0027\n \u0027levels than \u0027\n \u0027specified taxonomy \u0027\n \u0027ID levels.\u0027},\n \u0027filter_ancestors\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027default\u0027: False,\n \u0027description\u0027: \u0027Whether to filter \u0027\n \u0027reads classified \u0027\n \u0027at all taxonomy \u0027\n \u0027levels between \u0027\n \u0027root and the \u0027\n \u0027specified \u0027\n \u0027taxonomy ID \u0027\n \u0027levels.\u0027},\n \u0027save_memory\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027description\u0027: \u0027If true, kraken limits \u0027\n \u0027RAM memory usage but \u0027\n \u0027sacrifices speed.\u0027,\n \u0027default\u0027: True},\n \u0027generate_krona\u0027: {\u0027type\u0027: \u0027boolean\u0027,\n \u0027description\u0027: \u0027If true, krona is \u0027\n \u0027generated from \u0027\n \u0027kraken report.\u0027,\n \u0027default\u0027: False},\n \u0027krona_dir\u0027: {\u0027type\u0027: [\u0027string\u0027, \u0027null\u0027],\n \u0027description\u0027: \u0027Directory where krona \u0027\n \u0027dataset is located, or \u0027\n \u0027where will be \u0027\n \u0027downloaded.\u0027,\n \u0027examples\u0027: [\u0027/data/genome/taxonomy/krona/2023-12-03/\u0027]}},\n \u0027required\u0027: [\u0027taxa_ids\u0027,\n \u0027kraken_dir\u0027,\n \u0027filter_mode\u0027,\n \u0027filter_children\u0027,\n \u0027filter_ancestors\u0027,\n \u0027save_memory\u0027,\n \u0027generate_krona\u0027,\n \u0027krona_dir\u0027],\n \u0027title\u0027: \u0027ReadsDecontaminationKraken\u0027,\n \u0027if\u0027: {\u0027properties\u0027: {\u0027generate_krona\u0027: {\u0027const\u0027: True}}},\n \u0027then\u0027: {\u0027properties\u0027: {\u0027krona_dir\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027pattern\u0027: \u0027.*/\\\\d{4}-\\\\d{2}-\\\\d{2}\\\\/?$\u0027}},\n \u0027message\u0027: \u0027reads__decontamination__kraken-\u003ekrona_dir must \u0027\n \u0027be valid if generate_krona is True.\u0027}}\n\nOn instance[\u0027reads__decontamination__kraken\u0027]:\n {\u0027kraken_dir\u0027: \u0027/data/genome/metagenome/kraken/k2_pluspf_20240112\u0027,\n \u0027exclude_taxa_ids\u0027: [9606],\n \u0027exclude_children\u0027: False,\n \u0027exclude_ancestors\u0027: False,\n \u0027save_memory\u0027: True,\n \u0027generate_krona\u0027: False,\n \u0027krona_dir\u0027: \u0027/data/genome/taxonomy/krona/2023-12-03/\u0027}\n File \"https://:ghs_IeDJpmWTuQlQw4bViKzOm0InikjEi62zmraA@raw.githubusercontent.com/cuspuk/workflow_reads/v3.6.1/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n File \"https://:ghs_IeDJpmWTuQlQw4bViKzOm0InikjEi62zmraA@raw.githubusercontent.com/cuspuk/workflow_reads/v3.6.1/workflow/rules/common.smk\", line 9, in \u003cmodule\u003e\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1725521831.0 + "updated_at": 1725197236.0 }, { "config_readme": null, "data_format": 2, - "description": "reproducibly estimate parameters for VerifyBamID2 for a new reference genome", - "formatting": null, - "full_name": "lightning-auriga/estimate-verifybamid2-reference-data", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpdhb8wyp1/workflow/Snakefile:\n * Absolute path \"/bin/bash\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpdhb8wyp1/workflow/rules/estimate_parameters.smk:\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 38:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for snakefile /tmp/tmpdhb8wyp1/workflow/rules/performance_benchmarks.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule download_reference_data (line 1, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_fasta (line 38, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_input_vcf (line 57, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_vcf (line 78, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_and_shrink (line 1, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule report_markers (line 22, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule select_downsampled_markers (line 42, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule subset_vcf (line 61, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_vcfs (line 82, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule estimate_verify_parameters (line 1, /tmp/tmpdhb8wyp1/workflow/rules/estimate_parameters.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule copy_verify_files (line 30, /tmp/tmpdhb8wyp1/workflow/rules/estimate_parameters.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule performance_benchmarks (line 22, /tmp/tmpdhb8wyp1/workflow/rules/performance_benchmarks.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param parent_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "description": "Workflow module for read processing", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpu2gkglmx/cuspuk-workflow_reads-44925a2/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpu2gkglmx/cuspuk-workflow_reads-44925a2/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "cuspuk/workflow_reads", + "latest_release": "v3.6.7", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1725910520.0 + "updated_at": 1725197223.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/Snakefile\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpawms2scm/rules/qc.smk\": Keyword \"script\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpawms2scm/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/align-fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/cna.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/align-fastq_after_merge.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\ \u0027\n[DEBUG] In file \"/tmp/tmpawms2scm/rules/variants_analysis.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mdelcorvo/DeSeq-Free", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpck2p5egj/workflow/rules/download.smk\": NoParametersError: L22: In input definition.\n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/rules/download.smk\": \n[DEBUG] In file \"/tmp/tmpck2p5egj/workflow/rules/train_pop_gen_cnn.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "xin-huang/prml", "latest_release": null, - "linting": "/tmp/tmpawms2scm/rules/common.smk:24: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n if not str.endswith(\u0027/\u0027):\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 135, in import_optional_dependency\n module = importlib.import_module(name)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/importlib/__init__.py\", line 90, in import_module\n return _bootstrap._gcd_import(name[level:], package, level)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1387, in _gcd_import\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1360, in _find_and_load\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1324, in _find_and_load_unlocked\n\nModuleNotFoundError: No module named \u0027openpyxl\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpawms2scm/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpawms2scm/rules/common.smk\", line 156, in \u003cmodule\u003e\n samples = samples[~samples[\u0027fq1\u0027].apply(check_fastq) != 1]\n ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 495, in read_excel\n io = ExcelFile(\n ^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 1567, in __init__\n self._reader = self._engines[engine](\n ^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_openpyxl.py\", line 552, in __init__\n import_optional_dependency(\"openpyxl\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 138, in import_optional_dependency\n raise ImportError(msg)\n\nImportError: Missing optional dependency \u0027openpyxl\u0027. Use pip or conda to install openpyxl.\n\n", + "linting": "Lints for snakefile /tmp/tmpck2p5egj/workflow/rules/download.smk:\n * Absolute path \"/print \\\\(.*\\\\)/print(\\\\1)/\u0027 | sed s\" in line 50:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule download_training_data (line 20, /tmp/tmpck2p5egj/workflow/rules/download.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_test_data (line 47, /tmp/tmpck2p5egj/workflow/rules/download.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule training (line 20, /tmp/tmpck2p5egj/workflow/rules/train_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule original_model_performance (line 20, /tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule reproduced_model_performance (line 57, /tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot (line 90, /tmp/tmpck2p5egj/workflow/rules/test_pop_gen_cnn.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1031,82 +1013,67 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725483209.0 + "updated_at": 1725184830.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake pipeline for variant annotation with VEP", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3vdgxua/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/install_vep_cache.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/revel.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/disgenet.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/disgenet.smk\": \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/gnomad.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/gnomad.smk\": \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/rnacentral.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/rnacentral.smk\": \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/loftee.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/loftee.smk\": \n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/cadd.smk\": Formatted content is different from original\n[INFO] 4 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "hmartiniano/annot", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppgts66o_/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "bluegenes/2024-nsurp", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config.yml but it is not present or accessible (full checked path: /tmp/tmpj3vdgxua/config.yml).\n", + "linting": "Lints for rule branchwater_fastmultigather (line 75, /tmp/tmppgts66o_/Snakefile):\n * Param outd is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sourmash_taxonomy (line 123, /tmp/tmppgts66o_/Snakefile):\n * Param output_base is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1725479314.0 + "updated_at": 1725068190.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsqa3ksxm/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mdondrup/divergence_time", + "description": "Codebase exploring figure-ground segregation in texture stimuli through neural synchrony mechanisms. Contains simulations based on the theory of weakly coupled oscillators, psychophysics experiments, and statistical analyses.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpizzb9992/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ccnmaastricht/NeuralSynchrony-FigureGround", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpsqa3ksxm/workflow/Snakefile:\n * Absolute path \"/|\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 8:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule degenotate (line 61, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rename_chromosomes (line 99, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule index_vcf (line 147, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_vcf (line 182, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_genotype_matrix (line 232, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule difference_matrix (line 282, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, + "linting": "Lints for rule download_data (line 28, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_system_info (line 44, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_gee_accuracy (line 60, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_behavioral_arnold_tongue (line 81, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_transfer_session_model_comparison (line 105, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_parameter_exploration (line 126, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_crossval_estimation (line 147, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_crossval_prediction (line 168, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_high_resolution_simulations (line 190, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule test_model_predictions (line 211, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_figure_two (line 234, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_figure_three (line 260, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_figure_four (line 281, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_figure_five (line 305, /tmp/tmpizzb9992/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725458332.0 + "updated_at": 1725028128.0 }, { "config_readme": null, "data_format": 2, - "description": "Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data", - "formatting": null, - "full_name": "hermidalc/tcga-wgs-kraken-microbial-quant", + "description": "A tool designed specifically for analyzing RNA-seq data using Snakemake workflows", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/hisat2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/fastp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/salmon.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/DESeqFromFeatureCounts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/BigWig.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/featureCounts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/DESeqFromHTSeqCount.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/fastqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/arriba.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/htseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi4vzwe2l/workflow/rules/STAR.smk\": Formatted content is different from original\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "littleisland8/Transcriptomestic", "latest_release": null, - "linting": "Using workflow specific profile workflow/profiles/default for setting default command line arguments.\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpl5kimfd7/workflow/Snakefile\", line 129, in \u003cmodule\u003e\n\nAssertionError: GDC auth token not found in GDC_TOKEN, GDC_TOKEN_FILE, or ~/.gdc_token\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpi4vzwe2l/workflow/Snakefile\", line 5, in \u003cmodule\u003e\n include: \"rules/STAR.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpi4vzwe2l/workflow/rules/fastqc.smk\", line 4, in \u003cmodule\u003e\n output:\n\nTypeError: unsupported operand type(s) for +: \u0027NoneType\u0027 and \u0027str\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "bioinformatics-pipeline", - "bioinformatics-workflow", - "metagenomic-pipeline", - "metagenomics", - "metagenomics-taxon-profiling", - "snakemake-pipeline", - "snakemake-workflow" - ], - "updated_at": 1725457492.0 + "topics": [], + "updated_at": 1725015928.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp08ufac6a/Snakefile\": Keyword \"input\" at line 123 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp08ufac6a/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "lucianhu/rnaseq_snakemake", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[WARNING] In file \"/tmp/tmpgnn_t2gx/Snakefile\": Keyword \"output\" at line 178 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpgnn_t2gx/Snakefile\": Keyword \"output\" at line 1000 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpgnn_t2gx/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "LukasFrankenQ/pypsa-earth-sec", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp08ufac6a/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule import_genome (line 139, /tmp/tmp08ufac6a/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule import_annotation (line 160, /tmp/tmp08ufac6a/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule trim_galore_paired (line 462, /tmp/tmp08ufac6a/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule align_paired (line 588, /tmp/tmp08ufac6a/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule align_single (line 693, /tmp/tmp08ufac6a/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule read_distribution (line 1495, /tmp/tmp08ufac6a/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "SyntaxError in file /tmp/tmpgnn_t2gx/Snakefile, line 61:\nKeyword subworkflow is deprecated. Use module directive instead :\nNone\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1114,16 +1081,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725454058.0 + "updated_at": 1725005433.0 }, { "config_readme": null, "data_format": 2, - "description": "2023-2024 data-process pipeline-conversion project; Adapting havoc to utilise snakemake.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/indelqual_bamfile.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/mask_low-coverage_regions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/remove_primers.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/preprocess_reads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/lineage_identification.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/create_visual.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/variant_calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/process_SAM_and_BAM_files.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/consensus_calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/align_reads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/Snakefile\": Formatted content is different from original\n[INFO] 11 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "WisseSchuuring/NewDataProcessProject", + "description": "Lightweight snakemake pipeline for preprocessing, alignmen, and QC of PROseq/ChROseq data", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpf3ix66yp/rules/1b_rule.smk\": InvalidParameterSyntax: 3\"file1.extension\"\nINPUT_2=\"file2.extension\"\n\n[DEBUG] In file \"/tmp/tmpf3ix66yp/rules/1b_rule.smk\": \n[ERROR] In file \"/tmp/tmpf3ix66yp/rules/0_rule.smk\": InvalidParameterSyntax: 3\"file1.extension\"\nINPUT_2=\"file2.extension\"\n\n[DEBUG] In file \"/tmp/tmpf3ix66yp/rules/0_rule.smk\": \n[ERROR] In file \"/tmp/tmpf3ix66yp/rules/1a_rule.smk\": InvalidParameterSyntax: 3\"file1.extension\"\nINPUT_2=\"file2.extension\"\n\n[DEBUG] In file \"/tmp/tmpf3ix66yp/rules/1a_rule.smk\": \n[ERROR] In file \"/tmp/tmpf3ix66yp/Snakefile\": NoParametersError: L52: In input definition.\n[INFO] In file \"/tmp/tmpf3ix66yp/Snakefile\": 4 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "mckellardw/runon_snake", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile /homes/wsfschuuring/Desktop/DataProcess/SECRET-PROJECT/NewDataProcessProject/config/config.yaml but it is not present or accessible (full checked path: /homes/wsfschuuring/Desktop/DataProcess/SECRET-PROJECT/NewDataProcessProject/config/config.yaml).\n", + "linting": "WorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpf3ix66yp/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1131,33 +1098,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725447002.0 + "updated_at": 1724953436.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"input\" at line 145 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"resources\" at line 222 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"resources\" at line 257 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"output\" at line 536 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "highRES-model/highRES-Europe-WF", + "description": "Media Mix Modelling: Lecture 3 of Digital and Social Media Strategies (DSMS) at Tilburg U", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpcswibnm_/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcswibnm_/rules/renv.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "deer-marketing-lab/dsms-lecture-mediamix", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpms5_34th/workflow/Snakefile:\n * Absolute path \"/highres.lst\" in line 505:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/highres.log\" in line 506:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/highres.lst\" in line 534:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/highres.log\" in line 535:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 365:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 447:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 489:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 517:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 550:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule build_cplex_opt (line 155, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_zones_file (line 176, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_technoeconomic_inputs (line 199, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rename_demand_file (line 242, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_shapes (line 261, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_vre_cf_grid (line 292, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_vre_land_avail (line 331, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_vre_cf_inputs (line 389, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_hydro_capfac (line 421, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_areas_file (line 474, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_hydrores_inflow (line 516, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compress_hydrores_inflow (line 541, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule link_hydrores_inflow (line 563, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_file (line 585, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule build_vre_parquet (line 619, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_csv (line 646, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_gdx (line 673, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compress_vre_gdx (line 699, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_gams (line 795, /tmp/tmpms5_34th/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param modelpath is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule convert_results (line 846, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule convert_results_db_parquet (line 869, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Lints for rule build_html (line 16, /tmp/tmpcswibnm_/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 46, /tmp/tmpcswibnm_/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 89, /tmp/tmpcswibnm_/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 22, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 34, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 46, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 58, /tmp/tmpcswibnm_/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1725437645.0 + "updated_at": 1724950425.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow to re-batch POD5 files by pore/channel", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpe1yo8avq/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 70:0: res = defaultdict(set)\n```\n\n[INFO] In file \"/tmp/tmpe1yo8avq/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "tbooth/pod5_by_pore", + "description": "Basic RNA-seq snakemake workflow. Use as a module for larger workflows.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/SplicingAnalysis.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpxp575kpp/rules/IndexGenome.smk\": NoParametersError: L107: In params definition.\n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/IndexGenome.smk\": \n[ERROR] In file \"/tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk\": NoParametersError: L47: In params definition.\n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk\": \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/ExpressionAnalysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/QC.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/MakeBigwigs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxp575kpp/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxp575kpp/Snakefile\": Keyword \"input\" at line 37 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxp575kpp/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "bfairkun/snakemake-workflow_rna-seq", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpe1yo8avq/workflow/Snakefile:\n * Absolute path \"/{p5}.pod5\" in line 17:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{foo}.pod5\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 17:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule get_channels_in_pod (line 39, /tmp/tmpe1yo8avq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule batched_channels_in_pod (line 46, /tmp/tmpe1yo8avq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule get_channels_in_use (line 63, /tmp/tmpe1yo8avq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\n", + "linting": "Lints for snakefile /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk:\n * Absolute path \"/STARIndex\" in line 86:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpxp575kpp/rules/IndexGenome.smk:\n * Absolute path \"/^#/ || /tag \"basic\"/ || /transcript_biotype \"mRNA\"/ || /transcript_biotype \"protein_coding\"/ || $3==\"gene\" || /transcript_id \"[XN]M/\u0027 {input.gtf} | sed -e \" in line 28:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk:\n * Absolute path \"/Reference.basic.gtf\" in line 169:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 93:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpxp575kpp/rules/MakeBigwigs.smk:\n * Absolute path \"/project2/yangili1/bjf79/ChromatinSplicingQTLs/code/ReferenceGenome/Fasta/GRCh38.primary_assembly.genome.fa.fai\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule CopyFastq (line 1, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule CopyFastq_SE (line 39, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule STAR_Align (line 185, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule indexBam (line 238, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule idxstats (line 269, /tmp/tmpxp575kpp/rules/PreprocessAndAlign.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule DownloadFastaAndGtf (line 1, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule GetBasicGtf (line 30, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule faidxGenome (line 71, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gtf_to_bed12 (line 96, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_colored_bed12 (line 174, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule STAR_make_index (line 202, /tmp/tmpxp575kpp/rules/IndexGenome.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ConcatJuncFilesAndKeepUniq (line 92, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_leafcutter_juncfile (line 168, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule leafcutter_cluster (line 199, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bgzip_PSI_bed (line 288, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule Get5ssSeqs (line 331, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ConvertLeacfutterJuncNames_To_True_Bed_Coords (line 419, /tmp/tmpxp575kpp/rules/SplicingAnalysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule MultiQC (line 53, /tmp/tmpxp575kpp/rules/QC.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule CountReadsPerSample (line 88, /tmp/tmpxp575kpp/rules/QC.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule MakeBigwigs_NormalizedToGenomewideCoverage (line 2, /tmp/tmpxp575kpp/rules/MakeBigwigs.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1165,16 +1132,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726155010.0 + "updated_at": 1724948624.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpjaoq8q6y/workflow/Snakefile\": InvalidParameterSyntax: 189rule cplex_opt_EU\n\n\n\n[INFO] In file \"/tmp/tmpjaoq8q6y/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "celeryroastalpenglow/MENOFS", - "latest_release": null, - "linting": "PermissionError in file /tmp/tmpjaoq8q6y/workflow/Snakefile, line 146:\n[Errno 13] Permission denied: \u0027/a_folder_path\u0027\n File \"/tmp/tmpjaoq8q6y/workflow/Snakefile\", line 146, in \u003cmodule\u003e\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile\": Keyword \"output\" at line 37 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile\": Keyword \"shell\" at line 48 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "jiapeng-CP/Snakemake_MTG", + "latest_release": "v1.0.0", + "linting": "RuleException in rule catFq in file /tmp/tmppg830s7j/jiapeng-CP-Snakemake_MTG-6bf9c77/Snakefile, line 90:\nNot all output, log and benchmark files of rule catFq contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1182,50 +1149,67 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726145324.0 + "updated_at": 1724944578.0 }, { "config_readme": null, "data_format": 2, - "description": "Barcode Recovery and Comparison from Database", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/commons.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/reports.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\q\u0027\n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/pairwise_alignement.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/extract_barcodes.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "CVUA-RRW/BaRCoD", - "latest_release": "1.1.1", - "linting": "WorkflowError in file /tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/Snakefile, line 12:\nWorkflow defines configfile /tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/../.tests/config/config.yaml but it is not present or accessible (full checked path: /tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/.tests/config/config.yaml).\n", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptjcq7m2e/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "daisybio/DysRegNet_workflow", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmptjcq7m2e/workflow/Snakefile:\n * Absolute path \"/nfs/data/patients_networks/data\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule prepare_HTRIdb (line 115, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_string (line 142, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_pancan_tpm (line 173, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sample_infos (line 217, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscoring (line 251, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3 (line 284, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_shared (line 324, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_top (line 357, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet (line 392, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet_no_direction (line 428, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ssn (line 465, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compute_overlap_shared (line 500, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_shared (line 538, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_benchmark_shared (line 579, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_tests (line 614, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_tests (line 650, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_plots (line 686, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_plots (line 728, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mutation_plots (line 813, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule model_stats_plots (line 859, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats (line 896, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats_plots (line 925, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_tests (line 964, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_plots (line 998, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_dysregnet (line 1037, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_ssn (line 1078, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_plots (line 1117, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_meta (line 1151, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_dysregnet (line 1180, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_plots (line 1216, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule provide_db (line 1256, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule load_db (line 1295, /tmp/tmptjcq7m2e/workflow/Snakefile):\n * Shell command directly uses variable DB_PW from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 2, "topics": [], - "updated_at": 1726142474.0 + "updated_at": 1724916589.0 }, { "config_readme": null, "data_format": 2, - "description": "Find single-stranded DNA breaks with an error-prone DNA polymerase", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_sbd6gc0/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "NBISweden/Sloppymerase", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpgsdtaw6f/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "JohannesKersting/DysRegNet_workflow", "latest_release": null, - "linting": "Lints for rule count_illumina_reads (line 24, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_illumina (line 33, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule count_nanopore_pacbio_reads (line 49, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_nanopore (line 57, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_pacbio (line 71, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule detect_breaks (line 84, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_bed (line 106, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule subtract_illumina_controls (line 116, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simulate_nickase (line 128, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule random_sites (line 141, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule intersect_nickase_sites (line 153, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule intersect_random_sites (line 162, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index_bed (line 171, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index_bam (line 177, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bgzip_bed (line 182, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpgsdtaw6f/workflow/Snakefile:\n * Absolute path \"/nfs/data/patients_networks/data\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule prepare_HTRIdb (line 115, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_string (line 142, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_pancan_tpm (line 173, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sample_infos (line 217, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscoring (line 251, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3 (line 284, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_shared (line 324, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genie3_top (line 357, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet (line 392, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dysregnet_no_direction (line 428, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ssn (line 465, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compute_overlap_shared (line 500, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_shared (line 538, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clustering_benchmark_shared (line 579, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_tests (line 614, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_tests (line 650, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_plots (line 686, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule methylation_zscores_plots (line 728, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mutation_plots (line 813, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule model_stats_plots (line 859, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats (line 896, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule network_stats_plots (line 925, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_tests (line 964, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule cancer_stage_plots (line 998, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_dysregnet (line 1037, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_ssn (line 1078, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runtime_plots (line 1117, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_meta (line 1151, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_dysregnet (line 1180, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule downsample_plots (line 1216, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule provide_db (line 1256, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule load_db (line 1295, /tmp/tmpgsdtaw6f/workflow/Snakefile):\n * Shell command directly uses variable DB_PW from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 7, + "subscribers_count": 1, "topics": [], - "updated_at": 1726141738.0 + "updated_at": 1724916566.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "create long read (Nanopore with NanoSim) and short read (Illumina with Circle-Map) testing data for ecDNA analysis workflows", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpiw53r2g_/workflow/Snakefile\": Keyword \"params\" at line 56 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmpiw53r2g_/workflow/Snakefile\": IndexError: pop from empty list\n[INFO] In file \"/tmp/tmpiw53r2g_/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "dlaehnemann/create-ecdna-testing-data", + "description": "Clinical Genomics Uppsala inheritance disease pipeline for WGS", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/add_ref_to_vcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/extract_str_bed.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/concat_vcfs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/coverage.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/fix_sv_header.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/bcftools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/peddy.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/vcf_to_aed.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "clinical-genomics-uppsala/poirot_rd_wgs", + "latest_release": "v0.6.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbzqk2aol/clinical-genomics-uppsala-poirot_rd_wgs-59afb24/workflow/rules/common.smk\", line 10, in \u003cmodule\u003e\n from hydra_genetics.utils.misc import get_module_snakefile\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 0, + "topics": [], + "updated_at": 1724916636.0 + }, + { + "config_readme": "\u003cp\u003eUser needs to change the simulation parameters in the config file without changing the format.\u003c/p\u003e\n", + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "bethanyyk/DENV_simulations", "latest_release": null, - "linting": "Workflow defines that rule get_chromosomes_ref is eligible for caching between workflows (use the --cache argument to enable this).\nLints for snakefile /tmp/tmpiw53r2g_/workflow/Snakefile:\n * Absolute path \"/human_NA12878_DNA_FAB49712_guppy/training\" in line 12:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/human_NA12878_DNA_FAB49712_guppy/training\" in line 16:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule config_segment_to_bed (line 65, /tmp/tmpiw53r2g_/workflow/Snakefile):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule create_samples_sheet (line 277, /tmp/tmpiw53r2g_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule create_units_sheet (line 305, /tmp/tmpiw53r2g_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\n", + "linting": null, "mandatory_flags": { "desc": null, "flags": null @@ -1240,16 +1224,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726140775.0 + "updated_at": 1725495840.0 }, { "config_readme": null, "data_format": 2, - "description": "Just annotate the MAGs as in mg_assembly", - "formatting": null, - "full_name": "3d-omics/mg_annotate", + "description": "Performs analysis of mass spectrometry data for John Belisle\u0027s lab.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmprw7gf7pd/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ryanjob42/mass-spec-analysis", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpi0370ikk/workflow/rules/dram.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule checkm2__quality_report__ (line 27, /tmp/tmpi0370ikk/workflow/rules/checkm2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\nusage: snakemake [-h] [--dry-run] [--profile PROFILE]\n [--workflow-profile WORKFLOW_PROFILE] [--cache [RULE ...]]\n [--snakefile FILE] [--cores N] [--jobs N] [--local-cores N]\n [--resources NAME=INT [NAME=INT ...]]\n [--set-threads RULE=THREADS [RULE=THREADS ...]]\n [--max-threads MAX_THREADS]\n [--set-resources RULE:RESOURCE=VALUE [RULE:RESOURCE=VALUE ...]]\n [--set-scatter NAME=SCATTERITEMS [NAME=SCATTERITEMS ...]]\n [--set-resource-scopes RESOURCE=[global|local]\n [RESOURCE=[global|local] ...]]\n [--default-resources [NAME=INT ...]]\n [--preemptible-rules [PREEMPTIBLE_RULES ...]]\n [--preemptible-retries PREEMPTIBLE_RETRIES]\n [--configfile FILE [FILE ...]] [--config [KEY=VALUE ...]]\n [--envvars VARNAME [VARNAME ...]] [--directory DIR] [--touch]\n [--keep-going]\n [--rerun-triggers {code,input,mtime,params,software-env} [{code,input,mtime,params,software-env} ...]]\n [--force] [--executor {local,dryrun,touch}] [--forceall]\n [--forcerun [TARGET ...]] [--prioritize TARGET [TARGET ...]]\n [--batch RULE=BATCH/BATCHES] [--until TARGET [TARGET ...]]\n [--omit-from TARGET [TARGET ...]] [--rerun-incomplete]\n [--shadow-prefix DIR] [--scheduler [{ilp,greedy}]]\n [--wms-monitor [WMS_MONITOR]]\n [--wms-monitor-arg [NAME=VALUE ...]]\n [--scheduler-ilp-solver {PULP_CBC_CMD,COIN_CMD}]\n [--conda-base-path CONDA_BASE_PATH] [--no-subworkflows]\n [--precommand PRECOMMAND] [--groups GROUPS [GROUPS ...]]\n [--group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]]\n [--report [FILE]] [--report-stylesheet CSSFILE]\n [--reporter PLUGIN] [--draft-notebook TARGET]\n [--edit-notebook TARGET] [--notebook-listen IP:PORT]\n [--lint [{text,json}]] [--generate-unit-tests [TESTPATH]]\n [--containerize] [--export-cwl FILE] [--list-rules]\n [--list-target-rules] [--dag] [--rulegraph] [--filegraph]\n [--d3dag] [--summary] [--detailed-summary] [--archive FILE]\n [--cleanup-metadata FILE [FILE ...]] [--cleanup-shadow]\n [--skip-script-cleanup] [--unlock]\n [--list-changes {input,params,code}] [--list-input-changes]\n [--list-params-changes] [--list-untracked]\n [--delete-all-output | --delete-temp-output]\n [--keep-incomplete] [--drop-metadata] [--version]\n [--printshellcmds] [--debug-dag] [--nocolor]\n [--quiet [{all,progress,rules} ...]] [--print-compilation]\n [--verbose] [--force-use-threads] [--allow-ambiguity]\n [--nolock] [--ignore-incomplete]\n [--max-inventory-time SECONDS] [--latency-wait SECONDS]\n [--wait-for-files [FILE ...]] [--wait-for-files-file FILE]\n [--queue-input-wait-time SECONDS] [--notemp] [--all-temp]\n [--unneeded-temp-files FILE [FILE ...]]\n [--keep-storage-local-copies]\n [--target-files-omit-workdir-adjustment]\n [--allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]]\n [--max-jobs-per-timespan MAX_JOBS_PER_TIMESPAN]\n [--max-jobs-per-second MAX_JOBS_PER_SECOND]\n [--max-status-checks-per-second MAX_STATUS_CHECKS_PER_SECOND]\n [--seconds-between-status-checks SECONDS_BETWEEN_STATUS_CHECKS]\n [--retries RETRIES] [--wrapper-prefix WRAPPER_PREFIX]\n [--default-storage-provider DEFAULT_STORAGE_PROVIDER]\n [--default-storage-prefix DEFAULT_STORAGE_PREFIX]\n [--local-storage-prefix LOCAL_STORAGE_PREFIX]\n [--remote-job-local-storage-prefix REMOTE_JOB_LOCAL_STORAGE_PREFIX]\n [--shared-fs-usage {input-output,persistence,software-deployment,source-cache,sources,storage-local-copies,none} [{input-output,persistence,software-deployment,source-cache,sources,storage-local-copies,none} ...]]\n [--scheduler-greediness SCHEDULER_GREEDINESS] [--no-hooks]\n [--debug] [--runtime-profile FILE]\n [--local-groupid LOCAL_GROUPID] [--attempt ATTEMPT]\n [--show-failed-logs] [--log-handler-script FILE]\n [--log-service {none,slack,wms}] [--job-deploy-sources]\n [--benchmark-extended] [--container-image IMAGE]\n [--immediate-submit] [--jobscript SCRIPT] [--jobname NAME]\n [--flux]\n [--software-deployment-method {apptainer,conda,env-modules} [{apptainer,conda,env-modules} ...]]\n [--container-cleanup-images] [--use-conda]\n [--conda-not-block-search-path-envvars] [--list-conda-envs]\n [--conda-prefix DIR] [--conda-cleanup-envs]\n [--conda-cleanup-pkgs [{tarballs,cache}]]\n [--conda-create-envs-only] [--conda-frontend {conda,mamba}]\n [--use-apptainer] [--apptainer-prefix DIR]\n [--apptainer-args ARGS] [--use-envmodules]\n [--scheduler-solver-path SCHEDULER_SOLVER_PATH]\n [--deploy-sources QUERY CHECKSUM]\n [--target-jobs TARGET_JOBS [TARGET_JOBS ...]]\n [--mode {remote,subprocess,default}]\n [--report-html-path VALUE]\n [--report-html-stylesheet-path VALUE]\n [targets ...]\nsnakemake: error: argument --executor/-e: invalid choice: \u0027slurm\u0027 (choose from \u0027local\u0027, \u0027dryrun\u0027, \u0027touch\u0027)\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1257,70 +1241,67 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726134655.0 + "updated_at": 1724882363.0 }, { "config_readme": null, "data_format": 2, - "description": "A Snakemake pipeline to analyze RNA-seq expression data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/diffexp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/quantification.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp31et65mg/workflow/Snakefile\": Keyword \"input\" at line 44 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/plots.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/splicing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/align.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "kristinassong/RNAseq", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpt52y0ckk/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "IMCBioinformatics/dada2_ITS_workflow", "latest_release": null, - "linting": "Lints for rule star_index (line 1, /tmp/tmp31et65mg/workflow/rules/align.smk):\n * Param idx is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_align (line 27, /tmp/tmp31et65mg/workflow/rules/align.smk):\n * Param out_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param idx is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule genomecov (line 97, /tmp/tmp31et65mg/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule kallisto_quant (line 38, /tmp/tmp31et65mg/workflow/rules/quantification.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule tx2gene (line 67, /tmp/tmp31et65mg/workflow/rules/quantification.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_kallisto_quant (line 80, /tmp/tmp31et65mg/workflow/rules/quantification.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deseq2 (line 3, /tmp/tmp31et65mg/workflow/rules/diffexp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param kallisto_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule volcano_plot (line 22, /tmp/tmp31et65mg/workflow/rules/diffexp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule pca (line 1, /tmp/tmp31et65mg/workflow/rules/plots.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 17, /tmp/tmp31et65mg/workflow/rules/plots.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats (line 1, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_rmats (line 23, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_paired_env (line 46, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rmats_paired (line 62, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_rmats_paired (line 85, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpt52y0ckk/Snakefile\", line 10, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027samples/samples.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "rna-seq-pipeline", - "snakemake-workflow" - ], - "updated_at": 1726112847.0 + "topics": [], + "updated_at": 1724878213.0 }, { "config_readme": null, "data_format": 2, - "description": "Workflow for processing UAS imagery into data on bird location and species for near real-time monitoring in the Everglades", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpopwg9ani/weecology-everwatch-workflow-2e6fceb/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "weecology/everwatch-workflow", - "latest_release": "v0.2.0", - "linting": "WorkflowError in file /tmp/tmpopwg9ani/weecology-everwatch-workflow-2e6fceb/Snakefile, line 5:\nWorkflow defines configfile /blue/ewhite/everglades/everwatch-workflow/snakemake_config.yml but it is not present or accessible (full checked path: /blue/ewhite/everglades/everwatch-workflow/snakemake_config.yml).\n", + "description": null, + "formatting": "Could not parse .gitignore: Invalid git pattern: \u0027.Ruserdata\\\\\\n\u0027\nValueError: Escape character found with no next character to escape: \u0027.Ruserdata\\\\\u0027\n\nThe above exception was the direct cause of the following exception:\n\npathspec.patterns.gitwildmatch.GitWildMatchPatternError: Invalid git pattern: \u0027.Ruserdata\\\\\\n\u0027\n\nsnakefmt version: 0.10.2", + "full_name": "krferrier/EWAS", + "latest_release": null, + "linting": "SyntaxError in file /tmp/tmpexugv3hd/rules/annotate.smk, line 58:\ninvalid syntax:\n\tshell ( , bench_record=bench_record, bench_iteration=bench_iteration\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 1, "topics": [], - "updated_at": 1726093707.0 + "updated_at": 1724874419.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpb_4sx3jl/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 75:0: EOF in multi-line statement\n```\n\n[INFO] In file \"/tmp/tmpb_4sx3jl/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "SoftLivingMatter/5eU-seq-pipelines", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppulecl4m/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Fotowatikha/sc-sn-RNA-seq-Pre-Processing-Pipeline", "latest_release": null, - "linting": "Creating specified working directory /your/directory/here.\nPermissionError in file /tmp/tmpb_4sx3jl/workflow/Snakefile, line 7:\n[Errno 13] Permission denied: \u0027/your\u0027\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n", + "linting": "Traceback (most recent call last):\n\n File \"/tmp/tmppulecl4m/Snakefile\", line 21, in \u003cmodule\u003e\n name_of_configfile = args[args.index(\"--configfiles\") + 1] # hpc\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nValueError: \u0027--configfiles\u0027 is not in list\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmppulecl4m/Snakefile\", line 23, in \u003cmodule\u003e\n name_of_configfile = args[args.index(\"--configfile\") + 1] # one config\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nValueError: \u0027--configfile\u0027 is not in list\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1726177806.0 + "updated_at": 1724872193.0 }, { "config_readme": null, "data_format": 2, - "description": "Workflow to identify the centromere dip region (CDR) from methyl BAMs", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpumxp1g0a/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "koisland/CDR-Finder", + "description": "Seabreeze: an automated pipeline for structrual variant analysis of bacterial resequencing experiments", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpuws_dkki/Snakefile\": Keyword \"output\" at line 86 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpuws_dkki/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ira-zibbu/seabreeze-ltee-analysis", "latest_release": null, - "linting": null, + "linting": "Lints for rule rename_contigs (line 53, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule compute_genome_stats (line 85, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_ISEScan_summary (line 171, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param input_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule align_genomes_nucmer (line 212, /tmp/tmpuws_dkki/Snakefile):\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule call_variants_syri (line 279, /tmp/tmpuws_dkki/Snakefile):\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_synteny_plot (line 345, /tmp/tmpuws_dkki/Snakefile):\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule clean_syri_output (line 407, /tmp/tmpuws_dkki/Snakefile):\n * Param isescan_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_synteny_plot_clean (line 463, /tmp/tmpuws_dkki/Snakefile):\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule reindex_contigs_oric (line 515, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_ori_dif_locations (line 543, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule analyse_replichore_arms (line 588, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule annotate_SV_boundaries_IS (line 667, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_SV_mechanism (line 709, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule classify_inversion_replichore (line 756, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_genome_diffs_tables (line 812, /tmp/tmpuws_dkki/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param gd_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param html_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1328,16 +1309,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726071971.0 + "updated_at": 1724869348.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake pipeline for parsing simulation outputs across scaling factors", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpkpgy83jb/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "SchriderLab/simscale-snakemake", + "latest_release": null, + "linting": "TypeError in file /tmp/tmpkpgy83jb/workflow/Snakefile, line 11:\n\u0027NoneType\u0027 object is not subscriptable\n File \"/tmp/tmpkpgy83jb/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1725894756.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbyphbz3g/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "vkpat/short-read-mapping-and-QC-snakemake-pipeline", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/rules/toblow5.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/rules/fetch_data.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpiobvfk4r/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "loganylchen/prep_public_nanoporeDRS_data", "latest_release": null, - "linting": "WorkflowError in file /tmp/tmpbyphbz3g/workflow/Snakefile, line 1:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpbyphbz3g/config.yaml).\n", + "linting": "/tmp/tmpiobvfk4r/workflow/Snakefile:9: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n sample=\"[\\da-zA-Z]+\"\nFileNotFoundError in file /tmp/tmpiobvfk4r/workflow/rules/common.smk, line 6:\n[Errno 2] No such file or directory: \u0027config/samples.tsv\u0027\n File \"/tmp/tmpiobvfk4r/workflow/rules/common.smk\", line 6, in \u003cmodule\u003e\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n", "mandatory_flags": { "desc": null, "flags": null @@ -1352,50 +1350,67 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726070051.0 + "updated_at": 1725894100.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptmii62qa/rules/renv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmptmii62qa/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "deer-marketing-lab/dsms-lecture-ugc-ratings", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpy9boas6k/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "daiuc/splice-pub", "latest_release": null, - "linting": "Lints for rule build_html (line 16, /tmp/tmptmii62qa/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 29, /tmp/tmptmii62qa/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 48, /tmp/tmptmii62qa/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 15, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 20, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 25, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 30, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpy9boas6k/Snakefile:\n * Absolute path \"/project/yangili1/cdai/SpliFi\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/smk-plots/gtex-sqtl-enrichment-v4\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/data/WGS_Feature_overlap_collapsed_VEP_short_4torus.MAF01.txt.gz\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/SpliFi\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/smk-plots/gtex-sqtl-enrichment-v4-C\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/yangili1/cdai/splice-pub/data/WGS_Feature_overlap_collapsed_VEP_short_4torus.MAF01.txt.gz\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 15:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule plotGTExsQTLEnrichment (line 33, /tmp/tmpy9boas6k/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plotGTExsQTLEnrichment_test (line 76, /tmp/tmpy9boas6k/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepTorusInputData (line 63, /tmp/tmpy9boas6k/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outprefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule RunTorusEnrich (line 85, /tmp/tmpy9boas6k/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1726069627.0 + "updated_at": 1725892780.0 }, { "config_readme": null, "data_format": 2, - "description": "[INSERM U981] WGS\u0026WES Pipelines", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppavg8cvv/workflow/rules/init_pipeline.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmppavg8cvv/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 62:0: \u003cline number missing in source\u003e\n```\n\n[INFO] In file \"/tmp/tmppavg8cvv/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmppavg8cvv/workflow/Snakefile\": 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "jinxin-wang/Genome_Sequencing_Analysis", + "description": null, + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpl4vsaazr/Snakefile\": SyntaxError: L107: Unrecognised keyword \u0027savedir\u0027 in rule definition\n[INFO] In file \"/tmp/tmpl4vsaazr/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "ML4GW/gwak", "latest_release": null, - "linting": "FileNotFoundError in file /tmp/tmppavg8cvv/workflow/rules/init_pipeline.smk, line 118:\n[Errno 2] No such file or directory: \u0027config/variant_call_list_TvN.tsv\u0027\n File \"/tmp/tmppavg8cvv/workflow/rules/init_pipeline.smk\", line 118, in \u003cmodule\u003e\n", + "linting": "Lints for snakefile /tmp/tmpl4vsaazr/Snakefile:\n * Absolute path \"/home/katya.govorkova/gwak/{version}/data/{dataclass}.npz\" in line 87:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule find_valid_segments (line 31, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_omicron (line 40, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fetch_site_data (line 52, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_data (line 64, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PERIOD from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule upload_data (line 81, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule validate_data (line 92, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable VERSION from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule train_quak (line 101, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_timeslides_for_far (line 113, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule evaluate_signals (line 137, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_timeslides_for_fm (line 150, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule train_final_metric (line 173, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule recreation_and_quak_plots (line 192, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compute_far (line 208, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_far_hist (line 232, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule quak_plotting_prediction_and_recreation (line 242, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_results (line 257, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param evaluation_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule make_pipeline_plot (line 272, /tmp/tmpl4vsaazr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 4, "topics": [], - "updated_at": 1726062684.0 + "updated_at": 1725890954.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:14: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n[DEBUG] In file \"/tmp/tmpdyuhxgko/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "fredjarlier/ProjectCNN", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpijdr3wdn/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "iedun/XDEM-Project", "latest_release": null, - "linting": "/tmp/tmpdyuhxgko/Snakefile:78: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n \"{yes}.bam\"\n/tmp/tmpdyuhxgko/Snakefile:85: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n input:\nKeyError in file /tmp/tmpdyuhxgko/Snakefile, line 31:\n\u0027lanes\u0027\n File \"/tmp/tmpdyuhxgko/Snakefile\", line 31, in \u003cmodule\u003e\n", + "linting": "RuleException in file /tmp/tmpijdr3wdn/Snakefile, line 32:\nOnly input files can be specified as functions\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1725890597.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmplmj6xu4a/workflow/Snakefile\": Keyword \"input\" at line 71 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmplmj6xu4a/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "caballero/snakemake-pairtools-phased", + "latest_release": null, + "linting": "KeyError in file /tmp/tmplmj6xu4a/workflow/Snakefile, line 12:\n\u0027fastq_dir\u0027\n File \"/tmp/tmplmj6xu4a/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1403,16 +1418,16 @@ var data = "stargazers_count": 0, "subscribers_count": 2, "topics": [], - "updated_at": 1726058223.0 + "updated_at": 1725870943.0 }, { "config_readme": null, "data_format": 2, - "description": "Mu-seq Workflow Utility ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/insertion_identification.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 93 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 129 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 168 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 200 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk\": InvalidPython: Black error:\n```\nCannot parse: 18:4: run:\n```\n\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk\": \n[ERROR] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/trimming.smk\": InvalidPython: Black error:\n```\nCannot parse: 45:4: log:\n```\n\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/trimming.smk\": \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/common_utils.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/quality_control.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/insertion_annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref_utils.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk\": InvalidPython: Black error:\n```\nCannot parse: 14:7: output:\n```\n\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk\": \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/indexes_bam2sam.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/duplicate_removal.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/mapping.smk\": Inline-formatted keyword \"threads\" at line 80 had its comments relocated above it.\nPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/mapping.smk\": Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "tgstoecker/MuWU", - "latest_release": "v1.5.0", - "linting": "/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk:129: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \"logs/annotation_table/annotation_table.log\"\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk:142: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \".1.bt2\", \".2.bt2\", \".3.bt2\", \".4.bt2\", \".rev.1.bt2\", \".rev.2.bt2\",\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:45: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n sed -i \u00271i Name\\\\tStrand\\\\tType\u0027 {output}\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:53: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n read_typing=expand(\"results/te_typing/pre_sorting/{sample}/{sample}_te_types_merged.tsv\", sample=SAMPLES),\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:510: SyntaxWarning: invalid escape sequence \u0027\\(\u0027\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:519: SyntaxWarning: invalid escape sequence \u0027\\(\u0027\nLints for rule read_te_typing (line 8, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merging_read_te_typing (line 34, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule te_typing_annotation (line 51, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule te_typing_annotation_propagation_GRID (line 79, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_uncategorized_ins_reads_1 (line 134, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_uncategorized_ins_reads_2 (line 151, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_uncategorized_ins_reads (line 167, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_categorized_ins_reads (line 184, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule locate_motif (line 197, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extend_motif (line 217, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extract_unc_ins_motif_subregions (line 232, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rename_unc_ins_motif_subregions (line 250, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_motif_subregions_files (line 263, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clustering_unc_reads_final_set (line 276, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule reformat_clustering_results_1 (line 293, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule reformat_clustering_results_2 (line 306, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule final_cluster_sizes (line 323, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "description": null, + "formatting": null, + "full_name": "rababerladuseladim/megadudes-evaluation", + "latest_release": null, + "linting": "Lints for rule mmseqs2_top_10 (line 116, /tmp/tmptk_adkyi/workflow/rules/run_mmseqs2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1420,33 +1435,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726050889.0 + "updated_at": 1725821035.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp2dl8hrsu/Snakefile\": Keyword \"shell\" at line 260 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2dl8hrsu/Snakefile\": Keyword \"shell\" at line 548 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp2dl8hrsu/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "HealthML/MFD", + "description": "A self contained snakemake workflow to test new features", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp13a3ojow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ETH-NEXUS/basic_snakemake_workflow", "latest_release": null, - "linting": "WorkflowError in file /tmp/tmp2dl8hrsu/Snakefile, line 1:\nWorkflow defines configfile src/config.yaml but it is not present or accessible (full checked path: /tmp/tmp2dl8hrsu/src/config.yaml).\n", + "linting": "Lints for rule generate_data (line 27, /tmp/tmp13a3ojow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_data (line 53, /tmp/tmp13a3ojow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule aggregate_data (line 79, /tmp/tmp13a3ojow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 2, "topics": [], - "updated_at": 1726044610.0 + "updated_at": 1725772983.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpqoiceb5e/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 6:8: storage:\n```\n\n[INFO] In file \"/tmp/tmpqoiceb5e/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "dakesan/snakemake-s3-minimum-example", + "description": "Dockerized RNA-seq analysis pipeline built with Snakemake through steps like quality control, trimming, alignment, and quantification, ultimately generating a count matrix for downstream analysis. ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpwgq__i7v/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "irishevia/RNAseq-box", "latest_release": null, - "linting": "InvalidPluginException in file /tmp/tmpqoiceb5e/Snakefile, line 6:\nError loading Snakemake plugin s3: The package snakemake-storage-plugin-s3 is not installed.\n", + "linting": "Lints for rule fastqc (line 41, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule trim_galore (line 71, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TRIM_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule hisat2_index (line 109, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable REFERENCE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule hisat2_align (line 142, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable REFERENCE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule samtools_sort (line 169, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule featurecounts (line 191, /tmp/tmpwgq__i7v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1454,33 +1469,54 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726027343.0 + "updated_at": 1725723184.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp93c8a3i2/workflow/Snakefile\": Keyword \"output\" at line 39 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp93c8a3i2/workflow/Snakefile\": Keyword \"params\" at line 53 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp93c8a3i2/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_mag-qc", + "description": "A snakemake workflow that assemble diploid genome using HiFi and HiC sequencing reads", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/03.yahs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp8zh91gwq/rules/02.arima_hic_mapping.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ZexuanZhao/HiFi-HiC-genome-assembly", "latest_release": null, - "linting": "KeyError in file /tmp/tmp93c8a3i2/workflow/Snakefile, line 13:\n\u0027work_dir\u0027\n File \"/tmp/tmp93c8a3i2/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n", + "linting": "Lints for snakefile /tmp/tmp8zh91gwq/Snakefile:\n * Environment variable PATH used but not asserted with envvars directive in line 9.:\n Asserting existence of environment variables with the envvars directive\n ensures proper error messages if the user fails to invoke a workflow with\n all required environment variables defined. Further, it allows snakemake\n to pass them on in case of distributed execution.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#environment-variables\n * Environment variable PATH used but not asserted with envvars directive in line 10.:\n Asserting existence of environment variables with the envvars directive\n ensures proper error messages if the user fails to invoke a workflow with\n all required environment variables defined. Further, it allows snakemake\n to pass them on in case of distributed execution.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#environment-variables\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 9:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk:\n * Absolute path \"/^S/{{print \"\u003e\"$2;print $3}}\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc_hic_before_trimming (line 2, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastp_hic (line 42, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule fastqc_hic_after_trimming (line 93, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc_hifi_before_trimming (line 134, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule hifiAdapterFilt (line 173, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc_hifi_after_trimming (line 232, /tmp/tmp8zh91gwq/rules/00.reads_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule hifiasm (line 1, /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule gfa2fasta (line 61, /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule hifi_assembly_stats (line 91, /tmp/tmp8zh91gwq/rules/01.hifi_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1726024734.0 + "updated_at": 1725720694.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "A Snakemake workflow for using SLEAP and NAPS", + "formatting": null, + "full_name": "Wolfffff/snakemake-sleap-naps", + "latest_release": "v0.1.0", + "linting": "Lints for rule compute_metrics (line 1, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/sleap_model_qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_sleap (line 2, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/sleap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_naps (line 1, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/naps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule copy_config (line 1, /tmp/tmpor4lzrih/Wolfffff-snakemake-sleap-naps-d975189/workflow/rules/copy_config.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "behavior", + "pose", + "snakemake" + ], + "updated_at": 1725719913.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpij19n6zn/workflow/Snakefile\": Keyword \"input\" at line 38 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmpij19n6zn/workflow/Snakefile\": NoParametersError: L189: In output definition.\n[INFO] In file \"/tmp/tmpij19n6zn/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "palomnyk/NHANES_Complexity", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpd7qc3qgo/workflow/rules/gsea.smk\": SyntaxError: L16: Colon (not \u0027gsea\u0027) expected after \u0027checkpoint rule\u0027\n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/gsea.smk\": \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/delivery.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpd7qc3qgo/workflow/rules/rseqc.smk\": Keyword \"input\" at line 210 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/rseqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/star.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/fastp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7qc3qgo/workflow/rules/deseq.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "jprnz/rnaseq-deseq2-star", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpij19n6zn/workflow/Snakefile, line 104:\nCommand must be given as string after the shell keyword.:\nNone\n", + "linting": "Using workflow specific profile workflow/profiles/default for setting default command line arguments.\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/Snakefile:\n * Absolute path \"/{species}/{release}-{build}/star-index\" in line 52:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 52:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/reference.smk:\n * Absolute path \"/dev/null\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/dev/null\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-dna-fasta.log\" in line 93:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-gtf.log\" in line 102:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-gtf-genes.log\" in line 113:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{species}-{release}-{build}-dna-fai.log\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 93:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 102:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 113:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 124:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 138:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/fastp.smk:\n * Absolute path \"/fastqs/{sample}_{pair}.fastq.gz\" in line 13:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/combine-{sample}_{pair}.log\" in line 15:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqs/{sample}_R1.fastq.gz\" in line 29:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqs/{sample}_R2.fastq.gz\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R1.fastq.gz\" in line 32:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R2.fastq.gz\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/json_reports/{sample}.json\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/html_reports/{sample}.html\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}.log\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqs/{sample}_{pair}.fastq.gz\" in line 57:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/json_reports/{sample}.json\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 15:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 61:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/star.smk:\n * Absolute path \"/{sample}_R1.fastq.gz\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R2.fastq.gz\" in line 20:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_Aligned.sortedByCoord.out.bam\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_ReadsPerGene.out.tab\" in line 25:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}.log\" in line 27:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_\" in line 29:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_Aligned.sortedByCoord.out.bam\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}_link.log\" in line 66:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 75:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam.bai\" in line 77:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{sample}_index.log\" in line 79:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}_ReadsPerGene.out.tab\" in line 90:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 92:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/count-matrix.log\" in line 94:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 104:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam.bai\" in line 108:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 109:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 25:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 27:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 60:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 66:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 75:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 79:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 90:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 92:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 104:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/rseqc.smk:\n * Absolute path \"/annotation.bed\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.db\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/rseqc_gtf2bed.log\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 20:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.junction.bed\" in line 22:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/junction_annotation/{sample}.log\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 27:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.junctionSaturation_plot.pdf\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/junction_saturation/{sample}.log\" in line 48:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 67:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 68:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.stats.txt\" in line 70:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/bam_stats/{sample}.log\" in line 72:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 83:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 84:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.infer_experiment.txt\" in line 86:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/infer_experiment/{sample}.log\" in line 88:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 99:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 100:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.inner_distance.txt\" in line 102:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/inner_distance/{sample}.log\" in line 104:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 107:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 123:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.readdistribution.txt\" in line 126:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/read_distribution/{sample}.log\" in line 128:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 131:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 145:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.pos.DupRate.xls\" in line 147:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/read_duplication/{sample}.log\" in line 149:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 152:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 167:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.GC.xls\" in line 169:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/read_gc/{sample}.log\" in line 171:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 173:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.bam\" in line 184:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/annotation.bed\" in line 185:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.geneBodyCoverage.txt\" in line 187:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/genebody_coverage/{sample}.log\" in line 188:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/gene_body_coverage/{sample}.log\" in line 190:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}\" in line 193:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.stats.txt\" in line 209:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.readdistribution.txt\" in line 210:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.junctionSaturation_plot.pdf\" in line 211:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.pos.DupRate.xls\" in line 212:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}/{sample}.geneBodyCoverage.txt\" in line 213:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 8:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 22:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 27:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 46:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 48:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 51:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 67:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 70:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 83:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 86:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 88:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 99:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 102:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 104:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 107:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 123:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 126:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 128:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 131:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 145:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 149:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 152:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 167:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 171:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 173:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 184:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 187:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 188:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 190:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 193:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 209:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 210:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 211:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 212:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 213:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/multiqc.smk:\n * Absolute path \"/QC.html\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/multiqc.log\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/deseq.smk:\n * Absolute path \"/counts.csv\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.RData\" in line 12:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.xlsx\" in line 13:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/counts.csv\" in line 14:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/normalized-counts.csv\" in line 15:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{analysis}.log\" in line 17:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.xlsx\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 9:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 14:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 15:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 17:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/gsea.smk:\n * Absolute path \"/{wc.analysis}/rnk-files/*.rnk\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/analysis.xlsx\" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/GSEA-{geneset}.xlsx\" in line 23:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/logs/{analysis}/{geneset}.log\" in line 25:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{analysis}/GSEA-{set}.xlsx\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 21:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 23:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 25:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk:\n * Absolute path \"/{v}/analysis.xlsx\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{v}/GSEA-{s}.xlsx\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/analysis.xlsx\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/GSEA/GSEA-{s}.xlsx\" in line 40:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/{v}/analysis.xlsx\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Analysis/{v}/GSEA/GSEA-{s}.xlsx\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/Methods.docx\" in line 53:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/QC.html\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 84:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/counts.csv\" in line 103:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 53:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 71:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule star_link (line 87, /tmp/tmpd7qc3qgo/workflow/rules/star.smk):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule multiqc (line 1, /tmp/tmpd7qc3qgo/workflow/rules/multiqc.smk):\n * Param output_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule deliver_methods (line 49, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_qc (line 66, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_bamfiles (line 83, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_counts (line 104, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deliver_analysis (line 126, /tmp/tmpd7qc3qgo/workflow/rules/delivery.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1488,16 +1524,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726014098.0 + "updated_at": 1725656443.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/clustering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/gliph.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/plotting.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/conga.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/seurat_preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/tcr_dist.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/differential_expression.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "carpenter-lab/single-cell-workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/extra_env.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpau0wp52n/workflow/rules/cellranger_arc.smk\": Keyword \"input\" at line 26 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/cellranger_arc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/main_seurat.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpau0wp52n/workflow/Snakefile\": Keyword \"input\" at line 18 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpau0wp52n/workflow/rules/integration.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "yzeng-lol/iSHARC", "latest_release": null, - "linting": "\nEidoValidationError in file /tmp/tmp5xd23uhl/workflow/Snakefile, line 13:\nEidoValidationError (Validation failed): {\"\u0027_samples\u0027 is a required property\": [{\u0027type\u0027: \"\u0027_samples\u0027 is a required property\", \u0027message\u0027: \"\u0027_samples\u0027 is a required property on instance project\", \u0027sample_name\u0027: \u0027project\u0027}]}\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/eido/validation.py\", line 73, in validate_project\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/eido/validation.py\", line 56, in _validate_object\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpau0wp52n/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n include: \"rules/main_seurat.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpau0wp52n/workflow/rules/common.smk\", line 1, in \u003cmodule\u003e\n workdir: config[\u0027work_dir\u0027]\n ^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1505,50 +1541,67 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725999338.0 + "updated_at": 1725644105.0 }, { "config_readme": null, "data_format": 2, - "description": "A thin wrapper to simplify running cellprofiler on della", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsxp2ehq9/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "SoftLivingMatter/snakemake-cellprofiler", + "description": "Repository containing all code used for dataset construction, analysis and figure generation for Tubbs et al. 2024", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/04_Annotate-SNVs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/05_Final-Matrix.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/03_Annotate-Bases.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp9jy4ezwi/workflow/rules/01_Annotate-rDHS.smk\": Keyword \"input\" at line 29 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/01_Annotate-rDHS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/02_Process-Motifs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9jy4ezwi/workflow/rules/00_Setup.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "RuderferLab/CBS_FunctionalAnnotation", "latest_release": null, - "linting": "Creating specified working directory /path/to/output/directory.\nPermissionError in file /tmp/tmpsxp2ehq9/workflow/Snakefile, line 7:\n[Errno 13] Permission denied: \u0027/path\u0027\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1726177733.0 + "updated_at": 1725626810.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/searchgui.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/raw_file_parse.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/generate_db.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/peptide_shaker.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/post_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/gff_generation.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "PRIDE-reanalysis/MetaPUF", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp6ykksmrt/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 288:0: EOF in multi-line statement\n```\n\n[INFO] In file \"/tmp/tmp6ykksmrt/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "JavedMS/highRES-model", "latest_release": null, - "linting": "NotImplementedError in file /tmp/tmp5yqp4tmy/workflow/rules/raw_file_parse.smk, line 10:\nRemote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85/cluster/EFF/results\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85/cluster/EFF\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85/cluster\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm/ec85\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01/ec-javedm\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01/u01\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/fp/homes01\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6ykksmrt/workflow/Snakefile\", line 219, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n self.parent.mkdir(parents=True, exist_ok=True)\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n self.parent.mkdir(parents=True, exist_ok=True)\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n self.parent.mkdir(parents=True, exist_ok=True)\n\n [Previous line repeated 4 more times]\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n os.mkdir(self, mode)\n\nPermissionError: [Errno 13] Permission denied: \u0027/fp\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1725982636.0 + "updated_at": 1725626201.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Generating consistent TC and TC Surge hazard set event using Snakemake and CLIMADA", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpybi507vm/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "spjuhel/Climada_TC_TCSurge_Generation", + "description": "Snakemake workflow for mTags extraction and classification", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4ebanfcv/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "aleixop/mtags_snakemake", "latest_release": null, - "linting": "KeyError in file /tmp/tmpybi507vm/workflow/Snakefile, line 27:\n\u0027start\u0027\n File \"/tmp/tmpybi507vm/workflow/Snakefile\", line 27, in \u003cmodule\u003e\n", + "linting": "Lints for rule format_input (line 18, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule blast_search (line 48, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_blast_hits (line 82, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_mtags (line 103, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_mtags (line 127, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_consensus_taxonomy (line 163, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_otu_table (line 190, /tmp/tmp4ebanfcv/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1725616248.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": "Snakemake workflow for RNA-Seq differential transcript analysis using STAR/Deseq2", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/deseq2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/plotting.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/deeptools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/resources.smk\": Keyword \"shell\" at line 170 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/resources.smk\": Keyword \"shell\" at line 199 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/resources.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/rules/fastqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/Snakefile\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "niekwit/rna-seq-star-deseq2", + "latest_release": "v0.5.0", + "linting": "Workflow version: v0.5.0\nWrapper version: v4.2.0\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/Snakefile\", line 32, in \u003cmodule\u003e\n include: \"rules/trim.smk\"\n ^^^^^^^^^^^^^\n\n File \"/tmp/tmpi2i3irlt/niekwit-rna-seq-star-deseq2-3444676/workflow/scripts/general_functions.smk\", line 90, in paired_end\n assert len(reads) != 0, \"No fastq files found...\"\n ^^^^^^^^^^^^^^^^^^\n\nAssertionError: No fastq files found...\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -1563,33 +1616,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1725981203.0 + "updated_at": 1725611083.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp_8rvuhe_/workflow/rules/phylogeny.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "koisland/CenClustering", - "latest_release": null, - "linting": "Multiple includes of /tmp/tmp_8rvuhe_/workflow/rules/data.smk ignored\nLints for snakefile https://:ghs_9K7szIWhrwDYcwcKyxn0stCzzoXvKe0s9Fdn@raw.githubusercontent.com/koisland/asm-to-reference-alignment/minimal/workflow/Snakefile:\n * Absolute path \"/tmp\" in line 13:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp_8rvuhe_/workflow/rules/phylogeny.smk:\n * Deprecated singularity directive used for container definition in line 25.:\n Use the container directive instead (it is agnostic of the underlying\n container runtime).\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule wget (line 1, /tmp/tmp_8rvuhe_/workflow/rules/utils.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_chm13_asm (line 6, /tmp/tmp_8rvuhe_/workflow/rules/data.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_chimp_asm (line 28, /tmp/tmp_8rvuhe_/workflow/rules/data.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/bgzip.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/imagemagick.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/bedtools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/tabix.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/samtools.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "hydra-genetics/misc", + "latest_release": "v0.2.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9csu2p7m/hydra-genetics-misc-9dba1b9/workflow/rules/common.smk\", line 12, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 4, "topics": [], - "updated_at": 1725980621.0 + "updated_at": 1725608822.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow to basecall ONT reads with dorado.", - "formatting": null, - "full_name": "logsdon-lab/Snakemake-ONT-Basecalling", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpfwso929l/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfwso929l/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "yjkimmdphd/asthma_bal", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpctlra9d1/workflow/rules/common.smk:\n * Absolute path \"/\", \" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule dorado_basecaller (line 31, /tmp/tmpctlra9d1/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1597,50 +1650,57 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726364793.0 + "updated_at": 1725555964.0 }, { - "config_readme": null, + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "La idea es crear una p\u00e1gina web con especies de fauna y flora de Gran Canaria que vaya encontrando, vamos a ver como hacemos esto", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpvjxeid2v/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "JuanCarlosBio/BiodiversidadGJC", + "description": "The aim of this repository is to practice on how to create a workflow that allows automatic creation of a global map.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp8dx357ai/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "gonzarizzo/globe_map", "latest_release": null, - "linting": "Lints for rule download_images (line 26, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_canary_islands_shp (line 41, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_extra_layers (line 54, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_biota_data (line 71, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule process_canary_islands_shp (line 83, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule process_jardin_botanico_kml (line 99, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule process_biota_data (line 112, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule figures_and_stats (line 146, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule webpage_html (line 165, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726363040.0 + "updated_at": 1725546879.0 }, { "config_readme": null, "data_format": 2, - "description": "A repository to hold the workflow for running solutionAnalysis", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbwl8qsaq/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "amritagos/workflow_solutionAnalysis", + "description": "Deep mutational scanning phenotypes of clade 2.3.4.4b influenza H5 HA", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpout79y2u/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 22:6: conda:\n```\n\n[INFO] In file \"/tmp/tmpout79y2u/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "jbloomlab/Flu-HA-H5-2.3.4.4-DMS-informed-surveillance", "latest_release": null, - "linting": "Lints for rule param_sweep (line 14, /tmp/tmpbwl8qsaq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpout79y2u/Snakefile\", line 6, in \u003cmodule\u003e\n import ruamel.yaml as yaml\n\nModuleNotFoundError: No module named \u0027ruamel\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1726325547.0 + "updated_at": 1725538932.0 }, { "config_readme": null, "data_format": 2, - "description": "House of Congress Bills Cosponsorship", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0k8pusec/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "LMCasale/PP4RS_Final_Assignment_LMC_MM", + "description": "Variant effect prediction using Kipoi", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmplswqabat/workflow/rules/benchmark.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmplswqabat/workflow/Snakefile\": SyntaxError: L14: \u0027use rule benchmark, evaluation, comparison from benchmark_workflow\u0027 not of form \u0027\"use\" \"rule\" (identifier | \"*\") \"from\" identifier [\"exclude\" identifier {\",\" identifier}] [\"as\" identifier] [\"with\" \":\"]\u0027\n[DEBUG] In file \"/tmp/tmplswqabat/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmplswqabat/workflow/rules/enformer.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmplswqabat/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "gtsitsiridis/kipoi_veff_analysis", "latest_release": null, - "linting": "Lints for rule PY_data_collection (line 5, /tmp/tmp0k8pusec/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule generate_report (line 13, /tmp/tmp0k8pusec/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplswqabat/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n assert len(config) \u003e 0, \"The config file has not been defined or is empty\"\n ^^^^^^^^^^^^^^^^^^\n\nAssertionError: The config file has not been defined or is empty\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1648,16 +1708,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726311216.0 + "updated_at": 1725525923.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for RNA-Seq and TGIRT-Seq", - "formatting": null, - "full_name": "LPChaumont/rna-seq-smk", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpixwe1_8l/workflow/rules/00_modules.smk\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "core-unit-bioinformatics/workflow-smk-vcf-annotation", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp8z0ir3q0/workflow/rules/common.smk:\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule build_full_transcriptome (line 49, /tmp/tmp8z0ir3q0/workflow/rules/ref.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fastp_multiqc (line 26, /tmp/tmp8z0ir3q0/workflow/rules/fastp.smk):\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_index (line 1, /tmp/tmp8z0ir3q0/workflow/rules/star.smk):\n * Param index_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_align (line 27, /tmp/tmp8z0ir3q0/workflow/rules/star.smk):\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param index_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_multiqc (line 62, /tmp/tmp8z0ir3q0/workflow/rules/star.smk):\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule salmon_quant (line 26, /tmp/tmp8z0ir3q0/workflow/rules/salmon.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule salmon_tximport (line 50, /tmp/tmp8z0ir3q0/workflow/rules/salmon.smk):\n * Param quantdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule salmon_multiqc (line 69, /tmp/tmp8z0ir3q0/workflow/rules/salmon.smk):\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule install_coco (line 6, /tmp/tmp8z0ir3q0/workflow/rules/coco.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule install_pairedBamToBed12 (line 18, /tmp/tmp8z0ir3q0/workflow/rules/coco.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule coco_sort_bg (line 107, /tmp/tmp8z0ir3q0/workflow/rules/coco.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule install_pairadise (line 5, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rmats_config_prep (line 21, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_config_post (line 33, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_post (line 83, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * Param tmp is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_stat (line 113, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * Param stat_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param post_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_filtering (line 146, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule deseq2 (line 1, /tmp/tmp8z0ir3q0/workflow/rules/deseq2.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "/tmp/tmpixwe1_8l/workflow/rules/commons/30_settings.smk:205: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n RUN_SUFFIX = RUN_SUFFIX.replace(\".\", \"-\").replace(\"_\", \"-\")\n/tmp/tmpixwe1_8l/workflow/rules/commons/30_settings.smk:208: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n # consecutive hyphens, replace with single one\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpixwe1_8l/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n include: \"rules/commons/00_commons.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpixwe1_8l/workflow/rules/commons/00_commons.smk\", line 17, in \u003cmodule\u003e\n # Module containing generic\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpixwe1_8l/workflow/rules/commons/30_settings.smk\", line 55, in \u003cmodule\u003e\n VERBOSE = workflow.verbose\n ^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027verbose\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1665,16 +1725,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726282837.0 + "updated_at": 1725521831.0 }, { "config_readme": null, "data_format": 2, - "description": "construct pangenome from unaligned reads", + "description": "reproducibly estimate parameters for VerifyBamID2 for a new reference genome", "formatting": null, - "full_name": "lightning-auriga/pangenome-from-unaligned-reads", + "full_name": "lightning-auriga/estimate-verifybamid2-reference-data", "latest_release": null, - "linting": "NotImplementedError in file /tmp/tmp88b07zux/workflow/Snakefile, line 14:\nRemote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n", + "linting": "Lints for snakefile /tmp/tmpdhb8wyp1/workflow/Snakefile:\n * Absolute path \"/bin/bash\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpdhb8wyp1/workflow/rules/estimate_parameters.smk:\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 38:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for snakefile /tmp/tmpdhb8wyp1/workflow/rules/performance_benchmarks.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule download_reference_data (line 1, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_fasta (line 38, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_input_vcf (line 57, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_vcf (line 78, /tmp/tmpdhb8wyp1/workflow/rules/acquire_data.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_and_shrink (line 1, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule report_markers (line 22, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule select_downsampled_markers (line 42, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule subset_vcf (line 61, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_vcfs (line 82, /tmp/tmpdhb8wyp1/workflow/rules/prepare_vcfs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule estimate_verify_parameters (line 1, /tmp/tmpdhb8wyp1/workflow/rules/estimate_parameters.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule copy_verify_files (line 30, /tmp/tmpdhb8wyp1/workflow/rules/estimate_parameters.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule performance_benchmarks (line 22, /tmp/tmpdhb8wyp1/workflow/rules/performance_benchmarks.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param parent_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1682,85 +1742,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726256549.0 + "updated_at": 1725910520.0 }, { "config_readme": null, "data_format": 2, - "description": "This is the repository of the pipeline META-DIFF, which detects sequences in differential abundances between two conditions, and annotates them taxonomicaly and functionaly.", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpsu9u41ar/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 42)\n[INFO] In file \"/tmp/tmpsu9u41ar/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "Louis-MG/META-DIFF", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/Snakefile\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpawms2scm/rules/qc.smk\": Keyword \"script\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpawms2scm/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/align-fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/cna.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/align-fastq_after_merge.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpawms2scm/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\ \u0027\n[DEBUG] In file \"/tmp/tmpawms2scm/rules/variants_analysis.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mdelcorvo/DeSeq-Free", "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 42:\ninconsistent use of tabs and spaces in indentation:\n\texpand(config[\"project_path\"] + \"pipeline_output/functional_annotation/{condition}_unitigs_to_gene_functions.tsv\", condition = [\u0027case\u0027, \u0027control\u0027])\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "linting": "/tmp/tmpawms2scm/rules/common.smk:24: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n if not str.endswith(\u0027/\u0027):\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 135, in import_optional_dependency\n module = importlib.import_module(name)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/importlib/__init__.py\", line 90, in import_module\n return _bootstrap._gcd_import(name[level:], package, level)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1387, in _gcd_import\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1360, in _find_and_load\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1324, in _find_and_load_unlocked\n\nModuleNotFoundError: No module named \u0027openpyxl\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpawms2scm/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpawms2scm/rules/common.smk\", line 156, in \u003cmodule\u003e\n samples = samples[~samples[\u0027fq1\u0027].apply(check_fastq) != 1]\n ~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 495, in read_excel\n io = ExcelFile(\n ^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 1567, in __init__\n self._reader = self._engines[engine](\n ^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_openpyxl.py\", line 552, in __init__\n import_optional_dependency(\"openpyxl\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 138, in import_optional_dependency\n raise ImportError(msg)\n\nImportError: Missing optional dependency \u0027openpyxl\u0027. Use pip or conda to install openpyxl.\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "annotation", - "bioinformatics-pipeline", - "kmers", - "metagenomics", - "shotgun-pipeline", - "snakemake" - ], - "updated_at": 1726244891.0 + "topics": [], + "updated_at": 1725483209.0 }, { "config_readme": null, "data_format": 2, - "description": "Test of Uniformity for centrosome orientation at early timepoints during Wound Healing Assay", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpnsaf00li/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 83)\n[INFO] In file \"/tmp/tmpnsaf00li/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "rgomez-AI/CellOrientation", + "description": "Snakemake pipeline for variant annotation with VEP", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3vdgxua/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/install_vep_cache.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/revel.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/disgenet.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/disgenet.smk\": \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/gnomad.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/gnomad.smk\": \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/rnacentral.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/rnacentral.smk\": \n[ERROR] In file \"/tmp/tmpj3vdgxua/rules/loftee.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 5)\n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/loftee.smk\": \n[DEBUG] In file \"/tmp/tmpj3vdgxua/rules/cadd.smk\": Formatted content is different from original\n[INFO] 4 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "hmartiniano/annot", "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 83:\ninconsistent use of tabs and spaces in indentation:\n\tproj=\"ZSTD\",\t# Stack projection (\"ZMAX\", \"ZAVG\", \"ZSTD\" or \"None\")\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "linting": "WorkflowError:\nWorkflow defines configfile config.yml but it is not present or accessible (full checked path: /tmp/tmpj3vdgxua/config.yml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bioimage-analysis", - "cellprofiler-pipeline", - "fiji-macro-language", - "snakemake-workflow", - "workflow-automation", - "uniformity-tests" - ], - "updated_at": 1726236620.0 - }, - { - "config_readme": "\u003cp\u003eTriosCompass expects to use the parent folder of TriosCompass_v2 (the repo clone folder) as the working space, so as to separate the Snakemake workflow from the working space.\u003c/p\u003e\n\u003cp\u003eThree configure files are required:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cem\u003eProfile yaml file\u003c/em\u003e: workflow/profiles/\u0026lt;PROFILE_NAME\u0026gt;/config.yaml\u003c/li\u003e\n\u003cli\u003e\u003cem\u003eConfig yaml file\u003c/em\u003e\u003c/li\u003e\n\u003cli\u003e\u003cem\u003eSample yaml file\u003c/em\u003e\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eThe \u003cem\u003econfig yaml file\u003c/em\u003e can be specified by Snakemake command-line argument \"--configfile\" or in the \"\u003cem\u003eprofile yaml file\u003c/em\u003e, for example:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003econfigfile\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eTriosCompass_v2/config/fullbam_config.yaml\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esnakefile\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eTriosCompass_v2/workflow/Snakefile\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIn turn, the \u003cem\u003esample yaml file\u003c/em\u003e is specified in the \u003cem\u003econfig yaml file\u003c/em\u003e, to \u003ca href=\"https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#configuring-scientific-experiments-via-peps\" rel=\"nofollow\"\u003edefine sample input via PEPs\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003epepfile\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003econfig/fullbam_pep.yaml\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003epepschema\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e../schemas/bam_schema.yaml\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003eExample of the PEP configure file for FASTQ input files\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003econfig/fastq_pep.yaml\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003epep_version\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e2.0.0\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esample_table\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003esample_fastq.csv\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e In manifest file, Sample_ID + Flowcell should be unique\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esample_modifiers\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eappend\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esample_name\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esn\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ederive\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eattributes\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e[sample_name]\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003esources\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esn\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e{SAMPLE_ID}_{FLOWCELL}\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003econfig/sample_fastq.csv\u003c/p\u003e\n\u003cpre lang=\"csv\"\u003e\u003ccode\u003eSAMPLE_ID,FLOWCELL,LANE,INDEX,R1,R2\nHG002,BH2JWTDSX5,1,CGGTTGTT-GTGGTATG,data/fq/HG002_NA24385_son_80X_R1.fq.gz,data/fq/HG002_NA24385_son_80X_R2.fq.gz\nHG003,BH2JWTDSX5,1,GCGTCATT-CAGACGTT,data/fq/HG003_NA24149_father_80X_R1.fq.gz,data/fq/HG003_NA24149_father_80X_R2.fq.gz\nHG004,BH2JWTDSX5,1,CTGTTGAC-ACCTCAGT,data/fq/HG004_NA24143_mother_80X_R1.fq.gz,data/fq/HG004_NA24143_mother_80X_R2.fq.gz\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eworkflow/schemas/fastq_schema.yaml\n(schemas to validate config/fastq_pep.yaml)\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-s\"\u003eworkflow/schemas/fastq_schema.yaml \u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eA example schema for a pipeline.\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eimports\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003ehttp://schema.databio.org/pep/2.0.0.yaml\u003c/span\u003e\n \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e - TriosCompass_v2/workflow/schemas/2.0.0.yaml\u003c/span\u003e\n \n\u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003earray\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eitems\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eobject\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eSAMPLE_ID\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esample id\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eFLOWCELL\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eFlowcell\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eINDEX\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eLibrary index\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eLANE\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eLane number in flowcell\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eenum\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e[\"1\", \"2\"]\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eR1\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003epath to the R1 fastq file\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eR2\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003epath to the R2 fastq file\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003erequired\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003eFLOWCELL\u003c/span\u003e\n - \u003cspan class=\"pl-s\"\u003eSAMPLE_ID\u003c/span\u003e\n - \u003cspan class=\"pl-s\"\u003eINDEX\u003c/span\u003e\n - \u003cspan class=\"pl-c1\"\u003eR1\u003c/span\u003e\n - \u003cspan class=\"pl-c1\"\u003eR2\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003eExample of the PEP configure file for BAM input files\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003econfig/bam_pep.yaml\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003epep_version\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e2.0.0\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esample_table\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003esample_bam.csv\u003c/span\u003e\n\n\n\u003cspan class=\"pl-ent\"\u003esample_modifiers\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eappend\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esample_name\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esn\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ederive\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eattributes\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e[sample_name]\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003esources\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esn\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e{SAMPLE_ID}\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003econfig/sample_bam.csv\u003c/p\u003e\n\u003cpre lang=\"csv\"\u003e\u003ccode\u003eSAMPLE_ID,BAM\nHG002,sorted_bam/HG002_NA24385_son_80X.bam\nHG003,sorted_bam/HG003_NA24149_father_80X.bam\nHG004,sorted_bam/HG004_NA24143_mother_80X.bam\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eworkflow/schemas/fastq_schema.yaml\n(schemas to validate config/bam_pep.yaml)\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eA example schema for a pipeline.\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eimports\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003ehttp://schema.databio.org/pep/2.0.0.yaml\u003c/span\u003e\n \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e - TriosCompass_v2/workflow/schemas/2.0.0.yaml\u003c/span\u003e\n \n\u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003earray\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eitems\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eobject\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eSAMPLE_ID\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esample id\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eBAM\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003epath to the bam file\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003erequired\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003eSAMPLE_ID\u003c/span\u003e\n - \u003cspan class=\"pl-s\"\u003eBAM\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n", - "data_format": 2, - "description": "Trios analysis workflow written in Snakemake", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/phasing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/premap.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/deepvariant.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/jigv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/hipstr.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/dnSV.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/call_dnm.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\(\u0027\n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/dnSTR.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpp38wrjr_/workflow/rules/gatk_hc.smk\": NoParametersError: L82: In resources definition.\n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/gatk_hc.smk\": \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/bam_qc.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpp38wrjr_/workflow/rules/bam_input.smk\": InvalidPython: Black error:\n```\nCannot parse: 1:0: else:\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/bam_input.smk\": \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/pedigree.smk\": Formatted content is different from original\n[INFO] 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] 15 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "NCI-CGR/TriosCompass_v2", - "latest_release": null, - "linting": "ModuleNotFoundError in file /tmp/tmpp38wrjr_/workflow/rules/pedigree.smk, line 1:\nNo module named \u0027peds\u0027\n File \"/tmp/tmpp38wrjr_/workflow/rules/pedigree.smk\", line 1, in \u003cmodule\u003e\n", - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": false, - "singularity": false, - "singularity+conda": true - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 2, "topics": [], - "updated_at": 1726233222.0 + "updated_at": 1725479314.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmph6yomgza/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "loganylchen/snakemake-epitranscriptome", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsqa3ksxm/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mdondrup/divergence_time", "latest_release": null, - "linting": null, + "linting": "Lints for snakefile /tmp/tmpsqa3ksxm/workflow/Snakefile:\n * Absolute path \"/|\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 8:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule degenotate (line 61, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rename_chromosomes (line 99, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule index_vcf (line 147, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_vcf (line 182, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_genotype_matrix (line 232, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule difference_matrix (line 282, /tmp/tmpsqa3ksxm/workflow/Snakefile):\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -1775,33 +1800,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726227841.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpw4bznijb/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "BejaLab/TAT", - "latest_release": null, - "linting": "/tmp/tmpw4bznijb/workflow/Snakefile:406: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n genes = \"analysis/diamond_collect/gtdb.tsv\",\n/tmp/tmpw4bznijb/workflow/Snakefile:412: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n params:\nWorkflowError in file /tmp/tmpw4bznijb/workflow/Snakefile, line 2:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpw4bznijb/config.yaml).\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1726226602.0 + "updated_at": 1725458332.0 }, { "config_readme": null, "data_format": 2, - "description": "Measure distances between two types of markers during FISH Assay after Chromosomal Translocation event", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxd7nn4ku/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "rgomez-AI/3DChromTrans", + "description": "Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data", + "formatting": null, + "full_name": "hermidalc/tcga-wgs-kraken-microbial-quant", "latest_release": null, - "linting": "\u001b[92m\u001b[1mThanks for using 3DChromTrans and please remember to cite the tool!\u001b[0m\u001b[0m\n \u001b[36m Author: Raul Gomez-Riera.\n \u001b[0m\nTclError in file /tmp/tmpxd7nn4ku/workflow/Snakefile, line 91:\nno display name and no $DISPLAY environment variable\n File \"/tmp/tmpxd7nn4ku/workflow/Snakefile\", line 91, in \u003cmodule\u003e\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/filedialog.py\", line 442, in askdirectory\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/commondialog.py\", line 42, in show\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/__init__.py\", line 338, in _get_temp_root\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/__init__.py\", line 2346, in __init__\n", + "linting": "Using workflow specific profile workflow/profiles/default for setting default command line arguments.\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpl5kimfd7/workflow/Snakefile\", line 129, in \u003cmodule\u003e\n\nAssertionError: GDC auth token not found in GDC_TOKEN, GDC_TOKEN_FILE, or ~/.gdc_token\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1809,23 +1817,24 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [ - "bioimage-analysis", - "cellprofiler-pipeline", - "distance-calculation", - "napari-visualization", - "snakemake-workflow", - "workflow-automation" + "bioinformatics-pipeline", + "bioinformatics-workflow", + "metagenomic-pipeline", + "metagenomics", + "metagenomics-taxon-profiling", + "snakemake-pipeline", + "snakemake-workflow" ], - "updated_at": 1726234074.0 + "updated_at": 1725457492.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsenx2ah_/workflow/rules/version37_pca.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpsenx2ah_/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "tanavader0/smk_plink_QC", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp08ufac6a/Snakefile\": Keyword \"input\" at line 123 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp08ufac6a/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "lucianhu/rnaseq_snakemake", "latest_release": null, - "linting": "/tmp/tmpsenx2ah_/workflow/Snakefile:647: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n/tmp/tmpsenx2ah_/workflow/Snakefile:662: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\nLints for rule prepare_correct_x (line 12, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule logs (line 47, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule genotyping05 (line 67, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule SampleCallrate98_sex (line 87, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_sex_checked (line 107, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_heterozygosity (line 130, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule check_heterozygosity (line 156, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_het_samples (line 176, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule VariantCallrate98 (line 199, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_MissDiff_HWE (line 219, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule check_MissDiff_HWE (line 259, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_MissDiff_HWE (line 287, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_1000G_sample_info (line 309, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_chromosomes (line 12, /tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_fasta_files (line 25, /tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_1000G_for_ancestry_PCA_step1 (line 42, /tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prepare_1000G_for_ancestry_PCA_step2 (line 328, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param bed1 is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param bed2 is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule merge_data_w_1000G_run_PCA (line 369, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_pca_plots (line 411, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_pca_filter (line 427, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_plink_for_ancestry (line 451, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule kinship_analysis (line 475, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule kinship_analysis_R (line 495, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule remove_relateds (line 515, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule kinship_check2 (line 536, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule kinship_check2_R (line 556, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Lints for snakefile /tmp/tmp08ufac6a/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule import_genome (line 139, /tmp/tmp08ufac6a/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule import_annotation (line 160, /tmp/tmp08ufac6a/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule trim_galore_paired (line 462, /tmp/tmp08ufac6a/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule align_paired (line 588, /tmp/tmp08ufac6a/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule align_single (line 693, /tmp/tmp08ufac6a/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule read_distribution (line 1495, /tmp/tmp08ufac6a/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1833,55 +1842,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726224019.0 + "updated_at": 1725454058.0 }, { "config_readme": null, "data_format": 2, - "description": "Field Experiments I: A/B tests - Lecture 4 of Digital and Social Media Strategies at Tilburg U", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpihlf3il6/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihlf3il6/rules/renv.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "deer-marketing-lab/dsms-lecture-experiments", + "description": "2023-2024 data-process pipeline-conversion project; Adapting havoc to utilise snakemake.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/indelqual_bamfile.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/mask_low-coverage_regions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/remove_primers.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/preprocess_reads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/lineage_identification.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/create_visual.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/variant_calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/process_SAM_and_BAM_files.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/consensus_calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/rules/align_reads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpvaw4j4h6/workflow/Snakefile\": Formatted content is different from original\n[INFO] 11 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "WisseSchuuring/NewDataProcessProject", "latest_release": null, - "linting": "Lints for rule build_html (line 16, /tmp/tmpihlf3il6/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 29, /tmp/tmpihlf3il6/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 48, /tmp/tmpihlf3il6/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 15, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 20, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 25, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 30, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "WorkflowError:\nWorkflow defines configfile /homes/wsfschuuring/Desktop/DataProcess/SECRET-PROJECT/NewDataProcessProject/config/config.yaml but it is not present or accessible (full checked path: /homes/wsfschuuring/Desktop/DataProcess/SECRET-PROJECT/NewDataProcessProject/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1726223985.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003ePlease see the \u003ca href=\"https://github.com/jsquaredosquared/novocraft-sv-benchmarking?tab=readme-ov-file#usage\"\u003e\"Usage\" section of the main README.md file\u003c/a\u003e for more information on configuring the workflow.\u003c/p\u003e\n", - "data_format": 2, - "description": "Comparing performance of SV callers when using NovoAlign vs other aligners.", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3o0y9lkc/workflow/rules/01_align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 5 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "jsquaredosquared/novocraft-sv-benchmarking", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp3o0y9lkc/workflow/rules/01_align.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmp3o0y9lkc/workflow/rules/03_benchmark.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule download_reference (line 4, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule novoindex_reference (line 15, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule download_hg002_fastqs (line 59, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_hg002_tier1_sv_truth_set (line 71, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_delly_exclude (line 88, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule align_with_bwa_mem2 (line 15, /tmp/tmp3o0y9lkc/workflow/rules/01_align.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule align_with_novoalign (line 35, /tmp/tmp3o0y9lkc/workflow/rules/01_align.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule configure_manta (line 11, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_dysgu (line 49, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_delly (line 71, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_smoove (line 90, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_wham (line 119, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_tiddit (line 141, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule bgzip_and_index_sv_vcf (line 159, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule split_truth_set (line 20, /tmp/tmp3o0y9lkc/workflow/rules/03_benchmark.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule generate_plots (line 1, /tmp/tmp3o0y9lkc/workflow/rules/04_compare.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": null, - "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "sv-calling", - "novoalign" - ], - "updated_at": 1726218052.0 + "topics": [], + "updated_at": 1725447002.0 }, { "config_readme": null, "data_format": 2, - "description": "Synthesize functional scoring enrichment results from several sources (GSEApy, ClusterProfiler, STRING)", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_b4tt43h/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "pdegen/SynEnrich", + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"input\" at line 145 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"resources\" at line 222 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"resources\" at line 257 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Keyword \"output\" at line 536 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpms5_34th/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "highRES-model/highRES-Europe-WF", "latest_release": null, - "linting": "WorkflowError in file /tmp/tmp_b4tt43h/workflow/Snakefile, line 5:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmp_b4tt43h/config/config.yaml).\n", + "linting": "Lints for snakefile /tmp/tmpms5_34th/workflow/Snakefile:\n * Absolute path \"/highres.lst\" in line 505:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/highres.log\" in line 506:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/highres.lst\" in line 534:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/highres.log\" in line 535:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 365:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 447:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 489:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 517:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 550:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule build_cplex_opt (line 155, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_zones_file (line 176, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_technoeconomic_inputs (line 199, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rename_demand_file (line 242, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_shapes (line 261, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_vre_cf_grid (line 292, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_vre_land_avail (line 331, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_vre_cf_inputs (line 389, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_hydro_capfac (line 421, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_areas_file (line 474, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_hydrores_inflow (line 516, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compress_hydrores_inflow (line 541, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule link_hydrores_inflow (line 563, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_file (line 585, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule build_vre_parquet (line 619, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_csv (line 646, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_vre_gdx (line 673, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule compress_vre_gdx (line 699, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_gams (line 795, /tmp/tmpms5_34th/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param modelpath is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule convert_results (line 846, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule convert_results_db_parquet (line 869, /tmp/tmpms5_34th/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1889,16 +1876,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726179535.0 + "updated_at": 1725437645.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/phages.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpyp3dyapx/workflow/rules/assembly.smk\": Keyword \"input\" at line 4 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/refine_bins.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/coverm.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/taxonomy.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/binning.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/preprocessing.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "megjohnson1999/prophage-pipeline", + "description": "Snakemake workflow to re-batch POD5 files by pore/channel", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpe1yo8avq/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 70:0: res = defaultdict(set)\n```\n\n[INFO] In file \"/tmp/tmpe1yo8avq/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "tbooth/pod5_by_pore", "latest_release": null, - "linting": "WorkflowError in file /tmp/tmpyp3dyapx/workflow/Snakefile, line 6:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", + "linting": "Lints for snakefile /tmp/tmpe1yo8avq/workflow/Snakefile:\n * Absolute path \"/{p5}.pod5\" in line 17:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{foo}.pod5\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 17:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule get_channels_in_pod (line 39, /tmp/tmpe1yo8avq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule batched_channels_in_pod (line 46, /tmp/tmpe1yo8avq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule get_channels_in_use (line 63, /tmp/tmpe1yo8avq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1906,67 +1893,91 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1726175200.0 + "updated_at": 1726155010.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/snvreport.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/pathogenic_expansion_loci.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/outlier_expansions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/svreport.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ccmbioinfo/crg2-pacbio", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpjaoq8q6y/workflow/Snakefile\": InvalidParameterSyntax: 189rule cplex_opt_EU\n\n\n\n[INFO] In file \"/tmp/tmpjaoq8q6y/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "celeryroastalpenglow/MENOFS", "latest_release": null, - "linting": "KeyError in file /tmp/tmpm1ioupzr/rules/common.smk, line 15:\n\u0027run\u0027\n File \"/tmp/tmpm1ioupzr/rules/common.smk\", line 15, in \u003cmodule\u003e\n", + "linting": "PermissionError in file /tmp/tmpjaoq8q6y/workflow/Snakefile, line 146:\n[Errno 13] Permission denied: \u0027/a_folder_path\u0027\n File \"/tmp/tmpjaoq8q6y/workflow/Snakefile\", line 146, in \u003cmodule\u003e\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 1, "topics": [], - "updated_at": 1726161873.0 + "updated_at": 1726145324.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpcuskt1r9/workflow/rules/download_snake.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcuskt1r9/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpcuskt1r9/workflow/rules/blast_missing_seqs.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 14)\n[INFO] In file \"/tmp/tmpcuskt1r9/workflow/rules/blast_missing_seqs.smk\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmpcuskt1r9/workflow/rules/blast_missing_seqs.smk\": 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "LCrossman/ribosomal_snakemake", - "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpcuskt1r9/config.yaml).\n", + "description": "Barcode Recovery and Comparison from Database", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/commons.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/reports.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\q\u0027\n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/pairwise_alignement.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/rules/extract_barcodes.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "CVUA-RRW/BaRCoD", + "latest_release": "1.1.1", + "linting": "WorkflowError in file /tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/Snakefile, line 12:\nWorkflow defines configfile /tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/workflow/../.tests/config/config.yaml but it is not present or accessible (full checked path: /tmp/tmprlaxvokq/CVUA-RRW-BaRCoD-e366aef/.tests/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1721228607.0 + "updated_at": 1726142474.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqjsa968x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "brambloemen/FARMED_onsite", + "description": "Find single-stranded DNA breaks with an error-prone DNA polymerase", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_sbd6gc0/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "NBISweden/Sloppymerase", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpqjsa968x/Snakefile:\n * Absolute path \"/results/plots/Time_and_AMR.png\" in line 256:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/results/plots/ARG_exp_byclass.png\" in line 257:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule get_readstats (line 28, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_reads (line 59, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_reads_GMSdb (line 93, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_reads_ResFdb (line 150, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_reads_RefSeq (line 207, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule finish_mapping (line 264, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule finish_alingment_parsing (line 457, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plotseqrunstats (line 524, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_time_amr_stats (line 553, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Lints for rule count_illumina_reads (line 24, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_illumina (line 33, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule count_nanopore_pacbio_reads (line 49, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_nanopore (line 57, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_pacbio (line 71, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule detect_breaks (line 84, /tmp/tmp_sbd6gc0/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_bed (line 106, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule subtract_illumina_controls (line 116, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simulate_nickase (line 128, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule random_sites (line 141, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule intersect_nickase_sites (line 153, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule intersect_random_sites (line 162, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index_bed (line 171, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index_bam (line 177, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bgzip_bed (line 182, /tmp/tmp_sbd6gc0/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 7, "topics": [], - "updated_at": 1721208291.0 + "updated_at": 1726141738.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": "create long read (Nanopore with NanoSim) and short read (Illumina with Circle-Map) testing data for ecDNA analysis workflows", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpiw53r2g_/workflow/Snakefile\": Keyword \"params\" at line 56 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmpiw53r2g_/workflow/Snakefile\": IndexError: pop from empty list\n[INFO] In file \"/tmp/tmpiw53r2g_/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "dlaehnemann/create-ecdna-testing-data", + "latest_release": null, + "linting": "Workflow defines that rule get_chromosomes_ref is eligible for caching between workflows (use the --cache argument to enable this).\nLints for snakefile /tmp/tmpiw53r2g_/workflow/Snakefile:\n * Absolute path \"/human_NA12878_DNA_FAB49712_guppy/training\" in line 12:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/human_NA12878_DNA_FAB49712_guppy/training\" in line 16:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule config_segment_to_bed (line 65, /tmp/tmpiw53r2g_/workflow/Snakefile):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule create_samples_sheet (line 277, /tmp/tmpiw53r2g_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule create_units_sheet (line 305, /tmp/tmpiw53r2g_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1726140775.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbl5cjth2/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "PratikPathade/scRNA-seq-pipeline-with-Snakemake-Workflow", + "description": "Just annotate the MAGs as in mg_assembly", + "formatting": null, + "full_name": "3d-omics/mg_annotate", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile /lustre/Pratik/snakemake_local/snakemake_tutorial/configs/config.yaml but it is not present or accessible (full checked path: /lustre/Pratik/snakemake_local/snakemake_tutorial/configs/config.yaml).\n", + "linting": "Lints for snakefile /tmp/tmpi0370ikk/workflow/rules/dram.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule checkm2__quality_report__ (line 27, /tmp/tmpi0370ikk/workflow/rules/checkm2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -1974,67 +1985,87 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1721200768.0 + "updated_at": 1726134655.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": null, - "full_name": "deMoraes-Lab/variants", + "description": "A Snakemake pipeline to analyze RNA-seq expression data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/diffexp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/quantification.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp31et65mg/workflow/Snakefile\": Keyword \"input\" at line 44 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/plots.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/splicing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp31et65mg/workflow/rules/align.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "kristinassong/RNAseq", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpewsne6eq/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n # Paths to input files\n ^^^^^^^^^^^^^^\n\nAssertionError: Please provide a NCBI accession for reference genome.\n\n", + "linting": "Lints for rule star_index (line 1, /tmp/tmp31et65mg/workflow/rules/align.smk):\n * Param idx is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_align (line 27, /tmp/tmp31et65mg/workflow/rules/align.smk):\n * Param out_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param idx is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule genomecov (line 97, /tmp/tmp31et65mg/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule kallisto_quant (line 38, /tmp/tmp31et65mg/workflow/rules/quantification.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule tx2gene (line 67, /tmp/tmp31et65mg/workflow/rules/quantification.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_kallisto_quant (line 80, /tmp/tmp31et65mg/workflow/rules/quantification.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule deseq2 (line 3, /tmp/tmp31et65mg/workflow/rules/diffexp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param kallisto_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule volcano_plot (line 22, /tmp/tmp31et65mg/workflow/rules/diffexp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule pca (line 1, /tmp/tmp31et65mg/workflow/rules/plots.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 17, /tmp/tmp31et65mg/workflow/rules/plots.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats (line 1, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_rmats (line 23, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_paired_env (line 46, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rmats_paired (line 62, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_rmats_paired (line 85, /tmp/tmp31et65mg/workflow/rules/splicing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, + "topics": [ + "rna-seq-pipeline", + "snakemake-workflow" + ], + "updated_at": 1726112847.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Workflow for processing UAS imagery into data on bird location and species for near real-time monitoring in the Everglades", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpopwg9ani/weecology-everwatch-workflow-2e6fceb/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "weecology/everwatch-workflow", + "latest_release": "v0.2.0", + "linting": "WorkflowError in file /tmp/tmpopwg9ani/weecology-everwatch-workflow-2e6fceb/Snakefile, line 5:\nWorkflow defines configfile /blue/ewhite/everglades/everwatch-workflow/snakemake_config.yml but it is not present or accessible (full checked path: /blue/ewhite/everglades/everwatch-workflow/snakemake_config.yml).\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 4, "topics": [], - "updated_at": 1721178829.0 + "updated_at": 1726093707.0 }, { "config_readme": null, "data_format": 2, - "description": "Demo repo for new cluster setup with snakemake (excludes configs)", - "formatting": null, - "full_name": "aabiddanda/snakemake_demo", + "description": null, + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpb_4sx3jl/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 75:0: EOF in multi-line statement\n```\n\n[INFO] In file \"/tmp/tmpb_4sx3jl/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "SoftLivingMatter/5eU-seq-pipelines", "latest_release": null, - "linting": "/tmp/tmpui4ku78m/workflow/rules/sims.smk:21: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n script:\n/tmp/tmpui4ku78m/workflow/rules/sims.smk:22: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n \"../scripts/sim_msprime.py\"\n/tmp/tmpui4ku78m/workflow/rules/sims.smk:23: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n \nLints for snakefile /tmp/tmpui4ku78m/workflow/Snakefile:\n * Absolute path \"/bin/bash\" in line 22:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpui4ku78m/workflow/rules/sims.smk:\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule sim_popgen_data (line 4, /tmp/tmpui4ku78m/workflow/rules/sims.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule create_summary_stats (line 48, /tmp/tmpui4ku78m/workflow/rules/sims.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_summary_stats (line 75, /tmp/tmpui4ku78m/workflow/rules/sims.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Creating specified working directory /your/directory/here.\nPermissionError in file /tmp/tmpb_4sx3jl/workflow/Snakefile, line 7:\n[Errno 13] Permission denied: \u0027/your\u0027\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 0, "topics": [], - "updated_at": 1721168943.0 + "updated_at": 1726177806.0 }, { "config_readme": null, "data_format": 2, - "description": "TRANQUIL (TRna AbundaNce QUantification pIpeLine)", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/template.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/mimseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/init.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/preprocess.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/Snakefile\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "CCBR/TRANQUIL", - "latest_release": "v0.2.1", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/Snakefile\", line 2, in \u003cmodule\u003e\n include: join(\"rules\",\"init.smk\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/init.smk\", line 44, in \u003cmodule\u003e\n CONFIGFILE = str(workflow.overwrite_configfiles[0])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nIndexError: list index out of range\n\n", + "description": "Workflow to identify the centromere dip region (CDR) from methyl BAMs", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpumxp1g0a/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "koisland/CDR-Finder", + "latest_release": null, + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 6, + "subscribers_count": 1, "topics": [], - "updated_at": 1721136674.0 + "updated_at": 1726071971.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/regions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/candidate_calling.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp0nhbuito/workflow/rules/phylogeny.smk\": SyntaxError: L232: Unrecognised keyword \u0027best_model\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/phylogeny.smk\": \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 5 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "hzi-bifo/phylogeny-of-single-cells", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbyphbz3g/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "vkpat/short-read-mapping-and-QC-snakemake-pipeline", "latest_release": null, - "linting": "WorkflowError:\nError validating row 0 of data frame.\nValidationError: \u0027sample_name\u0027 is a required property\n\nFailed validating \u0027required\u0027 in schema:\n {\u0027$id\u0027: \u0027https://json-schema.org/draft/2020-12/schema\u0027,\n \u0027$schema\u0027: \u0027https://json-schema.org/draft/2020-12/schema\u0027,\n \u0027description\u0027: \u0027an entry (row) in the sample sheet, representing a \u0027\n \u0027DNA sequencing sample from either a bulk of cells or \u0027\n \u0027a multiple displacement amplified single cell DNA\u0027,\n \u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027sample_name\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027description\u0027: \u0027sample name/identifier \u0027\n \u0027(alphanumeric string, \u0027\n \u0027that may additionally \u0027\n \"contain \u0027_\u0027 and \u0027-\u0027)\",\n \u0027pattern\u0027: \u0027^[a-zA-Z_0-9-]+$\u0027},\n \u0027individual\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027description\u0027: \u0027individual whose cells \u0027\n \u0027to jointly use for \u0027\n \u0027phylogenetic \u0027\n \u0027reconstruction \u0027\n \u0027(alphanumeric string, \u0027\n \u0027that may additionally \u0027\n \"contain \u0027_\u0027 and \u0027-\u0027)\",\n \u0027pattern\u0027: \u0027^[a-zA-Z_0-9-]+$\u0027},\n \u0027sample_type\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027enum\u0027: [\u0027single_cell\u0027, \u0027bulk\u0027],\n \u0027description\u0027: \u0027indication whether a \u0027\n \u0027sequencing sample is \u0027\n \u0027made from a bulk of \u0027\n \u0027cells (without \u0027\n \u0027amplification) or from \u0027\n \u0027a single cell (with \u0027\n \u0027multiple displacement \u0027\n \u0027amplification)\u0027},\n \u0027platform\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027enum\u0027: [\u0027CAPILLARY\u0027,\n \u0027LS454\u0027,\n \u0027ILLUMINA\u0027,\n \u0027SOLID\u0027,\n \u0027HELICOS\u0027,\n \u0027IONTORRENT\u0027,\n \u0027ONT\u0027,\n \u0027PACBIO\u0027],\n \u0027description\u0027: \u0027used sequencing \u0027\n \u0027platform\u0027}},\n \u0027required\u0027: [\u0027sample_name\u0027, \u0027individual\u0027, \u0027sample_type\u0027, \u0027platform\u0027]}\n\nOn instance:\n {}\n", + "linting": "WorkflowError in file /tmp/tmpbyphbz3g/workflow/Snakefile, line 1:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpbyphbz3g/config.yaml).\n", "mandatory_flags": { "desc": null, "flags": null @@ -2047,103 +2078,103 @@ var data = }, "standardized": true, "stargazers_count": 0, - "subscribers_count": 6, + "subscribers_count": 1, "topics": [], - "updated_at": 1721132843.0 + "updated_at": 1726070051.0 }, { "config_readme": null, "data_format": 2, - "description": "compile a phylogenetic dataset from genewise CDS fasta files", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6jols31/rules/00-common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpq6jols31/rules/02-after_trimal.smk\": Keyword \"output\" at line 36 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpq6jols31/rules/02-after_trimal.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpq6jols31/rules/01-before_trimal.smk\": Keyword \"output\" at line 77 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpq6jols31/rules/01-before_trimal.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6jols31/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6jols31/rules/03-repeated_rules.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "etkayapar/pcc", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptmii62qa/rules/renv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmptmii62qa/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "deer-marketing-lab/dsms-lecture-ugc-ratings", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpq6jols31/Snakefile\", line 1, in \u003cmodule\u003e\n include: \"rules/00-common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpq6jols31/rules/00-common.smk\", line 8, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027gene_table.tsv\u0027\n\n", + "linting": "Lints for rule build_html (line 16, /tmp/tmptmii62qa/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 29, /tmp/tmptmii62qa/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 48, /tmp/tmptmii62qa/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 15, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 20, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 25, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 30, /tmp/tmptmii62qa/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 0, "topics": [], - "updated_at": 1721121990.0 + "updated_at": 1726069627.0 }, { "config_readme": null, "data_format": 2, - "description": "ss", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpya7tkufc/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Isha-Guptaa/snakemake_indel-snv_vcf-to-csv", + "description": "[INSERM U981] WGS\u0026WES Pipelines", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppavg8cvv/workflow/rules/init_pipeline.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmppavg8cvv/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 62:0: \u003cline number missing in source\u003e\n```\n\n[INFO] In file \"/tmp/tmppavg8cvv/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmppavg8cvv/workflow/Snakefile\": 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "jinxin-wang/Genome_Sequencing_Analysis", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpya7tkufc/Snakefile:\n * Absolute path \"/home/isha/Documents/repo/nextflow_VCF-to-CSV/second/HCC1395T_vs_HCC1395N.strelka.somatic_{vcf_type}_VEP.ann.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule index_vcf (line 24, /tmp/tmpya7tkufc/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_vcf (line 58, /tmp/tmpya7tkufc/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule convert (line 91, /tmp/tmpya7tkufc/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "FileNotFoundError in file /tmp/tmppavg8cvv/workflow/rules/init_pipeline.smk, line 118:\n[Errno 2] No such file or directory: \u0027config/variant_call_list_TvN.tsv\u0027\n File \"/tmp/tmppavg8cvv/workflow/rules/init_pipeline.smk\", line 118, in \u003cmodule\u003e\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1721117071.0 + "updated_at": 1726062684.0 }, { "config_readme": null, "data_format": 2, - "description": "Samar is a pipeline for speedy, assembly-free differential gene expression analysis in non-model organisms.", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp3o98dplp/workflow/Snakefile\": Keyword \"shell\" at line 130 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp3o98dplp/workflow/Snakefile\": Keyword \"shell\" at line 167 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp3o98dplp/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "bioinfodlsu/samar", + "description": null, + "formatting": "[DEBUG] \n\u003cunknown\u003e:14: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n[DEBUG] In file \"/tmp/tmpdyuhxgko/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "fredjarlier/ProjectCNN", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp3o98dplp/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n convert_fastq_fasta_SE = srcdir(\"scripts/convert_SE_fastq-fasta.sh\")\n ^^^^^^\n\nNameError: name \u0027srcdir\u0027 is not defined\n\n", + "linting": "/tmp/tmpdyuhxgko/Snakefile:78: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n \"{yes}.bam\"\n/tmp/tmpdyuhxgko/Snakefile:85: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n input:\nKeyError in file /tmp/tmpdyuhxgko/Snakefile, line 31:\n\u0027lanes\u0027\n File \"/tmp/tmpdyuhxgko/Snakefile\", line 31, in \u003cmodule\u003e\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1721116075.0 + "updated_at": 1726058223.0 }, { "config_readme": null, "data_format": 2, - "description": "Robust reproducible differential expression analysis based on edgeR with components in R and Python as a snakemake pipeline", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfwdz5oz4/workflow/rules/expr_tables.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[ERROR] In file \"/tmp/tmpfwdz5oz4/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 7:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpfwdz5oz4/workflow/Snakefile\": \n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "imgag/expression-analysis-smk", - "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config.yml but it is not present or accessible (full checked path: /tmp/tmpfwdz5oz4/config.yml).\n", + "description": "Mu-seq Workflow Utility ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/insertion_identification.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 93 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 129 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 168 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Keyword \"input\" at line 200 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk\": InvalidPython: Black error:\n```\nCannot parse: 18:4: run:\n```\n\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk\": \n[ERROR] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/trimming.smk\": InvalidPython: Black error:\n```\nCannot parse: 45:4: log:\n```\n\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/trimming.smk\": \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/common_utils.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/quality_control.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/insertion_annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref_utils.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk\": InvalidPython: Black error:\n```\nCannot parse: 14:7: output:\n```\n\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk\": \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/indexes_bam2sam.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/duplicate_removal.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/mapping.smk\": Inline-formatted keyword \"threads\" at line 80 had its comments relocated above it.\nPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/mapping.smk\": Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "tgstoecker/MuWU", + "latest_release": "v1.5.0", + "linting": "/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk:129: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \"logs/annotation_table/annotation_table.log\"\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/ref.smk:142: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \".1.bt2\", \".2.bt2\", \".3.bt2\", \".4.bt2\", \".rev.1.bt2\", \".rev.2.bt2\",\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:45: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n sed -i \u00271i Name\\\\tStrand\\\\tType\u0027 {output}\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:53: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n read_typing=expand(\"results/te_typing/pre_sorting/{sample}/{sample}_te_types_merged.tsv\", sample=SAMPLES),\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:510: SyntaxWarning: invalid escape sequence \u0027\\(\u0027\n/tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk:519: SyntaxWarning: invalid escape sequence \u0027\\(\u0027\nLints for rule read_te_typing (line 8, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merging_read_te_typing (line 34, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule te_typing_annotation (line 51, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule te_typing_annotation_propagation_GRID (line 79, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_uncategorized_ins_reads_1 (line 134, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_uncategorized_ins_reads_2 (line 151, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_uncategorized_ins_reads (line 167, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_categorized_ins_reads (line 184, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule locate_motif (line 197, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extend_motif (line 217, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extract_unc_ins_motif_subregions (line 232, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rename_unc_ins_motif_subregions (line 250, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_motif_subregions_files (line 263, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clustering_unc_reads_final_set (line 276, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule reformat_clustering_results_1 (line 293, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule reformat_clustering_results_2 (line 306, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule final_cluster_sizes (line 323, /tmp/tmpjsaaylsc/tgstoecker-MuWU-cbf7dbb/workflow/rules/te_typing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 1, "topics": [], - "updated_at": 1721111566.0 + "updated_at": 1726050889.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp1c9u6lxr/Snakefile\": Keyword \"shell\" at line 134 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp1c9u6lxr/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "PallaresLab/DNAPipeline", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp2dl8hrsu/Snakefile\": Keyword \"shell\" at line 260 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2dl8hrsu/Snakefile\": Keyword \"shell\" at line 548 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp2dl8hrsu/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "HealthML/MFD", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp1c9u6lxr/Snakefile:\n * Absolute path \"/logs\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/working\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.fastq.gz\" in line 11:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.fastq.gz\" in line 14:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R1_001.fastq.gz\" in line 15:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc/multiqc.html\" in line 29:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.fastq.gz\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/{sample}_fastqc.zip\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/{sample}.log\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc\" in line 45:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/*_fastqc.html\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}\" in line 65:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R1_001_val_1.fq.gz\" in line 66:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R2_001_val_2.fq.gz\" in line 67:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}.log\" in line 68:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}\" in line 71:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/*_fastqc.html\" in line 72:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa_index/index.log\" in line 97:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa_index\" in line 100:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R1_001_val_1.fq.gz\" in line 115:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R2_001_val_2.fq.gz\" in line 116:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.bam\" in line 120:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.txt\" in line 121:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.log\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa\" in line 127:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.bam\" in line 145:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}_deduplicated.bam\" in line 148:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}_deduplicated.metrics.txt\" in line 149:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}.log\" in line 152:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard\" in line 155:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/{sample}_fastqc.zip\" in line 168:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}\" in line 170:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}.log\" in line 172:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.txt\" in line 174:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}_deduplicated.metrics.txt\" in line 176:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc/multiqc.html\" in line 182:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc/multiqc.log\" in line 185:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc\" in line 188:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 2:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 97:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule fastqc (line 43, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule trim (line 94, /tmp/tmp1c9u6lxr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule bwa_index (line 145, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule bwa (line 191, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule picard (line 246, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule multiqc (line 291, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "WorkflowError in file /tmp/tmp2dl8hrsu/Snakefile, line 1:\nWorkflow defines configfile src/config.yaml but it is not present or accessible (full checked path: /tmp/tmp2dl8hrsu/src/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 4, "topics": [], - "updated_at": 1724663319.0 + "updated_at": 1726044610.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqeeav49r/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Applied-Genomics-UTD/template-intro-snakemake", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpqoiceb5e/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 6:8: storage:\n```\n\n[INFO] In file \"/tmp/tmpqoiceb5e/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "dakesan/snakemake-s3-minimum-example", "latest_release": null, - "linting": "Lints for rule bwa_map (line 13, /tmp/tmpqeeav49r/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "InvalidPluginException in file /tmp/tmpqoiceb5e/Snakefile, line 6:\nError loading Snakemake plugin s3: The package snakemake-storage-plugin-s3 is not installed.\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2151,116 +2182,101 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1720975285.0 + "updated_at": 1726027343.0 }, { - "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing only one\nkey: \u003ccode\u003egenomes\u003c/code\u003e, which value is the path to a file containing the list of\ngenomes to download as described below.\u003c/p\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003egenomes: config/genomes.csv\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_genome_indexer/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003especies: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003ebuild: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003erelease: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release\nhomo_sapiens,GRCh38,110\nmus_musculus,GRCm38,99\nmus_musculus,GRCm39,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_genome_indexer/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Download and index Ensembl sequences and annotations", - "formatting": null, - "full_name": "tdayris/fair_genome_indexer", - "latest_release": "3.8.1", - "linting": null, - "mandatory_flags": { - "desc": "Download and index Ensembl genome files", - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": true - }, - "standardized": true, + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp93c8a3i2/workflow/Snakefile\": Keyword \"output\" at line 39 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp93c8a3i2/workflow/Snakefile\": Keyword \"params\" at line 53 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp93c8a3i2/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_mag-qc", + "latest_release": null, + "linting": "KeyError in file /tmp/tmp93c8a3i2/workflow/Snakefile, line 13:\n\u0027work_dir\u0027\n File \"/tmp/tmp93c8a3i2/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "ensembl", - "fair", - "snakemake", - "snakemake-workflow", - "snakemake-wrappers" - ], - "updated_at": 1720931641.0 + "topics": [], + "updated_at": 1726024734.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpdtyqazm8/Snakefile\": SyntaxError: L34: Unrecognised keyword \u0027\u0027\u0027\u0027\n\tMask repeats in the genome using RepeatMasker\n\t\u0027\u0027\u0027\u0027 in rule definition\n[INFO] In file \"/tmp/tmpdtyqazm8/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "Nanobio1991/AmphioxusCNVs", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpij19n6zn/workflow/Snakefile\": Keyword \"input\" at line 38 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmpij19n6zn/workflow/Snakefile\": NoParametersError: L189: In output definition.\n[INFO] In file \"/tmp/tmpij19n6zn/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "palomnyk/NHANES_Complexity", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdtyqazm8/Snakefile\", line 764, in \u003cmodule\u003e\n\nAttributeError: \u0027Namedlist\u0027 object has no attribute \u0027cnv_not_merged\u0027\n\n", + "linting": "SyntaxError in file /tmp/tmpij19n6zn/workflow/Snakefile, line 104:\nCommand must be given as string after the shell keyword.:\nNone\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 1, "topics": [], - "updated_at": 1720900261.0 + "updated_at": 1726014098.0 }, { "config_readme": null, "data_format": 2, - "description": "https://agc.readthedocs.io/ on REANA", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpg9miwz9z/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "iris-hep/agc-reana", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/clustering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/gliph.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/plotting.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/conga.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/seurat_preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/tcr_dist.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5xd23uhl/workflow/rules/differential_expression.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "carpenter-lab/single-cell-workflow", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpg9miwz9z/Snakefile:\n * Absolute path \"/bin/bash -l \u0026\u0026 source fix-env.sh \u0026\u0026 python prepare_workspace.py sample_{params.sample_name}_{wildcards.filename} \u0026\u0026 papermill ttbar_analysis_reana.ipynb sample_{params.sample_name}_{wildcards.filename}_out.ipynb -p sample_name {params.sample_name} -p filename {url_prefix}{wildcards.filename} -k python3\" in line 66:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bin/bash -l \u0026\u0026 source fix-env.sh \u0026\u0026 papermill file_merging.ipynb merged_{params.sample_name}.ipynb -p sample_name {params.sample_name} -k python3\" in line 81:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bin/bash -l \u0026\u0026 source fix-env.sh \u0026\u0026 papermill final_merging.ipynb result_notebook.ipynb -k python3\" in line 102:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 21:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule process_sample_one_file_in_sample (line 61, /tmp/tmpg9miwz9z/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable url_prefix from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule process_sample (line 97, /tmp/tmpg9miwz9z/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merging_histograms (line 134, /tmp/tmpg9miwz9z/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "\nEidoValidationError in file /tmp/tmp5xd23uhl/workflow/Snakefile, line 13:\nEidoValidationError (Validation failed): {\"\u0027_samples\u0027 is a required property\": [{\u0027type\u0027: \"\u0027_samples\u0027 is a required property\", \u0027message\u0027: \"\u0027_samples\u0027 is a required property on instance project\", \u0027sample_name\u0027: \u0027project\u0027}]}\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/eido/validation.py\", line 73, in validate_project\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/eido/validation.py\", line 56, in _validate_object\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 5, + "subscribers_count": 1, "topics": [], - "updated_at": 1720866798.0 + "updated_at": 1725999338.0 }, { - "config_readme": "\u003cp\u003eMost of the parameters for CLIPs4U run have to be set up in your custom \u003ca href=\"https://en.wikipedia.org/wiki/YAML\" rel=\"nofollow\"\u003eYAML\u003c/a\u003e file (for example \u003ccode\u003econfig.yaml\u003c/code\u003e).\nYou can edit \u003ccode\u003econfig.yaml\u003c/code\u003e, which is an empty config file in any text editor and set all parameters.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e only 3\u0027adapter and 5\u0027adapter sequences are absolutely required.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e when you do not provide path to your input file(s) CLIPs4U will run with test dataset (ZFP36.fq.gz) and your config file.\u003c/p\u003e\n\u003cp\u003eThe configuration file contains seven main sections:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eexec and input paths and hardware settings\u003c/li\u003e\n\u003cli\u003egenome file and genomic annotations\u003c/li\u003e\n\u003cli\u003eadapter trimming and reads collapsing\u003c/li\u003e\n\u003cli\u003eremoving repetitive elements\u003c/li\u003e\n\u003cli\u003egenome alignment\u003c/li\u003e\n\u003cli\u003ePARalyzer params\u003c/li\u003e\n\u003cli\u003emotif enrichment params\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eDefault configuration file is stored in \u003ccode\u003econfig/default_config.yaml\u003c/code\u003e\u003c/p\u003e\n\u003cp\u003eExec and input paths and hardware settings section contains two fields; the \u003ccode\u003einput_files\u003c/code\u003e field where you specify path(s) to input fastq.gz file(s). When you have more than one input, separate paths by comma. In the \u003ccode\u003ethreads\u003c/code\u003e field you specify maximum naumber of processors used by the rules within workflow.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e{\n #exec and input paths and hardware settings\n \u0027input_files\u0027: \"\", #(REQUIRED)absolute path(s) must be provided by user in config file, if \u0026gt; 1, comma separated\n \u0027threads\u0027: 4,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eGenome file and genomic annotations contains five fields. The first one specify organism. Right now you can choose human or mouse (\u003ccode\u003e\"hs\"\u003c/code\u003e or \u003ccode\u003e\"mm\"\u003c/code\u003e). If you want to run your analysis with data from other organism(s) open an issue and|or write an e-mail to \u003ca href=\"mailto:marcin.sajek@gmail.com\"\u003emarcin.sajek@gmail.com\u003c/a\u003e and we will prepare the data and|or modify scripts.\n\u003ccode\u003egenome_fasta\u003c/code\u003e and \u003ccode\u003egtf\u003c/code\u003e fields contain paths to genome sequence and gtf files. When empty (\u003ccode\u003e\"\"\u003c/code\u003e) both genome and its annotation will be downloaded from gencode. Gencode version of genome and gtf is specified in the \u003ccode\u003egenome_version\u003c/code\u003e field. The default version for human genome is 45, and for mouse - 35.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e Gencode versions for both organism must be greater than 4\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eannot_rank\u003c/code\u003e field contains path to annotation ranking file. If empty, default annot rank file will be used. This file contain categories from \u003ccode\u003egene_type\u003c/code\u003e field of gtf file, and if the peak is mapping to region with multiple annotations, lowest rank is chosen. The most abundant RNA types have highest ranks.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre lang=\"#genome\"\u003e\u003ccode\u003e \u0027organism\u0027 : \"hs\", #(OPTIONAL) allowed values are \"hs\" for human and \"mm\" for mouse\n \u0027genome_fasta\u0027 : \"\", #(OPTIONAL) you can specify your own genome file, if not specified GRCh38/GRCm39 primary assembly from gencode v45 will be automatically downloaded\n \u0027gtf\u0027 : \"\", #(OPTIONAL) you can specify your own gtf file (compatible with genome), if not specified basic annotation for GRCh38/GRCm39 primary assembly from gencode v45 will be automatically downloaded\n \u0027genome_version\u0027 : \"\", #(OPTIONAL) you can specify your own genome/gtf version; default: GRCh38/GRCm39 primary assembly from gencode v45/35\n \u0027annot_rank\u0027 : \"\", #(OPTIONAL) you can specify your own annotation rank file, suggesed when using your own genome; default: CLIPs4U/annotation/{organism}/annot_ranks.txt\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eAdapter trimming and reads collapsing section contain adapter trimming parameters. Please familiarize yourself with \u003ca href=\"https://cutadapt.readthedocs.io/en/stable/guide.html\" rel=\"nofollow\"\u003ecutadapt\u003c/a\u003e before filling this section. For some analyses it may be better to split adapter trimming into two rounds. If you want to do it in one step fill \u003ccode\u003ecutadapt_params1\u003c/code\u003e field and leave \u003ccode\u003ecutadapt_params2\u003c/code\u003e field with empty quotes \u003ccode\u003ecutadapt_params2 : \"\"\u003c/code\u003e, which is a default setting. If yor sequencing was performed on NextSeq or NovaSeq machine consider setting \u003ccode\u003enextseq\u003c/code\u003e to \u003ccode\u003eTrue\u003c/code\u003e, to remove a \u2018dark cycle\u2019 encoded as string of Gs. If you have UMIs in your read set the length of UMI in \u003ccode\u003eumi\u003c/code\u003e field. If your UMIs are in the 5\u0027 end of the read use positive integer, if at the 3\u0027 end, negative integer.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #adapter trimming and reads collapsing\n \u0027three_prime_adapter\u0027 : \"\", #(REQUIRED!!!) put your 3\u0027adapter sequence\n \u0027five_prime_adapter\u0027 : \"\", #(REQUIRED!!!) your 5\u0027adapter sequence\n \u0027nextseq\u0027 : False, #(OPTIONAL) put True or 1 if your sequencing run was on NextSeq machine\n \u0027cutadapt_params1\u0027 : \"-b CGTACGCGGGTTTAAACGA -b CTCATCTTGGTCGTACGCGGAATAGTTTAAACTGT -n 3 -j 0 -m 15 -M 50 --max-n 1\", #(OPTIONAL) - additional cutadapt parameters\n \u0027cutadapt_params2\u0027 : \"\", #(OPTIONAL) leave empty to ommit this step, if you want to perform second trimming put all cutadapt parameters for 2nd trimming here (including adapters)\n \u0027umi\u0027 : \"\", #(OPTIONAL) leave empty if you don\u0027t have UMIs, for 5\u0027 UMIs positive integer equal UMI length, if 3\u0027UMIs - negative integer equal UMI length\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003e\u003cstrong\u003eTIP:\u003c/strong\u003e \u003ccode\u003e-j 0 \u003c/code\u003e in cutadapt determined automatically numbers of available threads.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTIP:\u003c/strong\u003e Reads that are to long can cause further issues with PARalyzer (e.g. reported \u003ca href=\"https://github.com/ohlerlab/PARpipe/issues/6\"\u003ehere\u003c/a\u003e). Consider setting a max read length parameter, e.g. \u003ccode\u003e-M 50\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eRemoving repetitive elements section is skipped with default settings. User can perform removing repetitive element before genome alignent by setting \u003ccode\u003erem_rep\u003c/code\u003e to \u003ccode\u003eTrue\u003c/code\u003e. CLIPs4U is using \u003ca href=\"https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf\" rel=\"nofollow\"\u003eSTAR\u003c/a\u003e for this task. It is using default repetitive elments index and STAR parameters if \u003ccode\u003erep_idx\u003c/code\u003e and \u003ccode\u003estar_rem_reps_params\u003c/code\u003e are empty.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #removing repetitive elements\n \u0027rem_rep\u0027 : \"\", #(OPTIONAL) leave empty to omit this step, put True or 1 if you want to remove repetitive elements\n \u0027rep_idx\u0027 : \"\", #(OPTIONAL) default: CLIPs4U/annotation/{organism}/rep_idx\n \u0027star_rem_reps_params\u0027 : \"--runMode alignReads --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMtype BAM Unsorted --outFilterType BySJout --outBAMcompression 10 --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full\", #(OPTIONAL)\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eGenome alignment section of the configuration file contains a parameters list passed to aligner. Default aligner is \u003ca href=\"https://bowtie-bio.sourceforge.net/index.shtml\" rel=\"nofollow\"\u003ebowtie\u003c/a\u003e. User can switch aligner to \u003ca href=\"https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf\" rel=\"nofollow\"\u003eSTAR\u003c/a\u003e by filling \u003ccode\u003ealigner\u003c/code\u003e field with one of \u003ccode\u003e\"STAR\"\u003c/code\u003e, \u003ccode\u003e\"star\"\u003c/code\u003e, \u003ccode\u003e\"S\"\u003c/code\u003e or \u003ccode\u003e\"s\"\u003c/code\u003e. Remaining fields contain paths to bowtie or STAR indexes (generated automatically for selected aligner if left empty) and aligner parameters (filled with default settings when empty).\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #genome alignment\n \u0027aligner\u0027 : \"\", #(OPTIONAL) default bowtie, use \u0027S\u0027, \u0027s\u0027, \u0027STAR\u0027 or \u0027star\u0027 to switch to STAR\n \u0027bowtie_index_dir\u0027 : \"\", #(OPTIONAL) default - will be created automatically in your working dir if aligner will be set to bowtie\n \u0027bowtie_index_params\u0027 : \"\", #(OPTIONAL)\n \u0027bowtie_map_params\u0027 : \"-v 1 -m 10 --best --strata -S\", #(OPTIONAL)\n \u0027star_index_dir\u0027 : \"\", #(OPTIONAL) default - will be created automatically in your working dir if aligner will be set to STAR\n \u0027star_index_params\u0027 : \"--runMode genomeGenerate --sjdbOverhang 100\", #(OPTIONAL)\n \u0027star_map_params\u0027 : \"--runMode alignReads --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMattributes All --outSAMtype BAM Unsorted --outFilterType BySJout --outFilterMismatchNoverReadLmax 0.05 --outSAMattrRGline ID:foo --outStd Log --outBAMcompression 10 --outSAMmode Full\", #(OPTIONAL)\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eThe PARalyzer parameters section is directly used to create .ini file for PARalyzer run and setup memory limit for PARalyzer (\u003ccode\u003eparalyzer_memory\u003c/code\u003e field). To properly fill all fields please read PARalyzer \u003ca href=\"https://ohlerlab.mdc-berlin.de/files/duke/PARalyzer/README.txt\" rel=\"nofollow\"\u003emanual\u003c/a\u003e. Field \u003ccode\u003eADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u003c/code\u003e is required only if \u003ccode\u003esignal_extension : ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u003c/code\u003e. In other cases it will be skipped. If your library does not contain UMIs you may consider switching \u003ccode\u003euse_pcr_duplicates\u003c/code\u003e to \u003ccode\u003eTrue\u003c/code\u003e. Then PARalyzer will take into account all reads without PCR duplicates discrimination.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #PARalyzer params\n \u0027paralyzer_memory\u0027 : \"4G\", #(OPTIONAL)\n \u0027BANDWIDTH\u0027 : 3, #(OPTIONAL)\n \u0027CONVERSION\u0027 : \"T\u0026gt;C\", #(OPTIONAL), possible choices \"T\u0026gt;C\", \"G\u0026gt;A\"\n \u0027MINIMUM_READ_COUNT_PER_GROUP\u0027 : 5, #(OPTIONAL),\n \u0027MINIMUM_READ_COUNT_PER_CLUSTER\u0027 : 2, #(OPTIONAL)\n \u0027MINIMUM_READ_COUNT_FOR_KDE\u0027 : 3, #(OPTIONAL)\n \u0027MINIMUM_CLUSTER_SIZE\u0027 : 11, #(OPTIONAL)\n \u0027MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER\u0027 : 2, #(OPTIONAL)\n \u0027MINIMUM_CONVERSION_COUNT_FOR_CLUSTER\u0027 : 2, #(OPTIONAL)\n \u0027MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION\u0027 : 1, #(OPTIONAL)\n \u0027MINIMUM_READ_LENGTH\u0027 : 15, #(OPTIONAL)\n \u0027MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES\u0027 : 1, #(OPTIONAL)\n \u0027signal_extension\u0027 : \"EXTEND_BY_READ\", ##(OPTIONAL) one of \u0027EXTEND_BY_READ\u0027, \u0027HAFNER_APPROACH\u0027, \u0027ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u0027\n \u0027ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u0027 : 2, #only valid when signal_extension : \u0027ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u0027\n \u0027use_pcr_duplicates\u0027 : False, #(OPTIONAL) change to True to force PARalyzer to treat pcr duplicates as individual reads (will increase number of clusters, but also false positives)\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eThe last section contains motif enrichment parameters. Motif enrichmantis performed by one of the tools from \u003ca href=\"https://meme-suite.org/meme/\" rel=\"nofollow\"\u003eMEME\u003c/a\u003e. Default value for \u003ccode\u003emotif_enrichment_method\u003c/code\u003e is \u003ca href=\"https://meme-suite.org/meme/tools/meme\" rel=\"nofollow\"\u003ememe\u003c/a\u003e, user can also choose \u003ca href=\"https://meme-suite.org/meme/doc/dreme-tutorial.html\" rel=\"nofollow\"\u003edreme\u003c/a\u003e or \u003ca href=\"https://meme-suite.org/meme/doc/streme-tutorial.html\" rel=\"nofollow\"\u003estreme\u003c/a\u003e. \u003ccode\u003emotif_enrichment_params\u003c/code\u003e field should be filled with parameters specific for selected method.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e For motif enrichment analysis keep alphabet as \u003ccode\u003e-dna\u003c/code\u003e. Do not switch it to \u003ccode\u003e-rna\u003c/code\u003e. Final motifs will be changed to RNA alphabet automatically in the next steps.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #motif enrichment params\n \u0027motif_enrichment_method\u0027 : \"meme\", #(OPTIONAL), possible choices \"meme\", \"dreme\", \"streme\"\n \u0027motif_enrichment_params\u0027 : \"-dna -mod anr -evt 0.05 -minw 3\", #(OPTIONAL); be aware that some prameters are specific for enrichment method chosen\n}\n\u003c/code\u003e\u003c/pre\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for PAR-CLIP data analysis", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/genomes_indexes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/quality.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpz4ql9bk1/workflow/rules/alignment.smk\": Keyword \"output\" at line 7 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/remove_rep_elements.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/generate_report.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/trimming.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/bigwigs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/motif_enr.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/collapse_reads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/paralyzer.smk\": Formatted content is different from original\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mukherjeelab/CLIPs4U", + "description": "A thin wrapper to simplify running cellprofiler on della", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsxp2ehq9/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "SoftLivingMatter/snakemake-cellprofiler", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpz4ql9bk1/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n from scripts.genomic_files_and_indexes import prepare_genomes_and_indexes\n\n File \"/tmp/tmpz4ql9bk1/workflow/scripts/genomic_files_and_indexes.py\", line 9, in \u003cmodule\u003e\n import wget\n\nModuleNotFoundError: No module named \u0027wget\u0027\n\n", - "mandatory_flags": null, + "linting": "Creating specified working directory /path/to/output/directory.\nPermissionError in file /tmp/tmpsxp2ehq9/workflow/Snakefile, line 7:\n[Errno 13] Permission denied: \u0027/path\u0027\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1315, in mkdir\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/pathlib.py\", line 1311, in mkdir\n", + "mandatory_flags": [], "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 0, "topics": [], - "updated_at": 1720826035.0 + "updated_at": 1726177733.0 }, { "config_readme": null, "data_format": 2, - "description": "An app that removes empty images from camera trap datasets using MD. Comes with a simple GUI.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpstp5ptea/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "dwheelerau/easily-triggered", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/searchgui.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/raw_file_parse.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/generate_db.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/peptide_shaker.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/post_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp5yqp4tmy/workflow/rules/gff_generation.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "PRIDE-reanalysis/MetaPUF", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpstp5ptea/Snakefile:\n * Absolute path \"/project/megadetector-summary.txt\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.json\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.json\" in line 18:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.csv\" in line 20:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.csv\" in line 28:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/megadetector-summary.txt\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule megadetector (line 16, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule json_to_csv (line 38, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_md (line 64, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 90, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule kill (line 101, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "NotImplementedError in file /tmp/tmp5yqp4tmy/workflow/rules/raw_file_parse.smk, line 10:\nRemote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1720824619.0 + "updated_at": 1725982636.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "Test", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpc4mm9twg/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "weizhu365/snakemake_template_test", + "description": "Generating consistent TC and TC Surge hazard set event using Snakemake and CLIMADA", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpybi507vm/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "spjuhel/Climada_TC_TCSurge_Generation", "latest_release": null, - "linting": null, + "linting": "KeyError in file /tmp/tmpybi507vm/workflow/Snakefile, line 27:\n\u0027start\u0027\n File \"/tmp/tmpybi507vm/workflow/Snakefile\", line 27, in \u003cmodule\u003e\n", "mandatory_flags": { "desc": null, "flags": null @@ -2275,50 +2291,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1720727511.0 + "updated_at": 1725981203.0 }, { "config_readme": null, "data_format": 2, - "description": "Predict variant calling performance across the genome", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpdo_o7atv/workflow/rules/inputs.smk\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 3 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "usnistgov/giab-stratomod", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp_8rvuhe_/workflow/rules/phylogeny.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "koisland/CenClustering", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdo_o7atv/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n from common.config import StratoMod\n\n File \"/tmp/tmpdo_o7atv/workflow/scripts/python/common/config.py\", line 43, in \u003cmodule\u003e\n from more_itertools import duplicates_everseen, unzip, partition, flatten\n\nModuleNotFoundError: No module named \u0027more_itertools\u0027\n\n", + "linting": "Multiple includes of /tmp/tmp_8rvuhe_/workflow/rules/data.smk ignored\nLints for snakefile https://:ghs_9K7szIWhrwDYcwcKyxn0stCzzoXvKe0s9Fdn@raw.githubusercontent.com/koisland/asm-to-reference-alignment/minimal/workflow/Snakefile:\n * Absolute path \"/tmp\" in line 13:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmp_8rvuhe_/workflow/rules/phylogeny.smk:\n * Deprecated singularity directive used for container definition in line 25.:\n Use the container directive instead (it is agnostic of the underlying\n container runtime).\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule wget (line 1, /tmp/tmp_8rvuhe_/workflow/rules/utils.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_chm13_asm (line 6, /tmp/tmp_8rvuhe_/workflow/rules/data.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_chimp_asm (line 28, /tmp/tmp_8rvuhe_/workflow/rules/data.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1720724424.0 + "updated_at": 1725980621.0 }, { "config_readme": null, "data_format": 2, - "description": "Genome-in-a-Bottle stratifications for major references", + "description": "Snakemake workflow to basecall ONT reads with dorado.", "formatting": null, - "full_name": "usnistgov/giab-stratifications", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5b_4yl7d/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n from common.config import GiabStrats\n\nModuleNotFoundError: No module named \u0027common\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1720719980.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A pipeline for quantification of antibody staining in TMA cores.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp841howes/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "StaafLab/TMArQ", + "full_name": "logsdon-lab/Snakemake-ONT-Basecalling", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp841howes/Snakefile:\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule detectROI (line 26, /tmp/tmp841howes/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule segment (line 48, /tmp/tmp841howes/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpctlra9d1/workflow/rules/common.smk:\n * Absolute path \"/\", \" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule dorado_basecaller (line 31, /tmp/tmpctlra9d1/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2326,37 +2325,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1720710680.0 + "updated_at": 1726364793.0 }, { "config_readme": null, "data_format": 2, - "description": "Example repository for analyzing many datasets at once from scperturb.org using snakemake", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp8_50y4r6/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "stefanpeidli/scperturb_snakemake_example", + "description": "La idea es crear una p\u00e1gina web con especies de fauna y flora de Gran Canaria que vaya encontrando, vamos a ver como hacemos esto", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpvjxeid2v/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "JuanCarlosBio/BiodiversidadGJC", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 135, in import_optional_dependency\n module = importlib.import_module(name)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/importlib/__init__.py\", line 90, in import_module\n return _bootstrap._gcd_import(name[level:], package, level)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1387, in _gcd_import\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1360, in _find_and_load\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1324, in _find_and_load_unlocked\n\nModuleNotFoundError: No module named \u0027openpyxl\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp8_50y4r6/Snakefile\", line 26, in \u003cmodule\u003e\n if DATASETS == \u0027all\u0027:\n ^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 495, in read_excel\n io = ExcelFile(\n ^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 1567, in __init__\n self._reader = self._engines[engine](\n ^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_openpyxl.py\", line 552, in __init__\n import_optional_dependency(\"openpyxl\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 138, in import_optional_dependency\n raise ImportError(msg)\n\nImportError: Missing optional dependency \u0027openpyxl\u0027. Use pip or conda to install openpyxl.\n\n", + "linting": "Lints for rule download_images (line 26, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_canary_islands_shp (line 41, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_extra_layers (line 54, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_biota_data (line 71, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule process_canary_islands_shp (line 83, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule process_jardin_botanico_kml (line 99, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule process_biota_data (line 112, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule figures_and_stats (line 146, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule webpage_html (line 165, /tmp/tmpvjxeid2v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "perturbation-methods", - "single-cell", - "transcriptomics" - ], - "updated_at": 1721584898.0 + "topics": [], + "updated_at": 1726363040.0 }, { "config_readme": null, "data_format": 2, - "description": "deep_snake - snakemake-based deepconsensus (Pacbio SequelII subreads - to deepconsensus.fastq)", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpv1rq1esq/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:6: needs to be here for the snakemake workflow catalogue\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[INFO] In file \"/tmp/tmpv1rq1esq/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "WestGermanGenomeCenter/deep_snake", + "description": "A repository to hold the workflow for running solutionAnalysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbwl8qsaq/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "amritagos/workflow_solutionAnalysis", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpv1rq1esq/Snakefile, line 1:\ninvalid syntax:\nneeds to be here for the snakemake workflow catalogue\n\n", + "linting": "Lints for rule param_sweep (line 14, /tmp/tmpbwl8qsaq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2364,33 +2359,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1720702186.0 + "updated_at": 1726325547.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\ \u0027\n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/selection.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/karyotype.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/utility.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/PopulationStructure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/Snakefile\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "sanjaynagi/probe", + "description": "House of Congress Bills Cosponsorship", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0k8pusec/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "LMCasale/PP4RS_Final_Assignment_LMC_MM", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp1alwu1f4/workflow/Snakefile\", line 28, in \u003cmodule\u003e\n PCAcohorts = getCohorts(metadata, columns=config[\u0027PopulationStructure\u0027][\u0027PCA\u0027][\u0027colourColumns\u0027]) # PCA\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027config/gaard_metadata.tsv\u0027\n\n", + "linting": "Lints for rule PY_data_collection (line 5, /tmp/tmp0k8pusec/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule generate_report (line 13, /tmp/tmp0k8pusec/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1720687708.0 + "updated_at": 1726311216.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow: DNA Single Nucleotide Variant Calling ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpx6bc4lku/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "lesleymaraina/snv_ensemble_variant_calling", + "description": "Snakemake workflow for RNA-Seq and TGIRT-Seq", + "formatting": null, + "full_name": "LPChaumont/rna-seq-smk", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpx6bc4lku/Snakefile:\n * Absolute path \"/data/AlexanderP3/SJCLOUD/RBL/retinoblastoma/germline/WGS/bam/{sample}.WholeGenome.bam\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/AlexanderP3/SJCLOUD/RBL/retinoblastoma/germline/WGS/bam/{sample}.WholeGenome.bam.bai\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule strelka (line 23, /tmp/tmpx6bc4lku/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable parapath from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule HC (line 59, /tmp/tmpx6bc4lku/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable parapath from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule DV (line 94, /tmp/tmpx6bc4lku/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable parapath from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "linting": "Lints for snakefile /tmp/tmp8z0ir3q0/workflow/rules/common.smk:\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule build_full_transcriptome (line 49, /tmp/tmp8z0ir3q0/workflow/rules/ref.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fastp_multiqc (line 26, /tmp/tmp8z0ir3q0/workflow/rules/fastp.smk):\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_index (line 1, /tmp/tmp8z0ir3q0/workflow/rules/star.smk):\n * Param index_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_align (line 27, /tmp/tmp8z0ir3q0/workflow/rules/star.smk):\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param index_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule star_multiqc (line 62, /tmp/tmp8z0ir3q0/workflow/rules/star.smk):\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule salmon_quant (line 26, /tmp/tmp8z0ir3q0/workflow/rules/salmon.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule salmon_tximport (line 50, /tmp/tmp8z0ir3q0/workflow/rules/salmon.smk):\n * Param quantdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule salmon_multiqc (line 69, /tmp/tmp8z0ir3q0/workflow/rules/salmon.smk):\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule install_coco (line 6, /tmp/tmp8z0ir3q0/workflow/rules/coco.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule install_pairedBamToBed12 (line 18, /tmp/tmp8z0ir3q0/workflow/rules/coco.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule coco_sort_bg (line 107, /tmp/tmp8z0ir3q0/workflow/rules/coco.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule install_pairadise (line 5, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule rmats_config_prep (line 21, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_config_post (line 33, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_post (line 83, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * Param tmp is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_stat (line 113, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * Param stat_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param post_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule rmats_filtering (line 146, /tmp/tmp8z0ir3q0/workflow/rules/rmats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule deseq2 (line 1, /tmp/tmp8z0ir3q0/workflow/rules/deseq2.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2398,89 +2393,100 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1720642160.0 + "updated_at": 1726282837.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake Pipeline with \"selectable\" modules", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/split_bams_v2.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpcr8yqsp5/rules/split_bams_gt.smk\": Keyword \"params\" at line 151 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/split_bams_gt.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpcr8yqsp5/rules/analyse_vireo.smk\": Keyword \"output\" at line 7 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/analyse_vireo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/deeptools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/create_logs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/input_processing.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpcr8yqsp5/rules/snv_aware_align.smk\": Keyword \"output\" at line 81 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/snv_aware_align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/helper_functions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/STARsolo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/calico_solo_demux.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/identify_swaps.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/produce_targets.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/picard_metrics.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/demultiplex.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/pheno_demux3.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/kite.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/split_bams.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/resources.smk\": Formatted content is different from original\n[INFO] 19 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "pnm27/snRNA_scRNA_Pipeline", + "description": "construct pangenome from unaligned reads", + "formatting": null, + "full_name": "lightning-auriga/pangenome-from-unaligned-reads", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpcr8yqsp5/Snakefile\", line 20, in \u003cmodule\u003e\n import glob2, re, math\n\nModuleNotFoundError: No module named \u0027glob2\u0027\n\n", + "linting": "NotImplementedError in file /tmp/tmp88b07zux/workflow/Snakefile, line 14:\nRemote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1720635153.0 + "updated_at": 1726256549.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/8_snRNAseq_LDSR_protein_coding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/4_snRNAseq_MAGMA.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/5_snRNAseq_MAGMA_protein_genes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/9_snRNAseq_LDSR_nonprotein_coding.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp9ubz3_ps/workflow/Snakefile\": NoParametersError: L43: In input definition.\n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/11_snRNAseq_LDSR_GO_term_genes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/10_snRNAseq_LDSR_top2000.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/3_snRNAseq_get_and_munge_GWAS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/7_snRNAseq_LDSR.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/6_snRNAseq_MAGMA_nonprotein_genes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/2_snRNAseq_prep_enrich_files.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/1_snRNAseq_get_and_prep_herring_data.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 11 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "cetume/Tume_BP-GOS_2024", + "description": "This is the repository of the pipeline META-DIFF, which detects sequences in differential abundances between two conditions, and annotates them taxonomicaly and functionaly.", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpsu9u41ar/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 42)\n[INFO] In file \"/tmp/tmpsu9u41ar/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "Louis-MG/META-DIFF", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", + "linting": "TabError in file \u003cstring\u003e, line 42:\ninconsistent use of tabs and spaces in indentation:\n\texpand(config[\"project_path\"] + \"pipeline_output/functional_annotation/{condition}_unitigs_to_gene_functions.tsv\", condition = [\u0027case\u0027, \u0027control\u0027])\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1720626320.0 + "topics": [ + "annotation", + "bioinformatics-pipeline", + "kmers", + "metagenomics", + "shotgun-pipeline", + "snakemake" + ], + "updated_at": 1726244891.0 }, { "config_readme": null, "data_format": 2, - "description": "Workflow to detect assembly and long read regions rich in GA or CT alleles. ", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpruu6iydt/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 185)\n[INFO] In file \"/tmp/tmpruu6iydt/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "adlnosk/GA-CT-rich-regions", + "description": "Test of Uniformity for centrosome orientation at early timepoints during Wound Healing Assay", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpnsaf00li/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 83)\n[INFO] In file \"/tmp/tmpnsaf00li/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "rgomez-AI/CellOrientation", "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 185:\ninconsistent use of tabs and spaces in indentation:\n \tplotting_flank=10000,\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "linting": "TabError in file \u003cstring\u003e, line 83:\ninconsistent use of tabs and spaces in indentation:\n\tproj=\"ZSTD\",\t# Stack projection (\"ZMAX\", \"ZAVG\", \"ZSTD\" or \"None\")\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1720625698.0 + "subscribers_count": 1, + "topics": [ + "bioimage-analysis", + "cellprofiler-pipeline", + "fiji-macro-language", + "snakemake-workflow", + "workflow-automation", + "uniformity-tests" + ], + "updated_at": 1726236620.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": "\u003cp\u003eTriosCompass expects to use the parent folder of TriosCompass_v2 (the repo clone folder) as the working space, so as to separate the Snakemake workflow from the working space.\u003c/p\u003e\n\u003cp\u003eThree configure files are required:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cem\u003eProfile yaml file\u003c/em\u003e: workflow/profiles/\u0026lt;PROFILE_NAME\u0026gt;/config.yaml\u003c/li\u003e\n\u003cli\u003e\u003cem\u003eConfig yaml file\u003c/em\u003e\u003c/li\u003e\n\u003cli\u003e\u003cem\u003eSample yaml file\u003c/em\u003e\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eThe \u003cem\u003econfig yaml file\u003c/em\u003e can be specified by Snakemake command-line argument \"--configfile\" or in the \"\u003cem\u003eprofile yaml file\u003c/em\u003e, for example:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003econfigfile\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eTriosCompass_v2/config/fullbam_config.yaml\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esnakefile\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eTriosCompass_v2/workflow/Snakefile\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIn turn, the \u003cem\u003esample yaml file\u003c/em\u003e is specified in the \u003cem\u003econfig yaml file\u003c/em\u003e, to \u003ca href=\"https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#configuring-scientific-experiments-via-peps\" rel=\"nofollow\"\u003edefine sample input via PEPs\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003epepfile\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003econfig/fullbam_pep.yaml\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003epepschema\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e../schemas/bam_schema.yaml\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003eExample of the PEP configure file for FASTQ input files\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003econfig/fastq_pep.yaml\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003epep_version\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e2.0.0\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esample_table\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003esample_fastq.csv\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e In manifest file, Sample_ID + Flowcell should be unique\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esample_modifiers\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eappend\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esample_name\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esn\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ederive\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eattributes\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e[sample_name]\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003esources\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esn\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e{SAMPLE_ID}_{FLOWCELL}\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003econfig/sample_fastq.csv\u003c/p\u003e\n\u003cpre lang=\"csv\"\u003e\u003ccode\u003eSAMPLE_ID,FLOWCELL,LANE,INDEX,R1,R2\nHG002,BH2JWTDSX5,1,CGGTTGTT-GTGGTATG,data/fq/HG002_NA24385_son_80X_R1.fq.gz,data/fq/HG002_NA24385_son_80X_R2.fq.gz\nHG003,BH2JWTDSX5,1,GCGTCATT-CAGACGTT,data/fq/HG003_NA24149_father_80X_R1.fq.gz,data/fq/HG003_NA24149_father_80X_R2.fq.gz\nHG004,BH2JWTDSX5,1,CTGTTGAC-ACCTCAGT,data/fq/HG004_NA24143_mother_80X_R1.fq.gz,data/fq/HG004_NA24143_mother_80X_R2.fq.gz\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eworkflow/schemas/fastq_schema.yaml\n(schemas to validate config/fastq_pep.yaml)\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-s\"\u003eworkflow/schemas/fastq_schema.yaml \u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eA example schema for a pipeline.\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eimports\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003ehttp://schema.databio.org/pep/2.0.0.yaml\u003c/span\u003e\n \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e - TriosCompass_v2/workflow/schemas/2.0.0.yaml\u003c/span\u003e\n \n\u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003earray\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eitems\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eobject\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eSAMPLE_ID\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esample id\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eFLOWCELL\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eFlowcell\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eINDEX\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eLibrary index\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eLANE\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eLane number in flowcell\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eenum\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e[\"1\", \"2\"]\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eR1\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003epath to the R1 fastq file\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eR2\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003epath to the R2 fastq file\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003erequired\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003eFLOWCELL\u003c/span\u003e\n - \u003cspan class=\"pl-s\"\u003eSAMPLE_ID\u003c/span\u003e\n - \u003cspan class=\"pl-s\"\u003eINDEX\u003c/span\u003e\n - \u003cspan class=\"pl-c1\"\u003eR1\u003c/span\u003e\n - \u003cspan class=\"pl-c1\"\u003eR2\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003eExample of the PEP configure file for BAM input files\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003econfig/bam_pep.yaml\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003epep_version\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e2.0.0\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esample_table\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003esample_bam.csv\u003c/span\u003e\n\n\n\u003cspan class=\"pl-ent\"\u003esample_modifiers\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eappend\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esample_name\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esn\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ederive\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eattributes\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e[sample_name]\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003esources\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esn\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e{SAMPLE_ID}\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003econfig/sample_bam.csv\u003c/p\u003e\n\u003cpre lang=\"csv\"\u003e\u003ccode\u003eSAMPLE_ID,BAM\nHG002,sorted_bam/HG002_NA24385_son_80X.bam\nHG003,sorted_bam/HG003_NA24149_father_80X.bam\nHG004,sorted_bam/HG004_NA24143_mother_80X.bam\n\u003c/code\u003e\u003c/pre\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eworkflow/schemas/fastq_schema.yaml\n(schemas to validate config/bam_pep.yaml)\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eA example schema for a pipeline.\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eimports\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003ehttp://schema.databio.org/pep/2.0.0.yaml\u003c/span\u003e\n \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e - TriosCompass_v2/workflow/schemas/2.0.0.yaml\u003c/span\u003e\n \n\u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003earray\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eitems\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eobject\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eproperties\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eSAMPLE_ID\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003esample id\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eBAM\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etype\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003estring\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003edescription\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003epath to the bam file\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003erequired\u003c/span\u003e:\n - \u003cspan class=\"pl-s\"\u003eSAMPLE_ID\u003c/span\u003e\n - \u003cspan class=\"pl-s\"\u003eBAM\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n", "data_format": 2, - "description": "JMF workflow", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiuq4ubre/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "W-L/megahit_metagenome_assembly_binning", + "description": "Trios analysis workflow written in Snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/phasing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/premap.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/deepvariant.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/jigv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/hipstr.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/dnSV.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/call_dnm.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\(\u0027\n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/dnSTR.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpp38wrjr_/workflow/rules/gatk_hc.smk\": NoParametersError: L82: In resources definition.\n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/gatk_hc.smk\": \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/bam_qc.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpp38wrjr_/workflow/rules/bam_input.smk\": InvalidPython: Black error:\n```\nCannot parse: 1:0: else:\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/bam_input.smk\": \n[DEBUG] In file \"/tmp/tmpp38wrjr_/workflow/rules/pedigree.smk\": Formatted content is different from original\n[INFO] 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] 15 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "NCI-CGR/TriosCompass_v2", "latest_release": null, - "linting": null, - "mandatory_flags": { - "desc": null, - "flags": null - }, + "linting": "ModuleNotFoundError in file /tmp/tmpp38wrjr_/workflow/rules/pedigree.smk, line 1:\nNo module named \u0027peds\u0027\n File \"/tmp/tmpp38wrjr_/workflow/rules/pedigree.smk\", line 1, in \u003cmodule\u003e\n", + "mandatory_flags": null, "report": true, "software_stack_deployment": { - "conda": true, + "conda": false, "singularity": false, - "singularity+conda": false + "singularity+conda": true }, "standardized": true, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 4, "topics": [], - "updated_at": 1720623398.0 + "updated_at": 1726233222.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "Template from Snakemake", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpod6opocj/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "charleshefer/snakemake-workflow-template", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmph6yomgza/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "loganylchen/snakemake-epitranscriptome", "latest_release": null, "linting": null, "mandatory_flags": { @@ -2497,50 +2503,57 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722297889.0 + "updated_at": 1726227841.0 }, { "config_readme": null, "data_format": 2, - "description": "Isolated chromosome sequencing analysis", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk\": Keyword \"output\" at line 103 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk\": Keyword \"input\" at line 174 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/Snakefile\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "lca-imcb/dopseq", - "latest_release": "v2.2.0", - "linting": "Lints for rule fastqc_init (line 1, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc_trimmed (line 148, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule samtools_faidx (line 237, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule samtools_filter (line 355, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule samtools_merge (line 393, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule regions (line 429, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule stats (line 468, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "description": null, + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpw4bznijb/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "BejaLab/TAT", + "latest_release": null, + "linting": "/tmp/tmpw4bznijb/workflow/Snakefile:406: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n genes = \"analysis/diamond_collect/gtdb.tsv\",\n/tmp/tmpw4bznijb/workflow/Snakefile:412: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n params:\nWorkflowError in file /tmp/tmpw4bznijb/workflow/Snakefile, line 2:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpw4bznijb/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 2, "topics": [], - "updated_at": 1722259232.0 + "updated_at": 1726226602.0 }, { "config_readme": null, "data_format": 2, - "description": "An example workflow with snakemake", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpe31fu8mt/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Luke-ebbis/snakemake-tutorial", + "description": "Measure distances between two types of markers during FISH Assay after Chromosomal Translocation event", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxd7nn4ku/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "rgomez-AI/3DChromTrans", "latest_release": null, - "linting": "Using workflow specific profile workflow/profiles/default for setting default command line arguments.\nLints for snakefile /tmp/tmpe31fu8mt/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule download_data (line 42, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move (line 77, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fastqc (line 105, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quality_report_fastqc (line 132, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trimming (line 159, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assembly (line 211, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assembly_qc (line 251, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quality_report_assembly (line 284, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mapping_index (line 307, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mapping_mem (line 329, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fix_mates (line 355, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sort_coordinate (line 383, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sort_group (line 410, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dedupe (line 437, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule map_summary (line 464, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule coverage_stats (line 486, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule coverage_stats_filter (line 513, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule coverage_stats_contig (line 536, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule db (line 563, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule help (line 584, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 602, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_overview (line 616, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule install_easy_graph (line 646, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_ascii_graph (line 678, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "\u001b[92m\u001b[1mThanks for using 3DChromTrans and please remember to cite the tool!\u001b[0m\u001b[0m\n \u001b[36m Author: Raul Gomez-Riera.\n \u001b[0m\nTclError in file /tmp/tmpxd7nn4ku/workflow/Snakefile, line 91:\nno display name and no $DISPLAY environment variable\n File \"/tmp/tmpxd7nn4ku/workflow/Snakefile\", line 91, in \u003cmodule\u003e\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/filedialog.py\", line 442, in askdirectory\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/commondialog.py\", line 42, in show\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/__init__.py\", line 338, in _get_temp_root\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tkinter/__init__.py\", line 2346, in __init__\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1722245071.0 + "topics": [ + "bioimage-analysis", + "cellprofiler-pipeline", + "distance-calculation", + "napari-visualization", + "snakemake-workflow", + "workflow-automation" + ], + "updated_at": 1726234074.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpz8ctbkht/workflow/Snakefile\": TokenError: (\u0027unexpected character after line continuation character\u0027, (15, 208))\n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/rules/pQuant_enc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "G2Lab/pQuant", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsenx2ah_/workflow/rules/version37_pca.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpsenx2ah_/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "tanavader0/smk_plink_QC", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpz8ctbkht/workflow/Snakefile, line 10:\nunexpected character after line continuation character:\nNone\n", + "linting": "/tmp/tmpsenx2ah_/workflow/Snakefile:647: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n/tmp/tmpsenx2ah_/workflow/Snakefile:662: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\nLints for rule prepare_correct_x (line 12, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule logs (line 47, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule genotyping05 (line 67, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule SampleCallrate98_sex (line 87, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_sex_checked (line 107, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_heterozygosity (line 130, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule check_heterozygosity (line 156, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_het_samples (line 176, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule VariantCallrate98 (line 199, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_MissDiff_HWE (line 219, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule check_MissDiff_HWE (line 259, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_MissDiff_HWE (line 287, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_1000G_sample_info (line 309, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_chromosomes (line 12, /tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_fasta_files (line 25, /tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_1000G_for_ancestry_PCA_step1 (line 42, /tmp/tmpsenx2ah_/workflow/rules/version38_pca.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prepare_1000G_for_ancestry_PCA_step2 (line 328, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param bed1 is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param bed2 is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule merge_data_w_1000G_run_PCA (line 369, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_pca_plots (line 411, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_pca_filter (line 427, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_plink_for_ancestry (line 451, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule kinship_analysis (line 475, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule kinship_analysis_R (line 495, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule remove_relateds (line 515, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule kinship_check2 (line 536, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule kinship_check2_R (line 556, /tmp/tmpsenx2ah_/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2548,67 +2561,89 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722008668.0 + "updated_at": 1726224019.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/rules/manip_seqs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/rules/make_rlooper.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/rules/run_rlooper.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "EthanHolleman/rlooper-plasmids", - "latest_release": "1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n paramspace = Paramspace(pd.read_csv(PARAMS_TABLE, sep=\"\\t\"))\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027../resources/rlooper_params.tsv\u0027\n\n", + "description": "Field Experiments I: A/B tests - Lecture 4 of Digital and Social Media Strategies at Tilburg U", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpihlf3il6/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpihlf3il6/rules/renv.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "deer-marketing-lab/dsms-lecture-experiments", + "latest_release": null, + "linting": "Lints for rule build_html (line 16, /tmp/tmpihlf3il6/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 29, /tmp/tmpihlf3il6/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 48, /tmp/tmpihlf3il6/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 15, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 20, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 25, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 30, /tmp/tmpihlf3il6/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1721945847.0 + "updated_at": 1726223985.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003ePlease see the \u003ca href=\"https://github.com/jsquaredosquared/novocraft-sv-benchmarking?tab=readme-ov-file#usage\"\u003e\"Usage\" section of the main README.md file\u003c/a\u003e for more information on configuring the workflow.\u003c/p\u003e\n", "data_format": 2, - "description": "Analysing options for Ukraine\u0027s future energy supply.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/utils.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/pypsa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/preprocess.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/analyse.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/sync.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "timtroendle/ukraine-energy-future", + "description": "Comparing performance of SV callers when using NovoAlign vs other aligners.", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3o0y9lkc/workflow/rules/01_align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 5 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "jsquaredosquared/novocraft-sv-benchmarking", "latest_release": null, - "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpm4_62zl8/Snakefile\", line 13, in \u003cmodule\u003e\n onstart:\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpm4_62zl8/./rules/pypsa.smk\", line 6, in \u003cmodule\u003e\n from snakemake.io import load_configfile\n\nImportError: cannot import name \u0027load_configfile\u0027 from \u0027snakemake.io\u0027 (/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/io.py)\n\n", - "mandatory_flags": [], + "linting": "Lints for snakefile /tmp/tmp3o0y9lkc/workflow/rules/01_align.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmp3o0y9lkc/workflow/rules/03_benchmark.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule download_reference (line 4, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule novoindex_reference (line 15, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule download_hg002_fastqs (line 59, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_hg002_tier1_sv_truth_set (line 71, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_delly_exclude (line 88, /tmp/tmp3o0y9lkc/workflow/rules/00_prepare.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule align_with_bwa_mem2 (line 15, /tmp/tmp3o0y9lkc/workflow/rules/01_align.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule align_with_novoalign (line 35, /tmp/tmp3o0y9lkc/workflow/rules/01_align.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule configure_manta (line 11, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_dysgu (line 49, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_delly (line 71, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_smoove (line 90, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_wham (line 119, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule run_tiddit (line 141, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule bgzip_and_index_sv_vcf (line 159, /tmp/tmp3o0y9lkc/workflow/rules/02_call.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n\nLints for rule split_truth_set (line 20, /tmp/tmp3o0y9lkc/workflow/rules/03_benchmark.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule generate_plots (line 1, /tmp/tmp3o0y9lkc/workflow/rules/04_compare.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": null, "report": false, - "software_stack_deployment": null, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "sv-calling", + "novoalign" + ], + "updated_at": 1726218052.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Synthesize functional scoring enrichment results from several sources (GSEApy, ClusterProfiler, STRING)", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_b4tt43h/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "pdegen/SynEnrich", + "latest_release": null, + "linting": "WorkflowError in file /tmp/tmp_b4tt43h/workflow/Snakefile, line 5:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmp_b4tt43h/config/config.yaml).\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1721894371.0 + "updated_at": 1726179535.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3uk94ng/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "AHassanpour88/Evolutionary_Snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/phages.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpyp3dyapx/workflow/rules/assembly.smk\": Keyword \"input\" at line 4 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/refine_bins.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/coverm.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/taxonomy.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/binning.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyp3dyapx/workflow/rules/preprocessing.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "megjohnson1999/prophage-pipeline", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpj3uk94ng/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule sampleVAl (line 98, /tmp/tmpj3uk94ng/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runSimulations (line 143, /tmp/tmpj3uk94ng/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runEvolutionary (line 203, /tmp/tmpj3uk94ng/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gatherResults (line 249, /tmp/tmpj3uk94ng/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "WorkflowError in file /tmp/tmpyp3dyapx/workflow/Snakefile, line 6:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1721914761.0 + "updated_at": 1726175200.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpoo1v7ba9/weinstockj-RNAseq-perturbation-CD4-pipeline-7bce298/Snakefile\": Keyword \"output\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpoo1v7ba9/weinstockj-RNAseq-perturbation-CD4-pipeline-7bce298/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "weinstockj/RNAseq-perturbation-CD4-pipeline", - "latest_release": "v0.0.1", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpoo1v7ba9/weinstockj-RNAseq-perturbation-CD4-pipeline-7bce298/Snakefile\", line 6, in \u003cmodule\u003e\n sample_sheet = pd.read_table(\u0027/oak/stanford/groups/pritch/users/jweinstk/perturbation_data/metadata/sample_meta_data_2022_12_08.tsv\u0027, index_col = False)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/oak/stanford/groups/pritch/users/jweinstk/perturbation_data/metadata/sample_meta_data_2022_12_08.tsv\u0027\n\n", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/snvreport.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/pathogenic_expansion_loci.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/outlier_expansions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm1ioupzr/rules/svreport.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ccmbioinfo/crg2-pacbio", + "latest_release": null, + "linting": "KeyError in file /tmp/tmpm1ioupzr/rules/common.smk, line 15:\n\u0027run\u0027\n File \"/tmp/tmpm1ioupzr/rules/common.smk\", line 15, in \u003cmodule\u003e\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2616,16 +2651,16 @@ var data = "stargazers_count": 0, "subscribers_count": 3, "topics": [], - "updated_at": 1721838345.0 + "updated_at": 1726161873.0 }, { "config_readme": null, "data_format": 2, - "description": "This repository includes the workflow for the main experiments in the Movi paper.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9glx65_0/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mohsenzakeri/Movi-experiments", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpcuskt1r9/workflow/rules/download_snake.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcuskt1r9/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpcuskt1r9/workflow/rules/blast_missing_seqs.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 14)\n[INFO] In file \"/tmp/tmpcuskt1r9/workflow/rules/blast_missing_seqs.smk\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmpcuskt1r9/workflow/rules/blast_missing_seqs.smk\": 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "LCrossman/ribosomal_snakemake", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmp9glx65_0/config.yaml).\n", + "linting": "WorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpcuskt1r9/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2633,16 +2668,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1721838244.0 + "updated_at": 1721228607.0 }, { "config_readme": null, "data_format": 2, - "description": "Peak-calling using Snakemake", - "formatting": null, - "full_name": "ParthDoshi97/ATAC-seq-peak-calling", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqjsa968x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "brambloemen/FARMED_onsite", "latest_release": null, - "linting": "WorkflowError:\nFailed to open source file /tmp/tmp94ou6u70/Snakefile\nIsADirectoryError: [Errno 21] Is a directory: \u0027/tmp/tmp94ou6u70/Snakefile\u0027\n", + "linting": "Lints for snakefile /tmp/tmpqjsa968x/Snakefile:\n * Absolute path \"/results/plots/Time_and_AMR.png\" in line 256:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/results/plots/ARG_exp_byclass.png\" in line 257:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule get_readstats (line 28, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_reads (line 59, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_reads_GMSdb (line 93, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_reads_ResFdb (line 150, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_reads_RefSeq (line 207, /tmp/tmpqjsa968x/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule finish_mapping (line 264, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule finish_alingment_parsing (line 457, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plotseqrunstats (line 524, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_time_amr_stats (line 553, /tmp/tmpqjsa968x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2650,33 +2685,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1721827337.0 + "updated_at": 1721208291.0 }, { "config_readme": null, "data_format": 2, - "description": "Pipeline to annotate peptide identifications when using protein databases made by of ProHap / ProVar", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:61: \"python src/peptides_annotate_variation.py -i {input.pep} \" +\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[INFO] In file \"/tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "ProGenNo/ProHap_PeptideAnnotator", - "latest_release": "v1.1", - "linting": "Lints for snakefile /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile:\n * Path composition with \u0027+\u0027 in line 16:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 48:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 2:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule download_reference_proteome (line 20, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule reference_fix_headers (line 37, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_gtf (line 62, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule parse_gtf_whole (line 79, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_peptides (line 104, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbl5cjth2/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "PratikPathade/scRNA-seq-pipeline-with-Snakemake-Workflow", + "latest_release": null, + "linting": "WorkflowError:\nWorkflow defines configfile /lustre/Pratik/snakemake_local/snakemake_tutorial/configs/config.yaml but it is not present or accessible (full checked path: /lustre/Pratik/snakemake_local/snakemake_tutorial/configs/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1721821051.0 + "updated_at": 1721200768.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/encoding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/make_viz.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/behaviors.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/spatial_comparisons.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/fmri.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/behaviors_pred.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 7 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "nyuolab/MooneyComputationModeling2024", + "formatting": null, + "full_name": "deMoraes-Lab/variants", "latest_release": null, - "linting": "WorkflowError:\nFailed to open source file /tmp/tmpj75e5yml/workflow/rules/visualizations/attention_map.smk\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/tmp/tmpj75e5yml/workflow/rules/visualizations/attention_map.smk\u0027\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpewsne6eq/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n # Paths to input files\n ^^^^^^^^^^^^^^\n\nAssertionError: Please provide a NCBI accession for reference genome.\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2684,80 +2719,91 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1721753076.0 + "updated_at": 1721178829.0 }, { - "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n # Optional parameters for fastp trimming and QC\n fastp: \"\"\n salmon:\n # Optional parameters for genome indexation with Salmon\n index: \"\"\n # Optional parameters for salmon quantification\n # One should always include bootstraping and Bulk RNASeq bias\n quant: \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Optional path to downstream fastq file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release\nhomo_sapiens,GRCh38,110\nmus_musculus,GRCm38,99\nmus_musculus,GRCm39,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqg4p51tu/tdayris-fair_rnaseq_salmon_quant-b983532/workflow/rules/multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 10 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "tdayris/fair_rnaseq_salmon_quant", - "latest_release": "1.2.3", - "linting": null, - "mandatory_flags": { - "desc": "Estimate read abundance with Salmon", - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": true - }, - "standardized": true, + "description": "Demo repo for new cluster setup with snakemake (excludes configs)", + "formatting": null, + "full_name": "aabiddanda/snakemake_demo", + "latest_release": null, + "linting": "/tmp/tmpui4ku78m/workflow/rules/sims.smk:21: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n script:\n/tmp/tmpui4ku78m/workflow/rules/sims.smk:22: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n \"../scripts/sim_msprime.py\"\n/tmp/tmpui4ku78m/workflow/rules/sims.smk:23: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n \nLints for snakefile /tmp/tmpui4ku78m/workflow/Snakefile:\n * Absolute path \"/bin/bash\" in line 22:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpui4ku78m/workflow/rules/sims.smk:\n * Path composition with \u0027+\u0027 in line 13:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule sim_popgen_data (line 4, /tmp/tmpui4ku78m/workflow/rules/sims.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule create_summary_stats (line 48, /tmp/tmpui4ku78m/workflow/rules/sims.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_summary_stats (line 75, /tmp/tmpui4ku78m/workflow/rules/sims.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "fair", - "rnaseq-pipeline", - "snakemake", - "snakemake-workflow", - "reproducible-science" - ], - "updated_at": 1721740853.0 + "subscribers_count": 2, + "topics": [], + "updated_at": 1721168943.0 }, { "config_readme": null, "data_format": 2, - "description": "Compute a sequence and structure based phylome based on uniprot proteomes.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/checks.smk\": Keyword \"output\" at line 25 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/checks.smk\": Keyword \"input\" at line 210 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/checks.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/analysis.smk\": Keyword \"input\" at line 27 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/analysis.smk\": Keyword \"input\" at line 103 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/analysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/structure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/sequence.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/prepare.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Gabaldonlab/structural_phylome", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnbztpwt0/workflow/Snakefile\", line 20, in \u003cmodule\u003e\n include: \u0027rules/common.smk\u0027\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnbztpwt0/workflow/rules/prepare.smk\", line 1, in \u003cmodule\u003e\n outdir=config[\u0027outdir\u0027]+config[\u0027dataset\u0027]\n ^^^^^^^^^^^\n\nKeyError: \u0027dataset\u0027\n\n", + "description": "TRANQUIL (TRna AbundaNce QUantification pIpeLine)", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/template.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/mimseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/init.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/preprocess.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/Snakefile\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "CCBR/TRANQUIL", + "latest_release": "v0.2.1", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/Snakefile\", line 2, in \u003cmodule\u003e\n include: join(\"rules\",\"init.smk\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbc46_6gw/CCBR-TRANQUIL-4350fe5/workflow/rules/init.smk\", line 44, in \u003cmodule\u003e\n CONFIGFILE = str(workflow.overwrite_configfiles[0])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nIndexError: list index out of range\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 6, "topics": [], - "updated_at": 1722338463.0 + "updated_at": 1721136674.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": "snakemake workflow for the phylogenetic reconstruction of single cell lineages from multiple displacement amplified single cell DNAseq", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/regions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/candidate_calling.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp0nhbuito/workflow/rules/phylogeny.smk\": SyntaxError: L232: Unrecognised keyword \u0027best_model\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/phylogeny.smk\": \n[DEBUG] In file \"/tmp/tmp0nhbuito/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 5 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "hzi-bifo/phylogeny-of-single-cells", + "latest_release": null, + "linting": "WorkflowError:\nError validating row 0 of data frame.\nValidationError: \u0027sample_name\u0027 is a required property\n\nFailed validating \u0027required\u0027 in schema:\n {\u0027$id\u0027: \u0027https://json-schema.org/draft/2020-12/schema\u0027,\n \u0027$schema\u0027: \u0027https://json-schema.org/draft/2020-12/schema\u0027,\n \u0027description\u0027: \u0027an entry (row) in the sample sheet, representing a \u0027\n \u0027DNA sequencing sample from either a bulk of cells or \u0027\n \u0027a multiple displacement amplified single cell DNA\u0027,\n \u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027sample_name\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027description\u0027: \u0027sample name/identifier \u0027\n \u0027(alphanumeric string, \u0027\n \u0027that may additionally \u0027\n \"contain \u0027_\u0027 and \u0027-\u0027)\",\n \u0027pattern\u0027: \u0027^[a-zA-Z_0-9-]+$\u0027},\n \u0027individual\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027description\u0027: \u0027individual whose cells \u0027\n \u0027to jointly use for \u0027\n \u0027phylogenetic \u0027\n \u0027reconstruction \u0027\n \u0027(alphanumeric string, \u0027\n \u0027that may additionally \u0027\n \"contain \u0027_\u0027 and \u0027-\u0027)\",\n \u0027pattern\u0027: \u0027^[a-zA-Z_0-9-]+$\u0027},\n \u0027sample_type\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027enum\u0027: [\u0027single_cell\u0027, \u0027bulk\u0027],\n \u0027description\u0027: \u0027indication whether a \u0027\n \u0027sequencing sample is \u0027\n \u0027made from a bulk of \u0027\n \u0027cells (without \u0027\n \u0027amplification) or from \u0027\n \u0027a single cell (with \u0027\n \u0027multiple displacement \u0027\n \u0027amplification)\u0027},\n \u0027platform\u0027: {\u0027type\u0027: \u0027string\u0027,\n \u0027enum\u0027: [\u0027CAPILLARY\u0027,\n \u0027LS454\u0027,\n \u0027ILLUMINA\u0027,\n \u0027SOLID\u0027,\n \u0027HELICOS\u0027,\n \u0027IONTORRENT\u0027,\n \u0027ONT\u0027,\n \u0027PACBIO\u0027],\n \u0027description\u0027: \u0027used sequencing \u0027\n \u0027platform\u0027}},\n \u0027required\u0027: [\u0027sample_name\u0027, \u0027individual\u0027, \u0027sample_type\u0027, \u0027platform\u0027]}\n\nOn instance:\n {}\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 6, + "topics": [], + "updated_at": 1721132843.0 }, { "config_readme": null, "data_format": 2, - "description": "Analysis NGS data from P53 ampicon-based assay", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp7sdb1mou/Snakefile\": NoParametersError: L26: In params definition.\n[INFO] In file \"/tmp/tmp7sdb1mou/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "bingfang/P53-mutation-screen", + "description": "compile a phylogenetic dataset from genewise CDS fasta files", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6jols31/rules/00-common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpq6jols31/rules/02-after_trimal.smk\": Keyword \"output\" at line 36 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpq6jols31/rules/02-after_trimal.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpq6jols31/rules/01-before_trimal.smk\": Keyword \"output\" at line 77 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpq6jols31/rules/01-before_trimal.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6jols31/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq6jols31/rules/03-repeated_rules.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "etkayapar/pcc", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp7sdb1mou/Snakefile:\n * Absolute path \"/Users/xubr/anaconda3/share/trimmomatic-0.39-2\" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule trim (line 24, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule debarcode (line 58, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genotyping (line 91, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule calculate_common_mutation_rate (line 125, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule calculate_mutation_rate (line 156, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpq6jols31/Snakefile\", line 1, in \u003cmodule\u003e\n include: \"rules/00-common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpq6jols31/rules/00-common.smk\", line 8, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027gene_table.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1721662519.0 + "updated_at": 1721121990.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"conda\" at line 10 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"shell\" at line 16 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"conda\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"shell\" at line 38 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0upnp1bm/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0upnp1bm/rules/picard_rmdup.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/fastp.smk\": Keyword \"conda\" at line 14 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp0upnp1bm/rules/fastp.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "china-fix/rq-count_v1", + "description": "ss", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpya7tkufc/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Isha-Guptaa/snakemake_indel-snv_vcf-to-csv", "latest_release": null, - "linting": null, + "linting": "Lints for snakefile /tmp/tmpya7tkufc/Snakefile:\n * Absolute path \"/home/isha/Documents/repo/nextflow_VCF-to-CSV/second/HCC1395T_vs_HCC1395N.strelka.somatic_{vcf_type}_VEP.ann.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule index_vcf (line 24, /tmp/tmpya7tkufc/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_vcf (line 58, /tmp/tmpya7tkufc/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule convert (line 91, /tmp/tmpya7tkufc/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2765,16 +2811,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1721511428.0 + "updated_at": 1721117071.0 }, { "config_readme": null, "data_format": 2, - "description": "Methylation tools repository", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpnk8egmli/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "MagdalenaZZ/methylation", + "description": "Samar is a pipeline for speedy, assembly-free differential gene expression analysis in non-model organisms.", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp3o98dplp/workflow/Snakefile\": Keyword \"shell\" at line 130 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp3o98dplp/workflow/Snakefile\": Keyword \"shell\" at line 167 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp3o98dplp/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "bioinfodlsu/samar", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnk8egmli/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnk8egmli/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp3o98dplp/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n convert_fastq_fasta_SE = srcdir(\"scripts/convert_SE_fastq-fasta.sh\")\n ^^^^^^\n\nNameError: name \u0027srcdir\u0027 is not defined\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2782,50 +2828,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1721375750.0 + "updated_at": 1721116075.0 }, { "config_readme": null, "data_format": 2, - "description": "Peptigate (\"peptide\" + \"investigate\") predicts bioactive peptides from transcriptome assemblies or sets of proteins.", - "formatting": null, - "full_name": "Arcadia-Science/peptigate", - "latest_release": "v1.0.0", - "linting": "/tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile:573: SyntaxWarning: invalid escape sequence \u0027\\*\u0027\n ## Charaterize \u0026 annotate predicted peptide sequences\n/tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile:585: SyntaxWarning: invalid escape sequence \u0027\\*\u0027\n conda:\nLints for rule get_coding_contig_names (line 53, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_contigs_to_no_predicted_ORF (line 90, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_uniref50_database (line 137, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_diamond_db_from_uniref50_database (line 158, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastx_transcripts_against_uniref50_database (line 194, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_transcript_uniref50_hits (line 252, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_no_predicted_ORF_contigs_to_no_uniref50_long_hits (line 290, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plmutils_translate (line 331, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule length_filter_plmutils_translate_output (line 367, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plmutils_embed (line 398, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plmutils_predict (line 444, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extract_plmutils_predicted_peptides (line 483, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extract_plmutils_predicted_peptides_as_nucleotides (line 518, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule remove_stop_codon_asterisk_from_transdecoder_ORFs (line 561, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_nlpprecursor_models (line 590, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_protein_sequences_with_nonstandard_amino_acids (line 619, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule nlpprecursor (line 655, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clone_deeppeptide (line 732, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule deeppeptide (line 763, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable WORKING_DIRPATH from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable WORKING_DIRPATH from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule extract_deeppeptide_sequences (line 802, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_faa_predictions (line 868, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule convert_peptide_faa_to_tsv (line 896, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_ffn_predictions (line 927, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule convert_peptide_ffn_to_tsv (line 955, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_peptipedia_database (line 996, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_diamond_db_from_peptipedia_database (line 1024, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp_peptide_predictions_against_peptipedia_database (line 1060, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_deepsig (line 1104, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule characterize_peptides (line 1141, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_autopeptideml_models (line 1192, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_autopeptideml (line 1226, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_predictions (line 1289, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_annotations (line 1336, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "description": "Robust reproducible differential expression analysis based on edgeR with components in R and Python as a snakemake pipeline", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfwdz5oz4/workflow/rules/expr_tables.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[ERROR] In file \"/tmp/tmpfwdz5oz4/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 7:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpfwdz5oz4/workflow/Snakefile\": \n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "imgag/expression-analysis-smk", + "latest_release": null, + "linting": "WorkflowError:\nWorkflow defines configfile config.yml but it is not present or accessible (full checked path: /tmp/tmpfwdz5oz4/config.yml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 3, "topics": [], - "updated_at": 1721332971.0 + "updated_at": 1721111566.0 }, { "config_readme": null, "data_format": 2, - "description": "Multiplex Accurate Sensitive Quantitation (MASQ) analysis and primer design", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_kkyaebk/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "amoffitt/MASQ", + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp1c9u6lxr/Snakefile\": Keyword \"shell\" at line 134 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp1c9u6lxr/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "PallaresLab/DNAPipeline", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp_kkyaebk/Snakefile:\n * Absolute path \"/r1.fastq.gz\" in line 143:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 144:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r1.fastq.gz\" in line 176:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 177:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 178:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 223:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 178:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 223:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 110:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 425:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 426:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule convert_SNV_table (line 122, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule barcode_split (line 150, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc (line 184, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule check_loci_extend_and_plot (line 219, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_data_by_tag_and_locus (line 255, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all_base_report (line 310, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_within_tag_errors (line 361, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_per_region (line 390, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_combined (line 426, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule rollup_tags (line 461, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_alignment (line 501, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_basecount (line 530, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_per_base (line 558, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_rollup (line 586, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_readspertag (line 614, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_variant_bases_from_report (line 643, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_rollup_results (line 671, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule final_report (line 704, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bad_loci (line 735, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule qc_plots (line 749, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule filter_base_report (line 776, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmp1c9u6lxr/Snakefile:\n * Absolute path \"/logs\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/working\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.fastq.gz\" in line 11:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.fastq.gz\" in line 14:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}_R1_001.fastq.gz\" in line 15:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc/multiqc.html\" in line 29:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{sample}.fastq.gz\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/{sample}_fastqc.zip\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/{sample}.log\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc\" in line 45:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/*_fastqc.html\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}\" in line 65:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R1_001_val_1.fq.gz\" in line 66:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R2_001_val_2.fq.gz\" in line 67:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}.log\" in line 68:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}\" in line 71:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/*_fastqc.html\" in line 72:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa_index/index.log\" in line 97:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa_index\" in line 100:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R1_001_val_1.fq.gz\" in line 115:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}/{sample}_R2_001_val_2.fq.gz\" in line 116:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.bam\" in line 120:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.txt\" in line 121:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.log\" in line 124:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa\" in line 127:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.bam\" in line 145:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}_deduplicated.bam\" in line 148:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}_deduplicated.metrics.txt\" in line 149:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}.log\" in line 152:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard\" in line 155:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/fastqc/{sample}_fastqc.zip\" in line 168:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}\" in line 170:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/trimmed/{sample}.log\" in line 172:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bwa/{sample}.txt\" in line 174:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/picard/{sample}_deduplicated.metrics.txt\" in line 176:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc/multiqc.html\" in line 182:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc/multiqc.log\" in line 185:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/multiqc\" in line 188:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 2:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 97:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule fastqc (line 43, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule trim (line 94, /tmp/tmp1c9u6lxr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule bwa_index (line 145, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule bwa (line 191, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule picard (line 246, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule multiqc (line 291, /tmp/tmp1c9u6lxr/Snakefile):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1723065291.0 + "updated_at": 1724663319.0 }, { "config_readme": null, "data_format": 2, - "description": "Significantly improved bam2bakR implementation", - "formatting": null, - "full_name": "isaacvock/fastq2EZbakR", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqeeav49r/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Applied-Genomics-UTD/template-intro-snakemake", "latest_release": null, - "linting": null, + "linting": "Lints for rule bwa_map (line 13, /tmp/tmpqeeav49r/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2833,18 +2879,18 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723042307.0 + "updated_at": 1720975285.0 }, { - "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n fair_bowtie2_mapping:\n bowtie2:\n # Optional parameters for bowtie2-build\n build: \"\"\n # Optional parameters for bowtie2-align\n align: \"\"\n sambamba:\n # Optional parameters for sambamba view\n view: \"--format \u0027bam\u0027 --filter \u0027mapping_quality \u0026gt;= 30 and not (unmapped or mate_is_unmapped)\u0027 \"\n # Optional parameters for sambamba markdup\n markdup: \"--remove-duplicates\"\n picard:\n # Mapping QC optional parameters\n metrics: \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Optional path to downstream fastq file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/samples.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe following columns are optional and are used to avoid downloading genomes:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efasta\u003c/code\u003e: Path to the reference genome sequence (FASTA formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efasta_index\u003c/code\u003e: Path to the reference genome sequence index (FAI formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebowtie2_dna_index\u003c/code\u003e: Path to the main directory containing reference index\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release,fasta,fasta_index,bowtie2_index\nhomo_sapiens,GRCh38,110,/path/to/sequence.fasta,/path/to/sequence.fasta.fai,/path/to/bowtie2_sequence/\nmus_musculus,GRCm38,99,,,\nmus_musculus,GRCm39,110,,,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", + "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing only one\nkey: \u003ccode\u003egenomes\u003c/code\u003e, which value is the path to a file containing the list of\ngenomes to download as described below.\u003c/p\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003egenomes: config/genomes.csv\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_genome_indexer/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003especies: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003ebuild: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003erelease: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release\nhomo_sapiens,GRCh38,110\nmus_musculus,GRCm38,99\nmus_musculus,GRCm39,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_genome_indexer/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", "data_format": 2, - "description": "Align reads over a reference genome, filter aligned-reads, and mark duplicates", + "description": "Download and index Ensembl sequences and annotations", "formatting": null, - "full_name": "tdayris/fair_bowtie2_mapping", - "latest_release": "4.2.0", + "full_name": "tdayris/fair_genome_indexer", + "latest_release": "3.8.1", "linting": null, "mandatory_flags": { - "desc": "Align ungapped reads to the genome with Bowtie2", + "desc": "Download and index Ensembl genome files", "flags": null }, "report": true, @@ -2857,127 +2903,188 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [ - "bowtie2", - "multiqc", - "sambamba", + "ensembl", + "fair", "snakemake", "snakemake-workflow", "snakemake-wrappers" ], - "updated_at": 1723031584.0 + "updated_at": 1720931641.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmp8pqah41f/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "jorgenriseth/gMRI2FEM", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpdtyqazm8/Snakefile\": SyntaxError: L34: Unrecognised keyword \u0027\u0027\u0027\u0027\n\tMask repeats in the genome using RepeatMasker\n\t\u0027\u0027\u0027\u0027 in rule definition\n[INFO] In file \"/tmp/tmpdtyqazm8/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "Nanobio1991/AmphioxusCNVs", "latest_release": null, - "linting": "/tmp/tmp8pqah41f/Snakefile:32: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n SUBJECTS=config[\"subjects\"]\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp8pqah41f/Snakefile\", line 14, in \u003cmodule\u003e\n + \"conda activate $CONDA_ENV_NAME \u0026\u0026 \"\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027use_singularity\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdtyqazm8/Snakefile\", line 764, in \u003cmodule\u003e\n\nAttributeError: \u0027Namedlist\u0027 object has no attribute \u0027cnv_not_merged\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 3, "topics": [], - "updated_at": 1723028673.0 + "updated_at": 1720900261.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": null, - "full_name": "3d-omics/mt_quant", - "latest_release": "v1.1.0", - "linting": null, + "description": "https://agc.readthedocs.io/ on REANA", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpg9miwz9z/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "iris-hep/agc-reana", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmpg9miwz9z/Snakefile:\n * Absolute path \"/bin/bash -l \u0026\u0026 source fix-env.sh \u0026\u0026 python prepare_workspace.py sample_{params.sample_name}_{wildcards.filename} \u0026\u0026 papermill ttbar_analysis_reana.ipynb sample_{params.sample_name}_{wildcards.filename}_out.ipynb -p sample_name {params.sample_name} -p filename {url_prefix}{wildcards.filename} -k python3\" in line 66:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bin/bash -l \u0026\u0026 source fix-env.sh \u0026\u0026 papermill file_merging.ipynb merged_{params.sample_name}.ipynb -p sample_name {params.sample_name} -k python3\" in line 81:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/bin/bash -l \u0026\u0026 source fix-env.sh \u0026\u0026 papermill final_merging.ipynb result_notebook.ipynb -k python3\" in line 102:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 21:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule process_sample_one_file_in_sample (line 61, /tmp/tmpg9miwz9z/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable url_prefix from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule process_sample (line 97, /tmp/tmpg9miwz9z/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merging_histograms (line 134, /tmp/tmpg9miwz9z/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 5, "topics": [], - "updated_at": 1722957411.0 + "updated_at": 1720866798.0 + }, + { + "config_readme": "\u003cp\u003eMost of the parameters for CLIPs4U run have to be set up in your custom \u003ca href=\"https://en.wikipedia.org/wiki/YAML\" rel=\"nofollow\"\u003eYAML\u003c/a\u003e file (for example \u003ccode\u003econfig.yaml\u003c/code\u003e).\nYou can edit \u003ccode\u003econfig.yaml\u003c/code\u003e, which is an empty config file in any text editor and set all parameters.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e only 3\u0027adapter and 5\u0027adapter sequences are absolutely required.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e when you do not provide path to your input file(s) CLIPs4U will run with test dataset (ZFP36.fq.gz) and your config file.\u003c/p\u003e\n\u003cp\u003eThe configuration file contains seven main sections:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eexec and input paths and hardware settings\u003c/li\u003e\n\u003cli\u003egenome file and genomic annotations\u003c/li\u003e\n\u003cli\u003eadapter trimming and reads collapsing\u003c/li\u003e\n\u003cli\u003eremoving repetitive elements\u003c/li\u003e\n\u003cli\u003egenome alignment\u003c/li\u003e\n\u003cli\u003ePARalyzer params\u003c/li\u003e\n\u003cli\u003emotif enrichment params\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eDefault configuration file is stored in \u003ccode\u003econfig/default_config.yaml\u003c/code\u003e\u003c/p\u003e\n\u003cp\u003eExec and input paths and hardware settings section contains two fields; the \u003ccode\u003einput_files\u003c/code\u003e field where you specify path(s) to input fastq.gz file(s). When you have more than one input, separate paths by comma. In the \u003ccode\u003ethreads\u003c/code\u003e field you specify maximum naumber of processors used by the rules within workflow.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e{\n #exec and input paths and hardware settings\n \u0027input_files\u0027: \"\", #(REQUIRED)absolute path(s) must be provided by user in config file, if \u0026gt; 1, comma separated\n \u0027threads\u0027: 4,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eGenome file and genomic annotations contains five fields. The first one specify organism. Right now you can choose human or mouse (\u003ccode\u003e\"hs\"\u003c/code\u003e or \u003ccode\u003e\"mm\"\u003c/code\u003e). If you want to run your analysis with data from other organism(s) open an issue and|or write an e-mail to \u003ca href=\"mailto:marcin.sajek@gmail.com\"\u003emarcin.sajek@gmail.com\u003c/a\u003e and we will prepare the data and|or modify scripts.\n\u003ccode\u003egenome_fasta\u003c/code\u003e and \u003ccode\u003egtf\u003c/code\u003e fields contain paths to genome sequence and gtf files. When empty (\u003ccode\u003e\"\"\u003c/code\u003e) both genome and its annotation will be downloaded from gencode. Gencode version of genome and gtf is specified in the \u003ccode\u003egenome_version\u003c/code\u003e field. The default version for human genome is 45, and for mouse - 35.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e Gencode versions for both organism must be greater than 4\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eannot_rank\u003c/code\u003e field contains path to annotation ranking file. If empty, default annot rank file will be used. This file contain categories from \u003ccode\u003egene_type\u003c/code\u003e field of gtf file, and if the peak is mapping to region with multiple annotations, lowest rank is chosen. The most abundant RNA types have highest ranks.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre lang=\"#genome\"\u003e\u003ccode\u003e \u0027organism\u0027 : \"hs\", #(OPTIONAL) allowed values are \"hs\" for human and \"mm\" for mouse\n \u0027genome_fasta\u0027 : \"\", #(OPTIONAL) you can specify your own genome file, if not specified GRCh38/GRCm39 primary assembly from gencode v45 will be automatically downloaded\n \u0027gtf\u0027 : \"\", #(OPTIONAL) you can specify your own gtf file (compatible with genome), if not specified basic annotation for GRCh38/GRCm39 primary assembly from gencode v45 will be automatically downloaded\n \u0027genome_version\u0027 : \"\", #(OPTIONAL) you can specify your own genome/gtf version; default: GRCh38/GRCm39 primary assembly from gencode v45/35\n \u0027annot_rank\u0027 : \"\", #(OPTIONAL) you can specify your own annotation rank file, suggesed when using your own genome; default: CLIPs4U/annotation/{organism}/annot_ranks.txt\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eAdapter trimming and reads collapsing section contain adapter trimming parameters. Please familiarize yourself with \u003ca href=\"https://cutadapt.readthedocs.io/en/stable/guide.html\" rel=\"nofollow\"\u003ecutadapt\u003c/a\u003e before filling this section. For some analyses it may be better to split adapter trimming into two rounds. If you want to do it in one step fill \u003ccode\u003ecutadapt_params1\u003c/code\u003e field and leave \u003ccode\u003ecutadapt_params2\u003c/code\u003e field with empty quotes \u003ccode\u003ecutadapt_params2 : \"\"\u003c/code\u003e, which is a default setting. If yor sequencing was performed on NextSeq or NovaSeq machine consider setting \u003ccode\u003enextseq\u003c/code\u003e to \u003ccode\u003eTrue\u003c/code\u003e, to remove a \u2018dark cycle\u2019 encoded as string of Gs. If you have UMIs in your read set the length of UMI in \u003ccode\u003eumi\u003c/code\u003e field. If your UMIs are in the 5\u0027 end of the read use positive integer, if at the 3\u0027 end, negative integer.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #adapter trimming and reads collapsing\n \u0027three_prime_adapter\u0027 : \"\", #(REQUIRED!!!) put your 3\u0027adapter sequence\n \u0027five_prime_adapter\u0027 : \"\", #(REQUIRED!!!) your 5\u0027adapter sequence\n \u0027nextseq\u0027 : False, #(OPTIONAL) put True or 1 if your sequencing run was on NextSeq machine\n \u0027cutadapt_params1\u0027 : \"-b CGTACGCGGGTTTAAACGA -b CTCATCTTGGTCGTACGCGGAATAGTTTAAACTGT -n 3 -j 0 -m 15 -M 50 --max-n 1\", #(OPTIONAL) - additional cutadapt parameters\n \u0027cutadapt_params2\u0027 : \"\", #(OPTIONAL) leave empty to ommit this step, if you want to perform second trimming put all cutadapt parameters for 2nd trimming here (including adapters)\n \u0027umi\u0027 : \"\", #(OPTIONAL) leave empty if you don\u0027t have UMIs, for 5\u0027 UMIs positive integer equal UMI length, if 3\u0027UMIs - negative integer equal UMI length\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003e\u003cstrong\u003eTIP:\u003c/strong\u003e \u003ccode\u003e-j 0 \u003c/code\u003e in cutadapt determined automatically numbers of available threads.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTIP:\u003c/strong\u003e Reads that are to long can cause further issues with PARalyzer (e.g. reported \u003ca href=\"https://github.com/ohlerlab/PARpipe/issues/6\"\u003ehere\u003c/a\u003e). Consider setting a max read length parameter, e.g. \u003ccode\u003e-M 50\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eRemoving repetitive elements section is skipped with default settings. User can perform removing repetitive element before genome alignent by setting \u003ccode\u003erem_rep\u003c/code\u003e to \u003ccode\u003eTrue\u003c/code\u003e. CLIPs4U is using \u003ca href=\"https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf\" rel=\"nofollow\"\u003eSTAR\u003c/a\u003e for this task. It is using default repetitive elments index and STAR parameters if \u003ccode\u003erep_idx\u003c/code\u003e and \u003ccode\u003estar_rem_reps_params\u003c/code\u003e are empty.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #removing repetitive elements\n \u0027rem_rep\u0027 : \"\", #(OPTIONAL) leave empty to omit this step, put True or 1 if you want to remove repetitive elements\n \u0027rep_idx\u0027 : \"\", #(OPTIONAL) default: CLIPs4U/annotation/{organism}/rep_idx\n \u0027star_rem_reps_params\u0027 : \"--runMode alignReads --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outSAMtype BAM Unsorted --outFilterType BySJout --outBAMcompression 10 --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full\", #(OPTIONAL)\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eGenome alignment section of the configuration file contains a parameters list passed to aligner. Default aligner is \u003ca href=\"https://bowtie-bio.sourceforge.net/index.shtml\" rel=\"nofollow\"\u003ebowtie\u003c/a\u003e. User can switch aligner to \u003ca href=\"https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf\" rel=\"nofollow\"\u003eSTAR\u003c/a\u003e by filling \u003ccode\u003ealigner\u003c/code\u003e field with one of \u003ccode\u003e\"STAR\"\u003c/code\u003e, \u003ccode\u003e\"star\"\u003c/code\u003e, \u003ccode\u003e\"S\"\u003c/code\u003e or \u003ccode\u003e\"s\"\u003c/code\u003e. Remaining fields contain paths to bowtie or STAR indexes (generated automatically for selected aligner if left empty) and aligner parameters (filled with default settings when empty).\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #genome alignment\n \u0027aligner\u0027 : \"\", #(OPTIONAL) default bowtie, use \u0027S\u0027, \u0027s\u0027, \u0027STAR\u0027 or \u0027star\u0027 to switch to STAR\n \u0027bowtie_index_dir\u0027 : \"\", #(OPTIONAL) default - will be created automatically in your working dir if aligner will be set to bowtie\n \u0027bowtie_index_params\u0027 : \"\", #(OPTIONAL)\n \u0027bowtie_map_params\u0027 : \"-v 1 -m 10 --best --strata -S\", #(OPTIONAL)\n \u0027star_index_dir\u0027 : \"\", #(OPTIONAL) default - will be created automatically in your working dir if aligner will be set to STAR\n \u0027star_index_params\u0027 : \"--runMode genomeGenerate --sjdbOverhang 100\", #(OPTIONAL)\n \u0027star_map_params\u0027 : \"--runMode alignReads --genomeLoad NoSharedMemory --alignEndsType EndToEnd --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outSAMattributes All --outSAMtype BAM Unsorted --outFilterType BySJout --outFilterMismatchNoverReadLmax 0.05 --outSAMattrRGline ID:foo --outStd Log --outBAMcompression 10 --outSAMmode Full\", #(OPTIONAL)\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eThe PARalyzer parameters section is directly used to create .ini file for PARalyzer run and setup memory limit for PARalyzer (\u003ccode\u003eparalyzer_memory\u003c/code\u003e field). To properly fill all fields please read PARalyzer \u003ca href=\"https://ohlerlab.mdc-berlin.de/files/duke/PARalyzer/README.txt\" rel=\"nofollow\"\u003emanual\u003c/a\u003e. Field \u003ccode\u003eADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u003c/code\u003e is required only if \u003ccode\u003esignal_extension : ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u003c/code\u003e. In other cases it will be skipped. If your library does not contain UMIs you may consider switching \u003ccode\u003euse_pcr_duplicates\u003c/code\u003e to \u003ccode\u003eTrue\u003c/code\u003e. Then PARalyzer will take into account all reads without PCR duplicates discrimination.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #PARalyzer params\n \u0027paralyzer_memory\u0027 : \"4G\", #(OPTIONAL)\n \u0027BANDWIDTH\u0027 : 3, #(OPTIONAL)\n \u0027CONVERSION\u0027 : \"T\u0026gt;C\", #(OPTIONAL), possible choices \"T\u0026gt;C\", \"G\u0026gt;A\"\n \u0027MINIMUM_READ_COUNT_PER_GROUP\u0027 : 5, #(OPTIONAL),\n \u0027MINIMUM_READ_COUNT_PER_CLUSTER\u0027 : 2, #(OPTIONAL)\n \u0027MINIMUM_READ_COUNT_FOR_KDE\u0027 : 3, #(OPTIONAL)\n \u0027MINIMUM_CLUSTER_SIZE\u0027 : 11, #(OPTIONAL)\n \u0027MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER\u0027 : 2, #(OPTIONAL)\n \u0027MINIMUM_CONVERSION_COUNT_FOR_CLUSTER\u0027 : 2, #(OPTIONAL)\n \u0027MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION\u0027 : 1, #(OPTIONAL)\n \u0027MINIMUM_READ_LENGTH\u0027 : 15, #(OPTIONAL)\n \u0027MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES\u0027 : 1, #(OPTIONAL)\n \u0027signal_extension\u0027 : \"EXTEND_BY_READ\", ##(OPTIONAL) one of \u0027EXTEND_BY_READ\u0027, \u0027HAFNER_APPROACH\u0027, \u0027ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u0027\n \u0027ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u0027 : 2, #only valid when signal_extension : \u0027ADDITIONAL_NUCLEOTIDES_BEYOND_SIGNAL\u0027\n \u0027use_pcr_duplicates\u0027 : False, #(OPTIONAL) change to True to force PARalyzer to treat pcr duplicates as individual reads (will increase number of clusters, but also false positives)\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eThe last section contains motif enrichment parameters. Motif enrichmantis performed by one of the tools from \u003ca href=\"https://meme-suite.org/meme/\" rel=\"nofollow\"\u003eMEME\u003c/a\u003e. Default value for \u003ccode\u003emotif_enrichment_method\u003c/code\u003e is \u003ca href=\"https://meme-suite.org/meme/tools/meme\" rel=\"nofollow\"\u003ememe\u003c/a\u003e, user can also choose \u003ca href=\"https://meme-suite.org/meme/doc/dreme-tutorial.html\" rel=\"nofollow\"\u003edreme\u003c/a\u003e or \u003ca href=\"https://meme-suite.org/meme/doc/streme-tutorial.html\" rel=\"nofollow\"\u003estreme\u003c/a\u003e. \u003ccode\u003emotif_enrichment_params\u003c/code\u003e field should be filled with parameters specific for selected method.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNOTE:\u003c/strong\u003e For motif enrichment analysis keep alphabet as \u003ccode\u003e-dna\u003c/code\u003e. Do not switch it to \u003ccode\u003e-rna\u003c/code\u003e. Final motifs will be changed to RNA alphabet automatically in the next steps.\u003c/p\u003e\n\u003cp\u003eSection from default config is shown below.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e #motif enrichment params\n \u0027motif_enrichment_method\u0027 : \"meme\", #(OPTIONAL), possible choices \"meme\", \"dreme\", \"streme\"\n \u0027motif_enrichment_params\u0027 : \"-dna -mod anr -evt 0.05 -minw 3\", #(OPTIONAL); be aware that some prameters are specific for enrichment method chosen\n}\n\u003c/code\u003e\u003c/pre\u003e\n", + "data_format": 2, + "description": "Snakemake workflow for PAR-CLIP data analysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/genomes_indexes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/quality.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpz4ql9bk1/workflow/rules/alignment.smk\": Keyword \"output\" at line 7 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/remove_rep_elements.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/generate_report.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/trimming.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/bigwigs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/motif_enr.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/collapse_reads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz4ql9bk1/workflow/rules/paralyzer.smk\": Formatted content is different from original\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mukherjeelab/CLIPs4U", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpz4ql9bk1/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n from scripts.genomic_files_and_indexes import prepare_genomes_and_indexes\n\n File \"/tmp/tmpz4ql9bk1/workflow/scripts/genomic_files_and_indexes.py\", line 9, in \u003cmodule\u003e\n import wget\n\nModuleNotFoundError: No module named \u0027wget\u0027\n\n", + "mandatory_flags": null, + "report": false, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 2, + "topics": [], + "updated_at": 1720826035.0 }, { "config_readme": null, "data_format": 2, - "description": "Repository containing bioinformatic code for macro-scale host transcriptomic data processing", - "formatting": null, - "full_name": "3d-omics/ht_quant", - "latest_release": "v0.2.0", - "linting": null, + "description": "An app that removes empty images from camera trap datasets using MD. Comes with a simple GUI.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpstp5ptea/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "dwheelerau/easily-triggered", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmpstp5ptea/Snakefile:\n * Absolute path \"/project/megadetector-summary.txt\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.json\" in line 9:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.json\" in line 18:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.csv\" in line 20:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/project.csv\" in line 28:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/project/megadetector-summary.txt\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule megadetector (line 16, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule json_to_csv (line 38, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_md (line 64, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 90, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule kill (line 101, /tmp/tmpstp5ptea/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "pipeline" - ], - "updated_at": 1722954021.0 + "topics": [], + "updated_at": 1720824619.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": "Test", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpc4mm9twg/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "weizhu365/snakemake_template_test", + "latest_release": null, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1720727511.0 }, { "config_readme": null, "data_format": 2, - "description": "Build genome references for RENEE", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpgvxd59l0/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "CCBR/build-renee-refs", + "description": "Predict variant calling performance across the genome", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpdo_o7atv/workflow/rules/inputs.smk\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 3 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "usnistgov/giab-stratomod", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpgvxd59l0/Snakefile\", line 7, in \u003cmodule\u003e\n raise ValueError(\"NCBI_API_KEY environment variable is not set.\\n\"\n\nValueError: NCBI_API_KEY environment variable is not set.\n\tPlease obtain an API Key for your NCBI account and set it to the environment variable NCBI_API_KEY.\n\thttps://support.nlm.nih.gov/knowledgebase/article/KA-05317/en-us\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdo_o7atv/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n from common.config import StratoMod\n\n File \"/tmp/tmpdo_o7atv/workflow/scripts/python/common/config.py\", line 43, in \u003cmodule\u003e\n from more_itertools import duplicates_everseen, unzip, partition, flatten\n\nModuleNotFoundError: No module named \u0027more_itertools\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 0, "topics": [], - "updated_at": 1722953693.0 + "updated_at": 1720724424.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp24uq7059/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "FreilichLab/NetCom2_snakemake", + "description": "Genome-in-a-Bottle stratifications for major references", + "formatting": null, + "full_name": "usnistgov/giab-stratifications", "latest_release": null, - "linting": "Lints for rule Removal_pipeline (line 12, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule split_count_table_by_treatment (line 70, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule claculate_enzyme_diversity_score (line 108, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule enzyme_diversity (line 154, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule determine_diffenetial_abundance (line 174, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Community_knockouts_simulations (line 232, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param sim_log_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule prepare_pathway_compounds_for_visual (line 273, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule visualize_knockout_network (line 316, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_netcom2 (line 419, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5b_4yl7d/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n from common.config import GiabStrats\n\nModuleNotFoundError: No module named \u0027common\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1722948499.0 + "updated_at": 1720719980.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpirza16q8/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "vari-bbc/methylation_array", + "description": "A pipeline for quantification of antibody staining in TMA cores.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp841howes/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "StaafLab/TMArQ", "latest_release": null, - "linting": "Lints for rule sesame_qc (line 30, /tmp/tmpirza16q8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Additionally specify a conda environment or container for each rule, environment modules are not enough:\n While environment modules allow to document and deploy the required\n software on a certain platform, they lock your workflow in there,\n disabling easy reproducibility on other machines that don\u0027t have exactly\n the same environment modules. Hence env modules (which might be beneficial\n in certain cluster environments), should always be complemented with\n equivalent conda environments.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param idat_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sesame_se (line 76, /tmp/tmpirza16q8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Additionally specify a conda environment or container for each rule, environment modules are not enough:\n While environment modules allow to document and deploy the required\n software on a certain platform, they lock your workflow in there,\n disabling easy reproducibility on other machines that don\u0027t have exactly\n the same environment modules. Hence env modules (which might be beneficial\n in certain cluster environments), should always be complemented with\n equivalent conda environments.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param idat_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sesame_DM (line 128, /tmp/tmpirza16q8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Additionally specify a conda environment or container for each rule, environment modules are not enough:\n While environment modules allow to document and deploy the required\n software on a certain platform, they lock your workflow in there,\n disabling easy reproducibility on other machines that don\u0027t have exactly\n the same environment modules. Hence env modules (which might be beneficial\n in certain cluster environments), should always be complemented with\n equivalent conda environments.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmp841howes/Snakefile:\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule detectROI (line 26, /tmp/tmp841howes/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule segment (line 48, /tmp/tmp841howes/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1722873728.0 + "updated_at": 1720710680.0 }, { "config_readme": null, "data_format": 2, - "description": "Python-based workflow for reproducible and scalable minimal processing with the HCPPipelines.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpre8pf8x8/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "leon-k-martin/hcpython", + "description": "Example repository for analyzing many datasets at once from scperturb.org using snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp8_50y4r6/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "stefanpeidli/scperturb_snakemake_example", "latest_release": null, - "linting": "/tmp/tmpre8pf8x8/hcpy/data/__init__.py:17: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n sep=\"\\s+\",\n/tmp/tmpre8pf8x8/hcpy/data/__init__.py:26: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n sep=\"\\s+\",\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpre8pf8x8/Snakefile\", line 64, in \u003cmodule\u003e\n f_dwi_res = join(rawdatadir, \"{subid}_{sequence}_{PEdir}_res.nii.gz\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n [Previous line repeated 2 more times]\n\n File \"\u003cfrozen os\u003e\", line 225, in makedirs\n\nPermissionError: [Errno 13] Permission denied: \u0027/Volumes\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 135, in import_optional_dependency\n module = importlib.import_module(name)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/importlib/__init__.py\", line 90, in import_module\n return _bootstrap._gcd_import(name[level:], package, level)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1387, in _gcd_import\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1360, in _find_and_load\n\n File \"\u003cfrozen importlib._bootstrap\u003e\", line 1324, in _find_and_load_unlocked\n\nModuleNotFoundError: No module named \u0027openpyxl\u0027\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp8_50y4r6/Snakefile\", line 26, in \u003cmodule\u003e\n if DATASETS == \u0027all\u0027:\n ^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 495, in read_excel\n io = ExcelFile(\n ^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_base.py\", line 1567, in __init__\n self._reader = self._engines[engine](\n ^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/excel/_openpyxl.py\", line 552, in __init__\n import_optional_dependency(\"openpyxl\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/compat/_optional.py\", line 138, in import_optional_dependency\n raise ImportError(msg)\n\nImportError: Missing optional dependency \u0027openpyxl\u0027. Use pip or conda to install openpyxl.\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "perturbation-methods", + "single-cell", + "transcriptomics" + ], + "updated_at": 1721584898.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "deep_snake - snakemake-based deepconsensus (Pacbio SequelII subreads - to deepconsensus.fastq)", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpv1rq1esq/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:6: needs to be here for the snakemake workflow catalogue\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[INFO] In file \"/tmp/tmpv1rq1esq/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "WestGermanGenomeCenter/deep_snake", + "latest_release": null, + "linting": "SyntaxError in file /tmp/tmpv1rq1esq/Snakefile, line 1:\ninvalid syntax:\nneeds to be here for the snakemake workflow catalogue\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -2985,33 +3092,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722868351.0 + "updated_at": 1720702186.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4pp0e8xo/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Mason-Lab-Code/NanoSeq-snakemake", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\ \u0027\n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/selection.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/karyotype.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/utility.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/rules/PopulationStructure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1alwu1f4/workflow/Snakefile\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "sanjaynagi/probe", "latest_release": null, - "linting": "Lints for rule fastqc (line 21, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule multiqc (line 66, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_tags (line 103, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bwa_index (line 140, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_mem (line 182, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_and_add_rc_mc_tags (line 238, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mark_dups (line 281, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_and_append_rb_tags (line 335, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule keep_random_read (line 384, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_analysis (line 433, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule check_contamination (line 607, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule estimate_efficiency (line 648, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule collate_efficiency (line 710, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule organise_outputs (line 749, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp1alwu1f4/workflow/Snakefile\", line 28, in \u003cmodule\u003e\n PCAcohorts = getCohorts(metadata, columns=config[\u0027PopulationStructure\u0027][\u0027PCA\u0027][\u0027colourColumns\u0027]) # PCA\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027config/gaard_metadata.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 2, "topics": [], - "updated_at": 1722844048.0 + "updated_at": 1720687708.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp7y71_ark/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "pruethemann/squeezemd", + "description": "Snakemake workflow: DNA Single Nucleotide Variant Calling ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpx6bc4lku/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "lesleymaraina/snv_ensemble_variant_calling", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config/params.yml but it is not present or accessible (full checked path: /tmp/tmp7y71_ark/config/params.yml).\n", + "linting": "Lints for snakefile /tmp/tmpx6bc4lku/Snakefile:\n * Absolute path \"/data/AlexanderP3/SJCLOUD/RBL/retinoblastoma/germline/WGS/bam/{sample}.WholeGenome.bam\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/AlexanderP3/SJCLOUD/RBL/retinoblastoma/germline/WGS/bam/{sample}.WholeGenome.bam.bai\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule strelka (line 23, /tmp/tmpx6bc4lku/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable parapath from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule HC (line 59, /tmp/tmpx6bc4lku/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable parapath from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule DV (line 94, /tmp/tmpx6bc4lku/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable parapath from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3019,16 +3126,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722802918.0 + "updated_at": 1720642160.0 }, { "config_readme": null, "data_format": 2, - "description": "Repository for varroa linkage mapping project", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp40tm3vxv/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "nurit-eliash/varroa-pedigree-study", + "description": "Snakemake Pipeline with \"selectable\" modules", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/split_bams_v2.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpcr8yqsp5/rules/split_bams_gt.smk\": Keyword \"params\" at line 151 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/split_bams_gt.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpcr8yqsp5/rules/analyse_vireo.smk\": Keyword \"output\" at line 7 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/analyse_vireo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/deeptools.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/create_logs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/input_processing.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpcr8yqsp5/rules/snv_aware_align.smk\": Keyword \"output\" at line 81 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/snv_aware_align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/helper_functions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/STARsolo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/calico_solo_demux.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/identify_swaps.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/produce_targets.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/picard_metrics.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/demultiplex.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/pheno_demux3.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/kite.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/split_bams.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpcr8yqsp5/rules/resources.smk\": Formatted content is different from original\n[INFO] 19 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "pnm27/snRNA_scRNA_Pipeline", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp40tm3vxv/Snakefile\", line 7, in \u003cmodule\u003e\n from scripts.split_fasta_regions import split_fasta\n\n File \"/tmp/tmp40tm3vxv/scripts/split_fasta_regions.py\", line 2, in \u003cmodule\u003e\n from Bio import SeqIO\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpcr8yqsp5/Snakefile\", line 20, in \u003cmodule\u003e\n import glob2, re, math\n\nModuleNotFoundError: No module named \u0027glob2\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3036,16 +3143,16 @@ var data = "stargazers_count": 0, "subscribers_count": 2, "topics": [], - "updated_at": 1722756095.0 + "updated_at": 1720635153.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppg6tzvci/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "hhshanto/RSEP", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/8_snRNAseq_LDSR_protein_coding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/4_snRNAseq_MAGMA.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/5_snRNAseq_MAGMA_protein_genes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/9_snRNAseq_LDSR_nonprotein_coding.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp9ubz3_ps/workflow/Snakefile\": NoParametersError: L43: In input definition.\n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/11_snRNAseq_LDSR_GO_term_genes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/10_snRNAseq_LDSR_top2000.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/3_snRNAseq_get_and_munge_GWAS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/7_snRNAseq_LDSR.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/6_snRNAseq_MAGMA_nonprotein_genes.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/2_snRNAseq_prep_enrich_files.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9ubz3_ps/workflow/rules/1_snRNAseq_get_and_prep_herring_data.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 11 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "cetume/Tume_BP-GOS_2024", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmppg6tzvci/Snakefile:\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 11:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule preprocess (line 14, /tmp/tmppg6tzvci/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PREPROCESS_SCRIPT from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "WorkflowError:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3053,33 +3160,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722714486.0 + "updated_at": 1720626320.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": null, - "full_name": "jayed87/rse-group-project", + "description": "Workflow to detect assembly and long read regions rich in GA or CT alleles. ", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpruu6iydt/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 185)\n[INFO] In file \"/tmp/tmpruu6iydt/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "adlnosk/GA-CT-rich-regions", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmphl7re638/config/config.yaml).\n", + "linting": "TabError in file \u003cstring\u003e, line 185:\ninconsistent use of tabs and spaces in indentation:\n \tplotting_flank=10000,\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1722632537.0 + "updated_at": 1720625698.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/rules/climate.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/rules/platform.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp44shwf1b/workflow/Snakefile\": Keyword \"input\" at line 70 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/Snakefile\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "simonmoulds/subseasonal-flood-prediction", + "description": "JMF workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiuq4ubre/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "W-L/megahit_metagenome_assembly_binning", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp44shwf1b/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n import pyarrow\n\nModuleNotFoundError: No module named \u0027pyarrow\u0027\n\n", + "linting": null, "mandatory_flags": { "desc": null, "flags": null @@ -3094,50 +3201,57 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722616971.0 + "updated_at": 1720623398.0 }, { - "config_readme": null, + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmps72zl_h4/SamBryce-Smith-bulk_polyatail_reads-8dc3509/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "SamBryce-Smith/bulk_polyatail_reads", - "latest_release": "v0.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmps72zl_h4/SamBryce-Smith-bulk_polyatail_reads-8dc3509/Snakefile\", line 4, in \u003cmodule\u003e\n sample_tbl = pd.read_csv(config[\"sample_table\"])\n ^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027sample_table\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, + "description": "Template from Snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpod6opocj/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "charleshefer/snakemake-workflow-template", + "latest_release": null, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722615397.0 + "updated_at": 1722297889.0 }, { "config_readme": null, "data_format": 2, - "description": "Code associated with \"Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages\"", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/pre-processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/phylodynamics.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpfm4m6vvs/workflow/Snakefile\": Keyword \"input\" at line 49 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/post-processing.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "EtthelWindels/snakemake-mtb-beast2", - "latest_release": null, - "linting": "RuleException in rule beast in file /tmp/tmpfm4m6vvs/workflow/rules/phylodynamics.smk, line 3:\nNot all output, log and benchmark files of rule beast contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.\n", + "description": "Isolated chromosome sequencing analysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk\": Keyword \"output\" at line 103 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk\": Keyword \"input\" at line 174 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/Snakefile\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "lca-imcb/dopseq", + "latest_release": "v2.2.0", + "linting": "Lints for rule fastqc_init (line 1, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc_trimmed (line 148, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule samtools_faidx (line 237, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule samtools_filter (line 355, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule samtools_merge (line 393, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule regions (line 429, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule stats (line 468, /tmp/tmp2ssfs4js/lca-imcb-dopseq-053d6ad/rules/dopseq.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 3, "topics": [], - "updated_at": 1722612479.0 + "updated_at": 1722259232.0 }, { "config_readme": null, "data_format": 2, - "description": "Hnld_Genetic_Diversity_Analysis", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpv567bg31/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "johnpatramanis/Hnld_Genetic_Diversity_Analysis", + "description": "An example workflow with snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpe31fu8mt/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Luke-ebbis/snakemake-tutorial", "latest_release": null, - "linting": "Lints for rule Index_VCF_File (line 85, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_Protein_Coverage (line 107, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Isolate_Genes_From_Each_VCF_File (line 142, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_GenomeWide_PI_from_VCF (line 169, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_GenomeWide_heterozyg_from_VCF (line 195, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule RunVEP_on_Filtered_VCF_File (line 229, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Second_Round_of_Filtering_Output_Positions (line 269, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Prepare_for_second_filtering (line 305, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Filter_Again_Using_VEP_Variants (line 339, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_Genotypes (line 377, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_Metric_From_Genotypes (line 413, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Using workflow specific profile workflow/profiles/default for setting default command line arguments.\nLints for snakefile /tmp/tmpe31fu8mt/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule download_data (line 42, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move (line 77, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fastqc (line 105, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quality_report_fastqc (line 132, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trimming (line 159, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assembly (line 211, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assembly_qc (line 251, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quality_report_assembly (line 284, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mapping_index (line 307, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mapping_mem (line 329, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fix_mates (line 355, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sort_coordinate (line 383, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sort_group (line 410, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dedupe (line 437, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule map_summary (line 464, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule coverage_stats (line 486, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule coverage_stats_filter (line 513, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule coverage_stats_contig (line 536, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule db (line 563, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule help (line 584, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 602, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_overview (line 616, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule install_easy_graph (line 646, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_ascii_graph (line 678, /tmp/tmpe31fu8mt/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3145,33 +3259,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722605198.0 + "updated_at": 1722245071.0 }, { "config_readme": null, "data_format": 2, - "description": "Generate single-cell reference dataset for deconvolution in Atlas", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp03uunm3o/Snakefile\": TokenError: (\u0027unexpected character after line continuation character\u0027, (102, 76))\n[INFO] In file \"/tmp/tmp03uunm3o/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "ebi-gene-expression-group/atlas-deconvolution-references", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpz8ctbkht/workflow/Snakefile\": TokenError: (\u0027unexpected character after line continuation character\u0027, (15, 208))\n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpz8ctbkht/workflow/rules/pQuant_enc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "G2Lab/pQuant", "latest_release": null, - "linting": "TokenError:\n(\u0027unexpected character after line continuation character\u0027, (102, 76))\n", + "linting": "SyntaxError in file /tmp/tmpz8ctbkht/workflow/Snakefile, line 10:\nunexpected character after line continuation character:\nNone\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 5, + "subscribers_count": 1, "topics": [], - "updated_at": 1722593796.0 + "updated_at": 1722008668.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/PopulationStructure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/karyotype.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/utility.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "sanjaynagi/ag3-relatedness", - "latest_release": null, - "linting": "WorkflowError:\nFailed to open source file /tmp/tmpqrumwp_e/workflow/rules/ibd.smk\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/tmp/tmpqrumwp_e/workflow/rules/ibd.smk\u0027\n", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/rules/manip_seqs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/rules/make_rlooper.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/rules/run_rlooper.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "EthanHolleman/rlooper-plasmids", + "latest_release": "1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmppd4vfp1g/EthanHolleman-rlooper-plasmids-5879b0f/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n paramspace = Paramspace(pd.read_csv(PARAMS_TABLE, sep=\"\\t\"))\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027../resources/rlooper_params.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3179,33 +3293,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722588226.0 + "updated_at": 1721945847.0 }, { "config_readme": null, "data_format": 2, - "description": "Lecture 1 of DSMS: Course Introduction", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp987lepvd/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp987lepvd/rules/renv.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "deer-marketing-lab/dsms-lecture-course-introduction", + "description": "Analysing options for Ukraine\u0027s future energy supply.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/utils.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/pypsa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/preprocess.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/analyse.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm4_62zl8/rules/sync.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "timtroendle/ukraine-energy-future", "latest_release": null, - "linting": "Lints for rule build_html (line 16, /tmp/tmp987lepvd/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 46, /tmp/tmp987lepvd/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 89, /tmp/tmp987lepvd/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 22, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 34, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 46, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 58, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpm4_62zl8/Snakefile\", line 13, in \u003cmodule\u003e\n onstart:\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpm4_62zl8/./rules/pypsa.smk\", line 6, in \u003cmodule\u003e\n from snakemake.io import load_configfile\n\nImportError: cannot import name \u0027load_configfile\u0027 from \u0027snakemake.io\u0027 (/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/io.py)\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 2, "topics": [], - "updated_at": 1722550844.0 + "updated_at": 1721894371.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/join_nest.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/generate_results_rds.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/process_actilife.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/reformat.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/resample.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/download_process.smk\": Formatted content is different from original\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "lilykoff/step_algorithms", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj3uk94ng/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "AHassanpour88/Evolutionary_Snakemake", "latest_release": null, - "linting": "Lints for rule download_data (line 26, /tmp/tmpojqzbhhd/workflow/rules/download_process.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_data_nom (line 56, /tmp/tmpojqzbhhd/workflow/rules/download_process.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule resample (line 26, /tmp/tmpojqzbhhd/workflow/rules/resample.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule resample_nom (line 62, /tmp/tmpojqzbhhd/workflow/rules/resample.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule reformat (line 28, /tmp/tmpojqzbhhd/workflow/rules/reformat.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule reformat_nom (line 75, /tmp/tmpojqzbhhd/workflow/rules/reformat.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_actilife_results (line 30, /tmp/tmpojqzbhhd/workflow/rules/process_actilife.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_actilife_results_nom (line 77, /tmp/tmpojqzbhhd/workflow/rules/process_actilife.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_stepcount (line 33, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_algorithms (line 71, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_stepcount_nom (line 118, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_algorithms_nom (line 146, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_results (line 32, /tmp/tmpojqzbhhd/workflow/rules/join_nest.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_results_nom (line 80, /tmp/tmpojqzbhhd/workflow/rules/join_nest.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_results_dfs (line 25, /tmp/tmpojqzbhhd/workflow/rules/generate_results_rds.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_results_dfs_nom (line 49, /tmp/tmpojqzbhhd/workflow/rules/generate_results_rds.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_acc_figures (line 25, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_step_figures (line 49, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_step_figures_nom (line 73, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_resamp_figures (line 96, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_resamp_figures_nom (line 118, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_speed_figures (line 141, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpj3uk94ng/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule sampleVAl (line 98, /tmp/tmpj3uk94ng/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runSimulations (line 143, /tmp/tmpj3uk94ng/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule runEvolutionary (line 203, /tmp/tmpj3uk94ng/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gatherResults (line 249, /tmp/tmpj3uk94ng/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3213,88 +3327,33 @@ var data = "stargazers_count": 0, "subscribers_count": 2, "topics": [], - "updated_at": 1722540937.0 - }, - { - "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n # Optional parameters for FastQC\n fastqc: \"\"\n # Optional parameters for FastP\n fastp:\n # Optional command line adapters\n adapters: \"\"\n # Optional command line parameters\n extra: \"\"\n bowtie2:\n # Optional parameters for bowtie2-build\n build: \"\"\n # Optional parameters for bowtie2-align\n align: \"\"\n sambamba:\n # Optional parameters for sambamba view\n view: \"--format \u0027bam\u0027 --filter \u0027mapping_quality \u0026gt;= 30 and not (unmapped or mate_is_unmapped)\u0027 \"\n # Optional parameters for sambamba markdup\n markdup: \"--remove-duplicates --overflow-size 500000\"\n picard:\n # Mapping QC optional parameters\n metrics: \"\"\n # Optional parameters for samtools stats\n samtools: \"\"\n macs2:\n # Optional parameters for Macs2 Callpeaks\n callpeak: \"\"\n homer:\n # Optional parameters for Homer AnnotatePeaks\n annotatepeaks: \"-homer2\"\n deeptools:\n # Optional parameters for DeepTools bamCoverage\n bamcoverage: \"--ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4 --ignoreForNormalization X Y MT\"\n # Optional parameters for DeepTools plotCoverage\n plot_coverage: \"--skipZeros --ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4\"\n # Optional parameters for DeepTools plotFingerprint\n plot_fingerprint: \"--skipZeros --ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4\"\n # Optional parameters for DeepTools plotPCA\n plot_pca: \"--ntop 1000\"\n # Optional parameters for DeepTools plotEnrichment\n plot_enrichment: \"--ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4 --smartLabels\"\n # Optional parameters for DeepTools plotCorrelations\n plot_correlation: \"--whatToPlot heatmap --corMethod spearman --skipZeros --plotNumbers --colorMap RdYlBu\"\n # Optional parameters for MultQC\n multiqc: \"--module deeptools --module macs2 --module picard --module fastqc --module fastp --module samtools --module bowtie2 --module sambamba --zip-data-dir --verbose --no-megaqc-upload --no-ansi --force\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003esample_id: Unique name of the sample\u003c/li\u003e\n\u003cli\u003eupstream_file: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003especies: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003ebuild: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003erelease: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003edownstream_file: Optional path to downstream fastq file\u003c/li\u003e\n\u003cli\u003einput: Sample id of the corresponding input signal\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release,input\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110,sac_a_input\nsac_a_input,data/reads/a.scerevisiaeI.1.fq,data/reads/a.scerevisiaeI.2.fq,saccharomyces_cerevisiae,R64-1-1,110,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", - "data_format": 2, - "description": "Snakemake workflow used to call peaks with Macs2", - "formatting": null, - "full_name": "tdayris/fair_macs2_calling", - "latest_release": "3.1.1", - "linting": null, - "mandatory_flags": { - "desc": "Call peaks with Macs2 and annotate them with Homer", - "flags": "--profile ./profiles/" - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bowtie2", - "homer", - "macs2", - "sambamba", - "snakemake", - "snakemake-workflow", - "snakemake-wrappers" - ], - "updated_at": 1722412389.0 + "updated_at": 1721914761.0 }, { "config_readme": null, "data_format": 2, - "description": "A machine learning project for the ML Seminar 2024 at the TU Dortmund (faculty of physics). A convolutional neural network is employed to classify bird species by audio recordings of their calls. ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5jb699qy/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "lukas-bert/CNN-based-Bird-Audio-Classification", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp5jb699qy/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 9:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 40:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 49:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule download_dataset (line 6, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable path_storage from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable dataset_name from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule get_spectrograms (line 28, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_audio_features (line 52, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule train_model (line 78, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpoo1v7ba9/weinstockj-RNAseq-perturbation-CD4-pipeline-7bce298/Snakefile\": Keyword \"output\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpoo1v7ba9/weinstockj-RNAseq-perturbation-CD4-pipeline-7bce298/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "weinstockj/RNAseq-perturbation-CD4-pipeline", + "latest_release": "v0.0.1", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpoo1v7ba9/weinstockj-RNAseq-perturbation-CD4-pipeline-7bce298/Snakefile\", line 6, in \u003cmodule\u003e\n sample_sheet = pd.read_table(\u0027/oak/stanford/groups/pritch/users/jweinstk/perturbation_data/metadata/sample_meta_data_2022_12_08.tsv\u0027, index_col = False)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/oak/stanford/groups/pritch/users/jweinstk/perturbation_data/metadata/sample_meta_data_2022_12_08.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 3, "topics": [], - "updated_at": 1722376796.0 + "updated_at": 1721838345.0 }, { "config_readme": null, "data_format": 2, - "description": "A Snakemake workflow for Chandra data reduction", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/extract_spectra.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/project_psf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_exposure_flux.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/reproject_events.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_spectral_weights.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/bin_events.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/fit_spectra.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/chandra_repro.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/simulate_psf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/post_process_psf.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/download_chandra_obsid.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/find_and_copy_asolfile.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_exposure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_background_simple.smk\": Formatted content is different from original\n[INFO] 15 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "adonath/snakemake-workflow-chandra", + "description": "This repository includes the workflow for the main experiments in the Movi paper.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9glx65_0/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mohsenzakeri/Movi-experiments", "latest_release": null, - "linting": "/tmp/tmpyhxsfesf/workflow/Snakefile:602: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n include: \"rules/chandra_repro.smk\"\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpyhxsfesf/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n from astropy import units as u\n\nModuleNotFoundError: No module named \u0027astropy\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 3, - "topics": [ - "chandra", - "ciao", - "data-reduction", - "snakemake", - "pylira" - ], - "updated_at": 1722373096.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/variables.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/alleles.smk\": Keyword \"shell\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/alleles.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/input.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/read_orientation.smk\": Keyword \"shell\" at line 80 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/read_orientation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 64 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 144 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"input\" at line 180 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 194 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "kilpert/FGF14_analyses", - "latest_release": "v1.0.0", - "linting": "/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile:131: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n \n/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile:132: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n ## include #############################################################################################################\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n from Bio.Seq import Seq\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", + "linting": "WorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmp9glx65_0/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3302,81 +3361,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1722336879.0 + "updated_at": 1721838244.0 }, { "config_readme": null, "data_format": 2, - "description": "Workspace for adding DFTs to Psi4 and testing them against ACCDB", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n[ERROR] In file \"/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile\": EmptyContextError: L164: rule has no keywords attached to it.\n[INFO] In file \"/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "UBCC3/adding-psi4-functionals", - "latest_release": "1", - "linting": "/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:34: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n basis=\u0027[-\\w]+\u0027,\n/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:35: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n restriction=\u0027RHF|UHF\u0027,\n/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:36: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n \n/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:146: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n energy = re.findall(regexp, qcengine_out.read())\nWorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/config.yaml).\n", + "description": "Peak-calling using Snakemake", + "formatting": null, + "full_name": "ParthDoshi97/ATAC-seq-peak-calling", + "latest_release": null, + "linting": "WorkflowError:\nFailed to open source file /tmp/tmp94ou6u70/Snakefile\nIsADirectoryError: [Errno 21] Is a directory: \u0027/tmp/tmp94ou6u70/Snakefile\u0027\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723760466.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": "Calling and plotting of differentially methylated regions between two or more biological samples in BAM format", - "formatting": null, - "full_name": "koesterlab/rossi-ips-dmr", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpulo4ybao/workflow/Snakefile\", line 26, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpulo4ybao/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n samples = read_sample_tsv(sample_tsv_path)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/tmp/tmpulo4ybao/workflow/rules/common.smk\", line 7, in read_sample_tsv\n with open(sample_tsv_path, \"r\") as file:\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/projects/koesterlab/rossi-ips-dmr/config/sample.tsv\u0027\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723738252.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "Addimator/compare_meth", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpn552y9ih/workflow/Snakefile\", line 26, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpn552y9ih/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n samples = read_sample_tsv(sample_tsv_path)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/tmp/tmpn552y9ih/workflow/rules/common.smk\", line 7, in read_sample_tsv\n with open(sample_tsv_path, \"r\") as file:\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/projects/koesterlab/benchmark-methylation/data_analysis_jochen/compare_meth/config/sample.tsv\u0027\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723727758.0 + "updated_at": 1721827337.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow to analyse hematological malignancies in whole genome data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/mutectcaller_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/fix_af.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/peddy_create_ped.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/export.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/dux4_rearrangements.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/manta_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/sample_order_multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/gatk_cnv_denoise_read_counts_by_sex.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/html_output.smk\": Formatted content is different from original\n[INFO] 13 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "clinical-genomics-uppsala/fluffy_hematology_wgs", - "latest_release": "v1.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\", line 12, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "description": "Pipeline to annotate peptide identifications when using protein databases made by of ProHap / ProVar", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:61: \"python src/peptides_annotate_variation.py -i {input.pep} \" +\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[INFO] In file \"/tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "ProGenNo/ProHap_PeptideAnnotator", + "latest_release": "v1.1", + "linting": "Lints for snakefile /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile:\n * Path composition with \u0027+\u0027 in line 16:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 48:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 2:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule download_reference_proteome (line 20, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule reference_fix_headers (line 37, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_gtf (line 62, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule parse_gtf_whole (line 79, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotate_peptides (line 104, /tmp/tmpn7gtdh99/ProGenNo-ProHap_PeptideAnnotator-aa96309/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3384,57 +3395,80 @@ var data = "stargazers_count": 0, "subscribers_count": 2, "topics": [], - "updated_at": 1723713011.0 + "updated_at": 1721821051.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp95qzm81x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MindTheGap-ERC/Triangle_workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/encoding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/make_viz.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/behaviors.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/spatial_comparisons.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/fmri.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpj75e5yml/workflow/rules/behaviors_pred.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 7 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "nyuolab/MooneyComputationModeling2024", "latest_release": null, - "linting": "WorkflowError:\nNo storage provider found for query irods://nluu12p/home/research-test-christine/triangle/{param_file}.mat. Either install the required storage plugin or check your query. Also consider to explicitly specify the storage provider to get a more informative error message.\n", + "linting": "WorkflowError:\nFailed to open source file /tmp/tmpj75e5yml/workflow/rules/visualizations/attention_map.smk\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/tmp/tmpj75e5yml/workflow/rules/visualizations/attention_map.smk\u0027\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 1, "topics": [], - "updated_at": 1723661311.0 + "updated_at": 1721753076.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n # Optional parameters for fastp trimming and QC\n fastp: \"\"\n salmon:\n # Optional parameters for genome indexation with Salmon\n index: \"\"\n # Optional parameters for salmon quantification\n # One should always include bootstraping and Bulk RNASeq bias\n quant: \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Optional path to downstream fastq file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release\nhomo_sapiens,GRCh38,110\nmus_musculus,GRCm38,99\nmus_musculus,GRCm39,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptaafhdwz/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "SveTho/bcl2fastq2_workflow", - "latest_release": null, + "description": "Snakemake workflow designed to perform RNASeq transcrpotime expression estimation with Salmon", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqg4p51tu/tdayris-fair_rnaseq_salmon_quant-b983532/workflow/rules/multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 10 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "tdayris/fair_rnaseq_salmon_quant", + "latest_release": "1.2.3", "linting": null, "mandatory_flags": { - "desc": null, + "desc": "Estimate read abundance with Salmon", "flags": null }, "report": true, "software_stack_deployment": { "conda": true, "singularity": false, - "singularity+conda": false + "singularity+conda": true }, "standardized": true, "stargazers_count": 0, "subscribers_count": 1, + "topics": [ + "fair", + "rnaseq-pipeline", + "snakemake", + "snakemake-workflow", + "reproducible-science" + ], + "updated_at": 1721740853.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Compute a sequence and structure based phylome based on uniprot proteomes.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/checks.smk\": Keyword \"output\" at line 25 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/checks.smk\": Keyword \"input\" at line 210 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/checks.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/analysis.smk\": Keyword \"input\" at line 27 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpnbztpwt0/workflow/rules/analysis.smk\": Keyword \"input\" at line 103 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/analysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/structure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/sequence.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/prepare.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnbztpwt0/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Gabaldonlab/structural_phylome", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnbztpwt0/workflow/Snakefile\", line 20, in \u003cmodule\u003e\n include: \u0027rules/common.smk\u0027\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnbztpwt0/workflow/rules/prepare.smk\", line 1, in \u003cmodule\u003e\n outdir=config[\u0027outdir\u0027]+config[\u0027dataset\u0027]\n ^^^^^^^^^^^\n\nKeyError: \u0027dataset\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 3, "topics": [], - "updated_at": 1723630209.0 + "updated_at": 1722338463.0 }, { "config_readme": null, "data_format": 2, - "description": "PacBio Jasmine pipeline, penalized regression, and DMR identification", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpup7dp332/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "aliciasillers/Preliminary-CpG-Data-Analysis", + "description": "Analysis NGS data from P53 ampicon-based assay", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp7sdb1mou/Snakefile\": NoParametersError: L26: In params definition.\n[INFO] In file \"/tmp/tmp7sdb1mou/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "bingfang/P53-mutation-screen", "latest_release": null, - "linting": "Lints for rule pbmm2 (line 18, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cpgtools (line 44, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Lints for snakefile /tmp/tmp7sdb1mou/Snakefile:\n * Absolute path \"/Users/xubr/anaconda3/share/trimmomatic-0.39-2\" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule trim (line 24, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule debarcode (line 58, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genotyping (line 91, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule calculate_common_mutation_rate (line 125, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule calculate_mutation_rate (line 156, /tmp/tmp7sdb1mou/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3442,67 +3476,67 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723591308.0 + "updated_at": 1721662519.0 }, { "config_readme": null, "data_format": 2, - "description": "Deep mutational scanning of the MERS-CoV and PDF-2180 receptor-binding domains", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp2b6mul21/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 351)\n[INFO] In file \"/tmp/tmp2b6mul21/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "tstarrlab/MERS-PDF2180-RBD_DMS", + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"conda\" at line 10 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"shell\" at line 16 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"conda\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Keyword \"shell\" at line 38 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp0upnp1bm/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0upnp1bm/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0upnp1bm/rules/picard_rmdup.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp0upnp1bm/rules/fastp.smk\": Keyword \"conda\" at line 14 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp0upnp1bm/rules/fastp.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "china-fix/rq-count_v1", "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 351:\ninconsistent use of tabs and spaces in indentation:\n \tconfig[\u0027codon_variant_table_file_MERS_rpk\u0027],\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1723589726.0 + "updated_at": 1721511428.0 }, { "config_readme": null, "data_format": 2, - "description": "Benchmark for the AI LLM integration project", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpmumhq60x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "xwiki-contrib/ai-llm-benchmark", + "description": "Methylation tools repository", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpnk8egmli/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "MagdalenaZZ/methylation", "latest_release": null, - "linting": "Lints for rule download (line 47, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_french (line 64, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_german (line 91, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index (line 118, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule split (line 140, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule collect (line 167, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule eval_summary (line 202, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_text_generation (line 234, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_rag_qa (line 265, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_plots (line 300, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule report (line 333, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_model_outputs_report (line 370, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule calculate_average_power (line 403, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule archive (line 431, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 465, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TASKS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable SNAKEOUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable REPORTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_SUMMARIZATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_TEXT_GENERATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_QA_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnk8egmli/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpnk8egmli/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 47, + "subscribers_count": 1, "topics": [], - "updated_at": 1723575430.0 + "updated_at": 1721375750.0 }, { "config_readme": null, "data_format": 2, - "description": "WIP HIBF benchmarks", + "description": "Peptigate (\"peptide\" + \"investigate\") predicts bioactive peptides from transcriptome assemblies or sets of proteins.", "formatting": null, - "full_name": "seqan/hibf_benchmarks", - "latest_release": null, - "linting": "Lints for rule plot_landingpage (line 42, /tmp/tmpjpma0sez/workflow/rules/plot.smk):\n * Param HTML_DIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "full_name": "Arcadia-Science/peptigate", + "latest_release": "v1.0.0", + "linting": "/tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile:573: SyntaxWarning: invalid escape sequence \u0027\\*\u0027\n ## Charaterize \u0026 annotate predicted peptide sequences\n/tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile:585: SyntaxWarning: invalid escape sequence \u0027\\*\u0027\n conda:\nLints for rule get_coding_contig_names (line 53, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_contigs_to_no_predicted_ORF (line 90, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_uniref50_database (line 137, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_diamond_db_from_uniref50_database (line 158, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastx_transcripts_against_uniref50_database (line 194, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_transcript_uniref50_hits (line 252, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule filter_no_predicted_ORF_contigs_to_no_uniref50_long_hits (line 290, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plmutils_translate (line 331, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule length_filter_plmutils_translate_output (line 367, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plmutils_embed (line 398, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plmutils_predict (line 444, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extract_plmutils_predicted_peptides (line 483, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule extract_plmutils_predicted_peptides_as_nucleotides (line 518, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule remove_stop_codon_asterisk_from_transdecoder_ORFs (line 561, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_nlpprecursor_models (line 590, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_protein_sequences_with_nonstandard_amino_acids (line 619, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule nlpprecursor (line 655, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clone_deeppeptide (line 732, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule deeppeptide (line 763, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable WORKING_DIRPATH from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable WORKING_DIRPATH from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule extract_deeppeptide_sequences (line 802, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_faa_predictions (line 868, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule convert_peptide_faa_to_tsv (line 896, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_ffn_predictions (line 927, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule convert_peptide_ffn_to_tsv (line 955, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_peptipedia_database (line 996, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule make_diamond_db_from_peptipedia_database (line 1024, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp_peptide_predictions_against_peptipedia_database (line 1060, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule run_deepsig (line 1104, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule characterize_peptides (line 1141, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_autopeptideml_models (line 1192, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_autopeptideml (line 1226, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_predictions (line 1289, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule combine_peptide_annotations (line 1336, /tmp/tmpzi_27_58/Arcadia-Science-peptigate-37d76f7/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 6, + "subscribers_count": 2, "topics": [], - "updated_at": 1723547496.0 + "updated_at": 1721332971.0 }, { "config_readme": null, "data_format": 2, - "description": "Remove and Quantify Organism Spike Reads from Sequencing Data", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpkzm451zl/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mskcc-microbiome/spikequant", + "description": "Multiplex Accurate Sensitive Quantitation (MASQ) analysis and primer design", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_kkyaebk/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "amoffitt/MASQ", "latest_release": null, - "linting": "/tmp/tmpkzm451zl/workflow/Snakefile:689: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n/tmp/tmpkzm451zl/workflow/Snakefile:715: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpkzm451zl/workflow/Snakefile\", line 19, in \u003cmodule\u003e\n #mapper = \"minimap2-sr\"\n ^^^^^^^^^^^^^^^^^\n\nAssertionError: spiketable is a required config argument!\n\n", + "linting": "Lints for snakefile /tmp/tmp_kkyaebk/Snakefile:\n * Absolute path \"/r1.fastq.gz\" in line 143:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 144:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r1.fastq.gz\" in line 176:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 177:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 178:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 223:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 178:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 223:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 110:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 425:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 426:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule convert_SNV_table (line 122, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule barcode_split (line 150, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc (line 184, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule check_loci_extend_and_plot (line 219, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_data_by_tag_and_locus (line 255, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all_base_report (line 310, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_within_tag_errors (line 361, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_per_region (line 390, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_combined (line 426, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule rollup_tags (line 461, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_alignment (line 501, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_basecount (line 530, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_per_base (line 558, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_rollup (line 586, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_readspertag (line 614, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_variant_bases_from_report (line 643, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_rollup_results (line 671, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule final_report (line 704, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bad_loci (line 735, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule qc_plots (line 749, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule filter_base_report (line 776, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3510,16 +3544,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723506913.0 + "updated_at": 1723065291.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/recomb.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/octomom.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "A1um/mixed-experiment-workflow", + "description": "Significantly improved bam2bakR implementation", + "formatting": null, + "full_name": "isaacvock/fastq2EZbakR", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/recomb.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\", line 9, in \u003cmodule\u003e\n samples = pd.read_json(config[\"sample_sheet\"], orient=\"records\") # noqa: F821\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 791, in read_json\n json_reader = JsonReader(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 904, in __init__\n data = self._get_data_from_filepath(filepath_or_buffer)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 960, in _get_data_from_filepath\n raise FileNotFoundError(f\"File {filepath_or_buffer} does not exist\")\n\nFileNotFoundError: File ./config/workflow.json does not exist\n\n", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3527,40 +3561,47 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723498924.0 + "updated_at": 1723042307.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n fair_bowtie2_mapping:\n bowtie2:\n # Optional parameters for bowtie2-build\n build: \"\"\n # Optional parameters for bowtie2-align\n align: \"\"\n sambamba:\n # Optional parameters for sambamba view\n view: \"--format \u0027bam\u0027 --filter \u0027mapping_quality \u0026gt;= 30 and not (unmapped or mate_is_unmapped)\u0027 \"\n # Optional parameters for sambamba markdup\n markdup: \"--remove-duplicates\"\n picard:\n # Mapping QC optional parameters\n metrics: \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Optional path to downstream fastq file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/samples.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe following columns are optional and are used to avoid downloading genomes:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efasta\u003c/code\u003e: Path to the reference genome sequence (FASTA formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efasta_index\u003c/code\u003e: Path to the reference genome sequence index (FAI formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebowtie2_dna_index\u003c/code\u003e: Path to the main directory containing reference index\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release,fasta,fasta_index,bowtie2_index\nhomo_sapiens,GRCh38,110,/path/to/sequence.fasta,/path/to/sequence.fasta.fai,/path/to/bowtie2_sequence/\nmus_musculus,GRCm38,99,,,\nmus_musculus,GRCm39,110,,,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", "data_format": 2, - "description": "Testing snakemake", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpljqu2g_d/workflow/rules/map2db.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpljqu2g_d/workflow/rules/concatenate_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpljqu2g_d/workflow/Snakefile\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "cmc-aau/snakemake_project_template", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpljqu2g_d/workflow/rules/concatenate_fastq.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule concatenate_fastq (line 9, /tmp/tmpljqu2g_d/workflow/rules/concatenate_fastq.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "description": "Align reads over a reference genome, filter aligned-reads, and mark duplicates", + "formatting": null, + "full_name": "tdayris/fair_bowtie2_mapping", + "latest_release": "4.2.0", + "linting": null, "mandatory_flags": { - "desc": null, + "desc": "Align ungapped reads to the genome with Bowtie2", "flags": null }, "report": true, "software_stack_deployment": { "conda": true, "singularity": false, - "singularity+conda": false + "singularity+conda": true }, "standardized": true, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1723456148.0 + "topics": [ + "bowtie2", + "multiqc", + "sambamba", + "snakemake", + "snakemake-workflow", + "snakemake-wrappers" + ], + "updated_at": 1723031584.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/04_left_trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/06_select_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/13_snpEff.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/11_annovar_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_fa_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_bam_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/12_annovar_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/07_filter_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/08_filter_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/05_select_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/02_combine_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_picard_dict.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/01_haplotype_caller.smk\": Formatted content is different from original\n[INFO] 17 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "DariaKIL/WES_Cardiomyopathy", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmp8pqah41f/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "jorgenriseth/gMRI2FEM", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpebsle3xl/Snakefile:\n * Absolute path \"/mnt/IMBG-NGS-Analysys/StudentsWork\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/reference\" in line 18:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/hs37d5\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 31:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 32:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 38:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 40:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_fa_index.smk\" in line 50:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_bam_index.smk\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_picard_dict.smk\" in line 52:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/01_haplotype_caller.smk\" in line 53:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/02_combine_gvcf.smk\" in line 54:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/03_genotype_gvcf.smk\" in line 55:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/04_left_trim.smk\" in line 56:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/05_select_snp.smk\" in line 57:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/06_select_indel.smk\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/07_filter_snp.smk\" in line 59:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/08_filter_indel.smk\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/09_bcftools_norm_snp.smk\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/10_bcftools_norm_ind.smk\" in line 62:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/11_annovar_snp.smk\" in line 63:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/12_annovar_ind.smk\" in line 64:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/13_snpEff.smk\" in line 65:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 18:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 33:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 38:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 40:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 42:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 50:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 51:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 52:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 53:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 55:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 59:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 60:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 61:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 62:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 64:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_fa_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_bam_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_picard_dict.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/04_left_trim.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/05_select_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/06_select_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/07_filter_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/08_filter_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/11_annovar_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/12_annovar_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/13_snpEff.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule fa_index (line 5, /tmp/tmpebsle3xl/rules/00_fa_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bam_index (line 5, /tmp/tmpebsle3xl/rules/00_bam_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule picard_dict (line 5, /tmp/tmpebsle3xl/rules/00_picard_dict.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule haplotype_caller (line 5, /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_gvcf (line 5, /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genotype_gvcf (line 5, /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable ref from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule left_trim (line 5, /tmp/tmpebsle3xl/rules/04_left_trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_snp (line 5, /tmp/tmpebsle3xl/rules/05_select_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_indel (line 5, /tmp/tmpebsle3xl/rules/06_select_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule snp_filter (line 5, /tmp/tmpebsle3xl/rules/07_filter_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule indel_filter (line 5, /tmp/tmpebsle3xl/rules/08_filter_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_snp (line 5, /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_ind (line 5, /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule anovar_snp (line 5, /tmp/tmpebsle3xl/rules/11_annovar_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule anovar_ind (line 5, /tmp/tmpebsle3xl/rules/12_annovar_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule snpEff_snp (line 5, /tmp/tmpebsle3xl/rules/13_snpEff.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "/tmp/tmp8pqah41f/Snakefile:32: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n SUBJECTS=config[\"subjects\"]\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp8pqah41f/Snakefile\", line 14, in \u003cmodule\u003e\n + \"conda activate $CONDA_ENV_NAME \u0026\u0026 \"\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027use_singularity\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3568,16 +3609,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723453165.0 + "updated_at": 1723028673.0 }, { "config_readme": null, "data_format": 2, "description": null, "formatting": null, - "full_name": "bjoernellens1/pypsa-eur-project", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplwxdek0h/Snakefile\", line 13, in \u003cmodule\u003e\n from scripts._helpers import path_provider, copy_default_files, get_scenarios, get_rdir\n\n File \"/tmp/tmplwxdek0h/scripts/_helpers.py\", line 23, in \u003cmodule\u003e\n from tqdm import tqdm\n\nModuleNotFoundError: No module named \u0027tqdm\u0027\n\n", + "full_name": "3d-omics/mt_quant", + "latest_release": "v1.1.0", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3585,192 +3626,154 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723384817.0 + "updated_at": 1722957411.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow to map PacBio HiFi reads back to an assembly and check for misassemblies at specific regions via NucFlag.", + "description": "Repository containing bioinformatic code for macro-scale host transcriptomic data processing", "formatting": null, - "full_name": "logsdon-lab/Snakemake-NucFlag", - "latest_release": "v0.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/rules/common.smk\", line 37, in get_sample_assemblies_and_reads\n for sm in config[\"samples\"]:\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027samples\u0027\n\n", + "full_name": "3d-omics/ht_quant", + "latest_release": "v0.2.0", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723304315.0 + "subscribers_count": 1, + "topics": [ + "pipeline" + ], + "updated_at": 1722954021.0 }, { "config_readme": null, "data_format": 2, - "description": "next step after recount-pump in the monorail pipeline", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj8zjb2fc/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "langmead-lab/recount-unify", + "description": "Build genome references for RENEE", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpgvxd59l0/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "CCBR/build-renee-refs", "latest_release": null, - "linting": "need to pass values for \u0027gene_rejoin_mapping\u0027 and \u0027exon_rejoin_mapping\u0027 and \u0027sample_ids_file\u0027 and \u0027num_samples\u0027 for the initial rejoining part of the pipeline!\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpgvxd59l0/Snakefile\", line 7, in \u003cmodule\u003e\n raise ValueError(\"NCBI_API_KEY environment variable is not set.\\n\"\n\nValueError: NCBI_API_KEY environment variable is not set.\n\tPlease obtain an API Key for your NCBI account and set it to the environment variable NCBI_API_KEY.\n\thttps://support.nlm.nih.gov/knowledgebase/article/KA-05317/en-us\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 5, + "subscribers_count": 3, "topics": [], - "updated_at": 1723235817.0 + "updated_at": 1722953693.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/demand.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/model.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/wind-and-solar.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/doc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/biofuels.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n[DEBUG] In file \"/tmp/tmp22brxynr/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/transmission.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/nuclear.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/hydro.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/shapes.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "calliope-project/euro-calliope-modular", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp24uq7059/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "FreilichLab/NetCom2_snakemake", "latest_release": null, - "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\n/tmp/tmp22brxynr/Snakefile:50: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \n/tmp/tmp22brxynr/Snakefile:114: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \"techs/supply/open-field-solar-and-wind-onshore.yaml\",\nLints for snakefile /tmp/tmp22brxynr/Snakefile:\n * Absolute path \"/\" if config[\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 89:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 100:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/biofuels.smk:\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/model.smk:\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/transmission.smk:\n * Path composition with \u0027+\u0027 in line 26:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule units (line 1, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule units_without_shape (line 29, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_potentials (line 9, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule potentials (line 40, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_capacity_factors_wind_and_solar (line 92, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule area_to_capacity_limits (line 123, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_onshore_wind_and_solar (line 161, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_eez (line 210, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eez (line 241, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule shared_coast (line 287, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_offshore (line 326, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_biofuel_potentials_and_costs (line 3, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule preprocess_biofuel_potentials_and_cost (line 34, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuels (line 73, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuel_tech_module (line 123, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_units (line 17, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_hydro_generation_data (line 69, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_pumped_hydro_data (line 102, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_runoff_data (line 135, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_basins_database (line 172, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_stations_database (line 205, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_basins_database (line 238, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_stations_database (line 269, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_basins (line 309, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_hydro_stations (line 345, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_m3 (line 382, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_mwh (line 417, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_hydro_capacities (line 457, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_capacity_factors_hydro (line 488, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule data_hydro (line 100, /tmp/tmp22brxynr/./rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_raw_load (line 4, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load_national (line 35, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load (line 71, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database_zipped (line 1, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database (line 32, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule nuclear_regional_capacity (line 60, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model_input_locations (line 1, /tmp/tmp22brxynr/./rules/model.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_entsoe_tyndp_zip (line 4, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule entsoe_tyndp_xlsx (line 35, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_entsoe_tyndp_tech_module (line 70, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_linked_neighbours_tech_module (line 110, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_with_location_specific_data (line 91, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_location_specific_data (line 134, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_specific_data (line 147, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule auxiliary_files (line 180, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model (line 213, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dag (line 290, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clean (line 311, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for rule Removal_pipeline (line 12, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule split_count_table_by_treatment (line 70, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule claculate_enzyme_diversity_score (line 108, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule enzyme_diversity (line 154, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule determine_diffenetial_abundance (line 174, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Community_knockouts_simulations (line 232, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param sim_log_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule prepare_pathway_compounds_for_visual (line 273, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule visualize_knockout_network (line 316, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_netcom2 (line 419, /tmp/tmp24uq7059/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 1, "topics": [], - "updated_at": 1723213764.0 + "updated_at": 1722948499.0 }, { "config_readme": null, "data_format": 2, - "description": "A Snakemake pipeline for copy number variant calling without normal tissue samples", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mutect2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mask_ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bowtie2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/bcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/umi_mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bwa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/qc_map.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": InvalidPython: Black error:\n```\nCannot parse: 54:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": \n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"shell\" at line 160 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"params\" at line 316 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/purecn.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/trimming_fastqc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "pedricolino/cnakepit", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpirza16q8/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "vari-bbc/methylation_array", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzqunecdj/workflow/Snakefile\", line 30, in \u003cmodule\u003e\n samples = read_sample(config[\u0027data\u0027][\u0027samples_in_directory\u0027])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027resources/data/sample_sheet.tsv\u0027\n\n", + "linting": "Lints for rule sesame_qc (line 30, /tmp/tmpirza16q8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Additionally specify a conda environment or container for each rule, environment modules are not enough:\n While environment modules allow to document and deploy the required\n software on a certain platform, they lock your workflow in there,\n disabling easy reproducibility on other machines that don\u0027t have exactly\n the same environment modules. Hence env modules (which might be beneficial\n in certain cluster environments), should always be complemented with\n equivalent conda environments.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param idat_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sesame_se (line 76, /tmp/tmpirza16q8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Additionally specify a conda environment or container for each rule, environment modules are not enough:\n While environment modules allow to document and deploy the required\n software on a certain platform, they lock your workflow in there,\n disabling easy reproducibility on other machines that don\u0027t have exactly\n the same environment modules. Hence env modules (which might be beneficial\n in certain cluster environments), should always be complemented with\n equivalent conda environments.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param idat_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule sesame_DM (line 128, /tmp/tmpirza16q8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Additionally specify a conda environment or container for each rule, environment modules are not enough:\n While environment modules allow to document and deploy the required\n software on a certain platform, they lock your workflow in there,\n disabling easy reproducibility on other machines that don\u0027t have exactly\n the same environment modules. Hence env modules (which might be beneficial\n in certain cluster environments), should always be complemented with\n equivalent conda environments.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bioinformatics", - "bwa", - "cna", - "cnv", - "cnvkit", - "conda", - "copynumbervariation", - "mutect2", - "panels", - "purecn", - "sequencing-data", - "snakemake", - "targeted-sequencing" - ], - "updated_at": 1723212951.0 + "subscribers_count": 2, + "topics": [], + "updated_at": 1722873728.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Snakemake workflow to call denovo dna variants on a RIL population", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9m5bzqwx/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Bioinflows-Bioversity-CIAT/denovo-dna-variant-calling", + "description": "Python-based workflow for reproducible and scalable minimal processing with the HCPPipelines.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpre8pf8x8/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "leon-k-martin/hcpython", "latest_release": null, - "linting": null, - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, + "linting": "/tmp/tmpre8pf8x8/hcpy/data/__init__.py:17: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n sep=\"\\s+\",\n/tmp/tmpre8pf8x8/hcpy/data/__init__.py:26: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n sep=\"\\s+\",\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpre8pf8x8/Snakefile\", line 64, in \u003cmodule\u003e\n f_dwi_res = join(rawdatadir, \"{subid}_{sequence}_{PEdir}_res.nii.gz\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n [Previous line repeated 2 more times]\n\n File \"\u003cfrozen os\u003e\", line 225, in makedirs\n\nPermissionError: [Errno 13] Permission denied: \u0027/Volumes\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1723209947.0 + "updated_at": 1722868351.0 }, { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral Configuration\u003c/h1\u003e\u003ca id=\"user-content-general-configuration\" class=\"anchor\" aria-label=\"Permalink: General Configuration\" href=\"#general-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eOutput folders\u003c/h2\u003e\u003ca id=\"user-content-output-folders\" class=\"anchor\" aria-label=\"Permalink: Output folders\" href=\"#output-folders\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBy default, this workflow stores the files obtained, parsed and aggregated into three different folders (\u003ccode\u003edownloaded/\u003c/code\u003e, \u003ccode\u003eparsed/\u003c/code\u003e \u003ccode\u003eaggregated/\u003c/code\u003e) in the working directory. This behavior can be changed with the entries \u003ccode\u003edownloaded_mriot_dir:\u003c/code\u003e, \u003ccode\u003eparsed_mriot_dir:\u003c/code\u003e and \u003ccode\u003eaggregated_mriot_dir:\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eFiles corresponding to a specific MRIOT will be stored in a subfolder of the corresponding name. For instance, Exiobase 3 (in ixi system) for year 1995 aggregated to 74 sectors will be stored under \u003ccode\u003eparsed/exiobase3_ixi/exiobase3_ixi_1995_74_sectors.pkl\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSector aggregation files\u003c/h2\u003e\u003ca id=\"user-content-sector-aggregation-files\" class=\"anchor\" aria-label=\"Permalink: Sector aggregation files\" href=\"#sector-aggregation-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow looks for aggregation files in the \u003ccode\u003eaggregation_csv_dir:\u003c/code\u003e (\u003ccode\u003econfig/aggregation_files\u003c/code\u003e) by default.\u003c/p\u003e\n\u003cp\u003eSome existing aggregation are included in the repository, and new ones can be added. If you think an aggregation file you designed would be a valuable contribution, don\u0027t hesitate to pull-request it !\u003c/p\u003e\n\u003cp\u003eThe folder structure follows the same as for outputs, for instance, the file used to aggregate Exiobase 3 to 74 sectors is looked under \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_74_sectors.csv\u003c/code\u003e\u003c/p\u003e\n\u003cp\u003eFiles should be in csv format, with a first column \u003ccode\u003esector\u003c/code\u003e with all the original sectors of the MRIOT, and \u003ccode\u003egroup\u003c/code\u003e and \u003ccode\u003ename\u003c/code\u003e columns with the new ID and names to map the original sectors too.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eCommon aggregation\u003c/h2\u003e\u003ca id=\"user-content-common-aggregation\" class=\"anchor\" aria-label=\"Permalink: Common aggregation\" href=\"#common-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAs an additional way to aggregate different MRIOTs into a common one, this workflow also embarks a \u003ccode\u003econfig/aggregation_files/sectors_common_aggreg.ods\u003c/code\u003e file for this purpose.\u003c/p\u003e\n\u003cp\u003eThe sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e of the file defines the sector to aggregate to via \u003ccode\u003egroup_id\u003c/code\u003e and \u003ccode\u003esector_name\u003c/code\u003e columns. The following sheets, \u003ccode\u003e\u0026lt;mriot_name\u0026gt;_to_common_aggreg\u003c/code\u003e, have \u003ccode\u003eoriginal sector\u003c/code\u003e, \u003ccode\u003eto_id\u003c/code\u003e and a \u003ccode\u003enew sector\u003c/code\u003e columns auto computed from \u003ccode\u003eto_id\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eAsking the workflow to build \u003ccode\u003eaggregated/icio2021/icio2021_2003_common_aggreg.pkl\u003c/code\u003e, for instance, will aggregate \u003ccode\u003eicio2021_2003_full.pkl\u003c/code\u003e to the sectors defined in the sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e based on the correspondence in \u003ccode\u003eicio2021_to_common_aggreg\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eDisclaimer: This work is still under progress and still requires to be streamlined.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eParameters aggregation\u003c/h2\u003e\u003ca id=\"user-content-parameters-aggregation\" class=\"anchor\" aria-label=\"Permalink: Parameters aggregation\" href=\"#parameters-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow also allows to build sector parameters files for the \u003ccode\u003eBoARIO\u003c/code\u003e model.\nWe provide a \u003ccode\u003econfig/mriot_params/exiobase3_ixi_full_sectors.csv\u003c/code\u003e \"master\" file that contains values we used with the model and this MRIOT, and from which similar files can be obtained for the other MRIOT, using \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_to_other_mrio_sectors.ods\u003c/code\u003e.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Pipelines to parse and aggregate MRIOT data for BoARIO", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/mrio_treatments.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/sectors_config.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "spjuhel/BoARIO-MRIOT-Tools", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4pp0e8xo/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Mason-Lab-Code/NanoSeq-snakemake", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpfciba8yw/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n from boario_tools.regex_patterns import (\n\nModuleNotFoundError: No module named \u0027boario_tools\u0027\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, + "linting": "Lints for rule fastqc (line 21, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule multiqc (line 66, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_tags (line 103, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bwa_index (line 140, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_mem (line 182, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_and_add_rc_mc_tags (line 238, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mark_dups (line 281, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_and_append_rb_tags (line 335, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule keep_random_read (line 384, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_analysis (line 433, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule check_contamination (line 607, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule estimate_efficiency (line 648, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule collate_efficiency (line 710, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule organise_outputs (line 749, /tmp/tmp4pp0e8xo/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], "report": false, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1723205425.0 + "updated_at": 1722844048.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s). ", - "formatting": null, - "full_name": "pmenzel/score-assemblies-MIT", - "latest_release": "v1.2", - "linting": null, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp7y71_ark/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "pruethemann/squeezemd", + "latest_release": null, + "linting": "WorkflowError:\nWorkflow defines configfile config/params.yml but it is not present or accessible (full checked path: /tmp/tmp7y71_ark/config/params.yml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "bacterial-genome-analysis", - "bioinformatics-pipeline", - "nanopore-sequencing", - "snakemake" - ], - "updated_at": 1723619591.0 + "topics": [], + "updated_at": 1722802918.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.", - "formatting": null, - "full_name": "pmenzel/ont-assembly-snake-MIT", - "latest_release": "v1.4", - "linting": "Lints for snakefile /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 28:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 67:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule filtlong (line 227, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMB (line 272, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongPC (line 318, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMBql (line 363, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule canu (line 918, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable target_genome_size from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "description": "Repository for varroa linkage mapping project", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp40tm3vxv/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "nurit-eliash/varroa-pedigree-study", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp40tm3vxv/Snakefile\", line 7, in \u003cmodule\u003e\n from scripts.split_fasta_regions import split_fasta\n\n File \"/tmp/tmp40tm3vxv/scripts/split_fasta_regions.py\", line 2, in \u003cmodule\u003e\n from Bio import SeqIO\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bacterial-genome-analysis", - "bioinformatics", - "bioinformatics-pipeline", - "nanopore-sequencing", - "snakemake", - "snakemake-workflow" - ], - "updated_at": 1723619513.0 + "subscribers_count": 2, + "topics": [], + "updated_at": 1722756095.0 }, { "config_readme": null, "data_format": 2, - "description": "A snakemake-based workflow for converting Illumina\u0027s bcl files to fastq files with the option of further downstream analysis (using FastQC, STAR+RSeQC, cutadapt) and encryption via gocryptfs", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": Keyword \"input\" at line 135 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": InvalidPython: Black error:\n```\nCannot parse: 143:4: log:\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 226 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"output\" at line 379 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/bcl2fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qcShort.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp690v5jwz/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:6: needs to be here for the snakemake workflow catalogue\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/Snakefile\": \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 95 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 114 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": NoParametersError: L170: In input definition.\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc_pe.smk\": Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "WestGermanGenomeCenter/bcl2fastq2_Pipeline", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppg6tzvci/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "hhshanto/RSEP", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmp690v5jwz/Snakefile, line 1:\ninvalid syntax:\nneeds to be here for the snakemake workflow catalogue\n\n", + "linting": "Lints for snakefile /tmp/tmppg6tzvci/Snakefile:\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 11:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule preprocess (line 14, /tmp/tmppg6tzvci/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PREPROCESS_SCRIPT from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3778,16 +3781,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723118553.0 + "updated_at": 1722714486.0 }, { "config_readme": null, "data_format": 2, - "description": "Mapping of RNAseq reads to sequences obtained from CryoEM in Toxoplasma gondii", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Keyword \"input\" at line 362 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "glaParaBio/cryoem-mitoribosome-rnaseq", + "description": null, + "formatting": null, + "full_name": "jayed87/rse-group-project", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdpo1e4ok/Snakefile\", line 7, in \u003cmodule\u003e\n TGMITO = os.path.basename(config[\u0027tgmito\u0027])\n ^^^^^^^^^^^^\n\nKeyError: \u0027tgmito\u0027\n\n", + "linting": "WorkflowError:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmphl7re638/config/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3795,16 +3798,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723114523.0 + "updated_at": 1722632537.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp81j129ms/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mdondrup/test", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/rules/climate.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/rules/platform.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp44shwf1b/workflow/Snakefile\": Keyword \"input\" at line 70 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp44shwf1b/workflow/Snakefile\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "simonmoulds/subseasonal-flood-prediction", "latest_release": null, - "linting": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp44shwf1b/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n import pyarrow\n\nModuleNotFoundError: No module named \u0027pyarrow\u0027\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -3819,16 +3822,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724322240.0 + "updated_at": 1722616971.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for mining Marchantia polymorpha DNA sequences for viruses. ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/megan_meganizer.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/fastq_gunzip.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/megan_export.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/megahit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/diamond.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/Snakefile\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "LanaVogrinec/snakemake-marchantia", - "latest_release": "v.1.0.0", - "linting": null, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmps72zl_h4/SamBryce-Smith-bulk_polyatail_reads-8dc3509/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "SamBryce-Smith/bulk_polyatail_reads", + "latest_release": "v0.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmps72zl_h4/SamBryce-Smith-bulk_polyatail_reads-8dc3509/Snakefile\", line 4, in \u003cmodule\u003e\n sample_tbl = pd.read_csv(config[\"sample_table\"])\n ^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027sample_table\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3836,16 +3839,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724320101.0 + "updated_at": 1722615397.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for bulk RNA sequencing with pytximport.", - "formatting": null, - "full_name": "complextissue/snakemake-bulk-rna-seq-workflow", - "latest_release": "Initial", - "linting": "WorkflowError:\nError validating row 0 of data frame.\nValidationError: 1 is not of type \u0027string\u0027\n\nFailed validating \u0027type\u0027 in schema[\u0027properties\u0027][\u0027sample_id\u0027]:\n {\u0027type\u0027: \u0027string\u0027, \u0027description\u0027: \u0027Unique identifier for the sample\u0027}\n\nOn instance[\u0027sample_id\u0027]:\n 1\n", + "description": "Code associated with \"Onset of infectiousness explains differences in transmissibility across Mycobacterium tuberculosis lineages\"", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/pre-processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/phylodynamics.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpfm4m6vvs/workflow/Snakefile\": Keyword \"input\" at line 49 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfm4m6vvs/workflow/rules/post-processing.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "EtthelWindels/snakemake-mtb-beast2", + "latest_release": null, + "linting": "RuleException in rule beast in file /tmp/tmpfm4m6vvs/workflow/rules/phylodynamics.smk, line 3:\nNot all output, log and benchmark files of rule beast contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file.\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -3853,74 +3856,104 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724319910.0 + "updated_at": 1722612479.0 }, { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eWorkflow config\u003c/h2\u003e\u003ca id=\"user-content-workflow-config\" class=\"anchor\" aria-label=\"Permalink: Workflow config\" href=\"#workflow-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires configuration by modification of \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\nFollow the explanations provided as comments in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample \u0026amp; unit config\u003c/h2\u003e\u003ca id=\"user-content-sample--unit-config\" class=\"anchor\" aria-label=\"Permalink: Sample \u0026amp; unit config\" href=\"#sample--unit-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration of samples and units is specified as tab-separated value (\u003ccode\u003e.tsv\u003c/code\u003e) files.\nEach \u003ccode\u003e.tsv\u003c/code\u003e requires specific columns (see below), but extra columns may be present (however, will not be used).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-samplestsv\" class=\"anchor\" aria-label=\"Permalink: samples.tsv\" href=\"#samplestsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the sample sheet is \u003ccode\u003econfig/samples.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e requires only one column named \u003ccode\u003esample\u003c/code\u003e, which contains the desired names of the samples.\nSample names must be unique, corresponding to a physical sample.\nBiological and technical replicates should be specified as separate samples.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-unitstsv\" class=\"anchor\" aria-label=\"Permalink: units.tsv\" href=\"#unitstsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the unit sheet is \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e requires four columns, named \u003ccode\u003esample\u003c/code\u003e, \u003ccode\u003eunit\u003c/code\u003e, \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e.\nEach row of the units sheet corresponds to a single sequencing unit.\nTherefore, for each sample specified in \u003ccode\u003esamples.tsv\u003c/code\u003e, one or more sequencing units should be present.\n\u003ccode\u003eunit\u003c/code\u003e values must be unique within each sample.\nA common example of an experiment with multiple sequencing units is a sample split across several runs/lanes.\u003c/p\u003e\n\u003cp\u003eFor each unit, the respective path to \u003ccode\u003eFASTQ\u003c/code\u003e files must be specified in the \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e columns.\nBoth columns must exist, however, the \u003ccode\u003efq2\u003c/code\u003e column may be left empty in the case of single-end sequencing experiments.\nThis is how one specifies whether single- or paired-end rules are run by the workflow.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Snakemake implementation of the GATK best-practices workflow for RNA-seq short variant discovery", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 12 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "baerlachlan/smk-rnaseq-gatk-variants", - "latest_release": "v1.0.3", - "linting": "Lints for rule genome_get (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule genome_index (line 26, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule genome_dict (line 53, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotation_get (line 80, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule star_index (line 105, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule known_variants_get (line 134, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule known_variants_index (line 164, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule gtf_to_bed (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/intervals.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bed_to_intervals (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/intervals.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_raw (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_trim (line 29, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_align (line 57, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_se (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_pe (line 30, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_md5 (line 64, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule align (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule align_md5 (line 31, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule assign_read_groups (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assign_read_groups_index (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assign_read_groups_md5 (line 50, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule group_umis_se (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule group_umis_pe (line 52, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule group_umis_md5 (line 105, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mark_duplicates (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/mark_duplicates.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mark_duplicates_umi (line 24, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/mark_duplicates.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mark_duplicates_md5 (line 52, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/mark_duplicates.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule split_n_cigar_reads (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/split_n_cigar_reads.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule split_n_cigar_reads_md5 (line 26, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/split_n_cigar_reads.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bqsr_firstpass (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/bqsr.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bqsr_apply (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/bqsr.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bqsr_apply_md5 (line 60, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/bqsr.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule variation_call (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_combine (line 36, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_genotype (line 62, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_select (line 88, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_filter (line 119, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_cleanup (line 157, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_gvcf_md5 (line 188, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule variation_vcf_md5 (line 217, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": null, + "description": "Hnld_Genetic_Diversity_Analysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpv567bg31/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "johnpatramanis/Hnld_Genetic_Diversity_Analysis", + "latest_release": null, + "linting": "Lints for rule Index_VCF_File (line 85, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_Protein_Coverage (line 107, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Isolate_Genes_From_Each_VCF_File (line 142, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_GenomeWide_PI_from_VCF (line 169, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_GenomeWide_heterozyg_from_VCF (line 195, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule RunVEP_on_Filtered_VCF_File (line 229, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Second_Round_of_Filtering_Output_Positions (line 269, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Prepare_for_second_filtering (line 305, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Filter_Again_Using_VEP_Variants (line 339, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_Genotypes (line 377, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule Get_Metric_From_Genotypes (line 413, /tmp/tmpv567bg31/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724293620.0 + "updated_at": 1722605198.0 }, { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eWorkflow config\u003c/h2\u003e\u003ca id=\"user-content-workflow-config\" class=\"anchor\" aria-label=\"Permalink: Workflow config\" href=\"#workflow-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires configuration by modification of \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\nFollow the explanations provided as comments in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample \u0026amp; unit config\u003c/h2\u003e\u003ca id=\"user-content-sample--unit-config\" class=\"anchor\" aria-label=\"Permalink: Sample \u0026amp; unit config\" href=\"#sample--unit-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration of samples and units is specified as tab-separated value (\u003ccode\u003e.tsv\u003c/code\u003e) files.\nEach \u003ccode\u003e.tsv\u003c/code\u003e requires specific columns (see below), but extra columns may be present (however, will not be used).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-samplestsv\" class=\"anchor\" aria-label=\"Permalink: samples.tsv\" href=\"#samplestsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the sample sheet is \u003ccode\u003econfig/samples.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e requires only one column named \u003ccode\u003esample\u003c/code\u003e, which contains the desired names of the samples.\nSample names must be unique, corresponding to a physical sample.\nBiological and technical replicates should be specified as separate samples.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-unitstsv\" class=\"anchor\" aria-label=\"Permalink: units.tsv\" href=\"#unitstsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the unit sheet is \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e requires four columns, named \u003ccode\u003esample\u003c/code\u003e, \u003ccode\u003eunit\u003c/code\u003e, \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e.\nEach row of the units sheet corresponds to a single sequencing unit.\nTherefore, for each sample specified in \u003ccode\u003esamples.tsv\u003c/code\u003e, one or more sequencing units should be present.\n\u003ccode\u003eunit\u003c/code\u003e values must be unique within each sample.\nA common example of an experiment with multiple sequencing units is a sample split across several runs/lanes.\u003c/p\u003e\n\u003cp\u003eFor each unit, the respective path to \u003ccode\u003eFASTQ\u003c/code\u003e files must be specified in the \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e columns.\nBoth columns must exist, however, the \u003ccode\u003efq2\u003c/code\u003e column may be left empty in the case of single-end sequencing experiments.\nThis is how one specifies whether single- or paired-end rules are run by the workflow.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for generating gene-level counts from RNA-seq data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 7 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "baerlachlan/smk-rnaseq-star-featurecounts", - "latest_release": "v1.1.2", - "linting": "Lints for rule genome_get (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotation_get (line 26, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule star_index (line 51, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_raw (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_trim (line 29, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_align (line 57, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_se (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_pe (line 30, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_md5 (line 64, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/merge.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_md5 (line 27, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/merge.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule align (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule align_md5 (line 31, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule count_s0 (line 2, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/count.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule count_s1 (line 37, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/count.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule count_s2 (line 72, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/count.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": null, + "description": "Generate single-cell reference dataset for deconvolution in Atlas", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp03uunm3o/Snakefile\": TokenError: (\u0027unexpected character after line continuation character\u0027, (102, 76))\n[INFO] In file \"/tmp/tmp03uunm3o/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "ebi-gene-expression-group/atlas-deconvolution-references", + "latest_release": null, + "linting": "TokenError:\n(\u0027unexpected character after line continuation character\u0027, (102, 76))\n", + "mandatory_flags": [], "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 5, + "topics": [], + "updated_at": 1722593796.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/PopulationStructure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/karyotype.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqrumwp_e/workflow/rules/utility.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "sanjaynagi/ag3-relatedness", + "latest_release": null, + "linting": "WorkflowError:\nFailed to open source file /tmp/tmpqrumwp_e/workflow/rules/ibd.smk\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/tmp/tmpqrumwp_e/workflow/rules/ibd.smk\u0027\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724291750.0 + "updated_at": 1722588226.0 }, { "config_readme": null, "data_format": 2, - "description": "Here be dragons.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/cohorts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/utility.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/site.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/gwss.smk\": NoParametersError: L61: In params definition.\n[INFO] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/gwss.smk\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/gwss.smk\": 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "anopheles-genomic-surveillance/selection-atlas", - "latest_release": "v0.0.1", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/Snakefile\", line 2, in \u003cmodule\u003e\n import geopandas as gpd\n\nModuleNotFoundError: No module named \u0027geopandas\u0027\n\n", + "description": "Lecture 1 of DSMS: Course Introduction", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp987lepvd/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp987lepvd/rules/renv.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "deer-marketing-lab/dsms-lecture-course-introduction", + "latest_release": null, + "linting": "Lints for rule build_html (line 16, /tmp/tmp987lepvd/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 46, /tmp/tmp987lepvd/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 89, /tmp/tmp987lepvd/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 22, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 34, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 46, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 58, /tmp/tmp987lepvd/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 0, "topics": [], - "updated_at": 1725379785.0 + "updated_at": 1722550844.0 }, { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "config_readme": null, "data_format": 2, - "description": "Tree sequence workflow", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmperkt4kl2/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "percyfal/tswf-smk", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/join_nest.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/generate_results_rds.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/process_actilife.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/reformat.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/resample.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpojqzbhhd/workflow/rules/download_process.smk\": Formatted content is different from original\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "lilykoff/step_algorithms", "latest_release": null, + "linting": "Lints for rule download_data (line 26, /tmp/tmpojqzbhhd/workflow/rules/download_process.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_data_nom (line 56, /tmp/tmpojqzbhhd/workflow/rules/download_process.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule resample (line 26, /tmp/tmpojqzbhhd/workflow/rules/resample.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule resample_nom (line 62, /tmp/tmpojqzbhhd/workflow/rules/resample.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule reformat (line 28, /tmp/tmpojqzbhhd/workflow/rules/reformat.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule reformat_nom (line 75, /tmp/tmpojqzbhhd/workflow/rules/reformat.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_actilife_results (line 30, /tmp/tmpojqzbhhd/workflow/rules/process_actilife.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule process_actilife_results_nom (line 77, /tmp/tmpojqzbhhd/workflow/rules/process_actilife.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_stepcount (line 33, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_algorithms (line 71, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_stepcount_nom (line 118, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fit_algorithms_nom (line 146, /tmp/tmpojqzbhhd/workflow/rules/fit_algorithms.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_results (line 32, /tmp/tmpojqzbhhd/workflow/rules/join_nest.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_results_nom (line 80, /tmp/tmpojqzbhhd/workflow/rules/join_nest.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_results_dfs (line 25, /tmp/tmpojqzbhhd/workflow/rules/generate_results_rds.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_results_dfs_nom (line 49, /tmp/tmpojqzbhhd/workflow/rules/generate_results_rds.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_acc_figures (line 25, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_step_figures (line 49, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_step_figures_nom (line 73, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_resamp_figures (line 96, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_resamp_figures_nom (line 118, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_speed_figures (line 141, /tmp/tmpojqzbhhd/workflow/rules/generate_figures.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 2, + "topics": [], + "updated_at": 1722540937.0 + }, + { + "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n # Optional parameters for FastQC\n fastqc: \"\"\n # Optional parameters for FastP\n fastp:\n # Optional command line adapters\n adapters: \"\"\n # Optional command line parameters\n extra: \"\"\n bowtie2:\n # Optional parameters for bowtie2-build\n build: \"\"\n # Optional parameters for bowtie2-align\n align: \"\"\n sambamba:\n # Optional parameters for sambamba view\n view: \"--format \u0027bam\u0027 --filter \u0027mapping_quality \u0026gt;= 30 and not (unmapped or mate_is_unmapped)\u0027 \"\n # Optional parameters for sambamba markdup\n markdup: \"--remove-duplicates --overflow-size 500000\"\n picard:\n # Mapping QC optional parameters\n metrics: \"\"\n # Optional parameters for samtools stats\n samtools: \"\"\n macs2:\n # Optional parameters for Macs2 Callpeaks\n callpeak: \"\"\n homer:\n # Optional parameters for Homer AnnotatePeaks\n annotatepeaks: \"-homer2\"\n deeptools:\n # Optional parameters for DeepTools bamCoverage\n bamcoverage: \"--ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4 --ignoreForNormalization X Y MT\"\n # Optional parameters for DeepTools plotCoverage\n plot_coverage: \"--skipZeros --ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4\"\n # Optional parameters for DeepTools plotFingerprint\n plot_fingerprint: \"--skipZeros --ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4\"\n # Optional parameters for DeepTools plotPCA\n plot_pca: \"--ntop 1000\"\n # Optional parameters for DeepTools plotEnrichment\n plot_enrichment: \"--ignoreDuplicates --minMappingQuality 30 --samFlagExclude 4 --smartLabels\"\n # Optional parameters for DeepTools plotCorrelations\n plot_correlation: \"--whatToPlot heatmap --corMethod spearman --skipZeros --plotNumbers --colorMap RdYlBu\"\n # Optional parameters for MultQC\n multiqc: \"--module deeptools --module macs2 --module picard --module fastqc --module fastp --module samtools --module bowtie2 --module sambamba --zip-data-dir --verbose --no-megaqc-upload --no-ansi --force\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003esample_id: Unique name of the sample\u003c/li\u003e\n\u003cli\u003eupstream_file: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003especies: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003ebuild: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003erelease: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003edownstream_file: Optional path to downstream fastq file\u003c/li\u003e\n\u003cli\u003einput: Sample id of the corresponding input signal\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release,input\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110,sac_a_input\nsac_a_input,data/reads/a.scerevisiaeI.1.fq,data/reads/a.scerevisiaeI.2.fq,saccharomyces_cerevisiae,R64-1-1,110,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", + "data_format": 2, + "description": "Snakemake workflow used to call peaks with Macs2", + "formatting": null, + "full_name": "tdayris/fair_macs2_calling", + "latest_release": "3.1.1", "linting": null, "mandatory_flags": { - "desc": null, - "flags": null + "desc": "Call peaks with Macs2 and annotate them with Homer", + "flags": "--profile ./profiles/" }, "report": true, "software_stack_deployment": { @@ -3931,85 +3964,123 @@ var data = "standardized": true, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1724259444.0 + "topics": [ + "bowtie2", + "homer", + "macs2", + "sambamba", + "snakemake", + "snakemake-workflow", + "snakemake-wrappers" + ], + "updated_at": 1722412389.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/bcftools.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\{\u0027\n[DEBUG] In file \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/filter_vcf.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "hydra-genetics/filtering", - "latest_release": "v1.0.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/common.smk\", line 10, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "description": "A machine learning project for the ML Seminar 2024 at the TU Dortmund (faculty of physics). A convolutional neural network is employed to classify bird species by audio recordings of their calls. ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5jb699qy/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "lukas-bert/CNN-based-Bird-Audio-Classification", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmp5jb699qy/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 9:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 40:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 49:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule download_dataset (line 6, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable path_storage from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable dataset_name from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule get_spectrograms (line 28, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_audio_features (line 52, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule train_model (line 78, /tmp/tmp5jb699qy/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 2, "topics": [], - "updated_at": 1724242954.0 + "updated_at": 1722376796.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpio56hnnd/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "srinzema/viralfind", + "description": "A Snakemake workflow for Chandra data reduction", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/extract_spectra.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/project_psf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_exposure_flux.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/reproject_events.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_spectral_weights.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/bin_events.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/fit_spectra.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/chandra_repro.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/simulate_psf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/post_process_psf.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/download_chandra_obsid.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/find_and_copy_asolfile.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_exposure.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyhxsfesf/workflow/rules/compute_background_simple.smk\": Formatted content is different from original\n[INFO] 15 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "adonath/snakemake-workflow-chandra", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpio56hnnd/Snakefile, line 516:\ninvalid syntax:\n\tshell ( , bench_record=bench_record, bench_iteration=bench_iteration\n\n", + "linting": "/tmp/tmpyhxsfesf/workflow/Snakefile:602: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n include: \"rules/chandra_repro.smk\"\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpyhxsfesf/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n from astropy import units as u\n\nModuleNotFoundError: No module named \u0027astropy\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724230991.0 + "subscribers_count": 3, + "topics": [ + "chandra", + "ciao", + "data-reduction", + "snakemake", + "pylira" + ], + "updated_at": 1722373096.0 }, { "config_readme": null, "data_format": 2, - "description": "Analysis of a multi-mutant, barcoded influenza H3 library in the A/HongKong/45/2019 background.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp46xl89ss/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "dms-vep/flu_h3_hk19_dms", - "latest_release": null, - "linting": "WorkflowError:\nFailed to open source file /tmp/tmp46xl89ss/dms-vep-pipeline/pipeline.smk\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/tmp/tmp46xl89ss/dms-vep-pipeline/pipeline.smk\u0027\n", + "description": null, + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/variables.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/alleles.smk\": Keyword \"shell\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/alleles.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/input.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/read_orientation.smk\": Keyword \"shell\" at line 80 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/read_orientation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 64 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 144 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"input\" at line 180 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 194 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/rules/repeat_region_spanning.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "kilpert/FGF14_analyses", + "latest_release": "v1.0.0", + "linting": "/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile:131: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n \n/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile:132: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n ## include #############################################################################################################\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpn3rr62b0/kilpert-FGF14_analyses-d0f98a9/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n from Bio.Seq import Seq\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 4, + "subscribers_count": 1, "topics": [], - "updated_at": 1724175546.0 + "updated_at": 1722336879.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6f7oe7t3/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6f7oe7t3/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6f7oe7t3/workflow/rules/picard.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ikarls/simple_pipeline", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6f7oe7t3/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6f7oe7t3/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "description": "Workspace for adding DFTs to Psi4 and testing them against ACCDB", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n[ERROR] In file \"/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile\": EmptyContextError: L164: rule has no keywords attached to it.\n[INFO] In file \"/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "UBCC3/adding-psi4-functionals", + "latest_release": "1", + "linting": "/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:34: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n basis=\u0027[-\\w]+\u0027,\n/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:35: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n restriction=\u0027RHF|UHF\u0027,\n/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:36: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n \n/tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/Snakefile:146: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n energy = re.findall(regexp, qcengine_out.read())\nWorkflowError:\nWorkflow defines configfile config.yaml but it is not present or accessible (full checked path: /tmp/tmpqmo1mdln/UBCC3-adding-psi4-functionals-2848851/config.yaml).\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1724152053.0 + "updated_at": 1723760466.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": "Calling and plotting of differentially methylated regions between two or more biological samples in BAM format", + "formatting": null, + "full_name": "koesterlab/rossi-ips-dmr", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpulo4ybao/workflow/Snakefile\", line 26, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpulo4ybao/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n samples = read_sample_tsv(sample_tsv_path)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/tmp/tmpulo4ybao/workflow/rules/common.smk\", line 7, in read_sample_tsv\n with open(sample_tsv_path, \"r\") as file:\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/projects/koesterlab/rossi-ips-dmr/config/sample.tsv\u0027\n\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 0, + "topics": [], + "updated_at": 1723738252.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp7sa742oj/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "LET19/snakemake-template", + "formatting": null, + "full_name": "Addimator/compare_meth", "latest_release": null, - "linting": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpn552y9ih/workflow/Snakefile\", line 26, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpn552y9ih/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n samples = read_sample_tsv(sample_tsv_path)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/tmp/tmpn552y9ih/workflow/rules/common.smk\", line 7, in read_sample_tsv\n with open(sample_tsv_path, \"r\") as file:\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/projects/koesterlab/benchmark-methylation/data_analysis_jochen/compare_meth/config/sample.tsv\u0027\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -4024,135 +4095,159 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724118252.0 + "updated_at": 1723727758.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp9p9mnt6s/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 183:7: params:\n```\n\n[INFO] In file \"/tmp/tmp9p9mnt6s/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "ebp-nor/GenomeAnnotation", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9p9mnt6s/workflow/Snakefile\", line 51, in \u003cmodule\u003e\n expand(\"galba/busco_galba_{lineage}\", lineage=config[\"busco_lineage\"]),\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027prefix\u0027\n\n", + "description": "Snakemake workflow to analyse hematological malignancies in whole genome data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/mutectcaller_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/fix_af.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/peddy_create_ped.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/export.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/dux4_rearrangements.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/manta_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/sample_order_multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/gatk_cnv_denoise_read_counts_by_sex.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/html_output.smk\": Formatted content is different from original\n[INFO] 13 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "clinical-genomics-uppsala/fluffy_hematology_wgs", + "latest_release": "v1.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\", line 12, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1724071470.0 + "updated_at": 1723713011.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp49jsbt49/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "scarlatti-nz/MEIHAWAI", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp95qzm81x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MindTheGap-ERC/Triangle_workflow", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp49jsbt49/Snakefile:\n * Absolute path \"/plots/initial_land_use.tif\" in line 25:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/agents_25.arrow\" in line 31:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/plots/initial_land_use.tif\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{grid_cell}/complete.txt\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/agents_25.arrow\" in line 45:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{grid_cell}/complete.txt\" in line 54:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 25:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 31:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 45:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule cleanup (line 25, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule plots (line 41, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable verbosePlots from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule join (line 63, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule main (line 88, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable data_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "linting": "WorkflowError:\nNo storage provider found for query irods://nluu12p/home/research-test-christine/triangle/{param_file}.mat. Either install the required storage plugin or check your query. Also consider to explicitly specify the storage provider to get a more informative error message.\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, + "subscribers_count": 4, + "topics": [], + "updated_at": 1723661311.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptaafhdwz/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "SveTho/bcl2fastq2_workflow", + "latest_release": null, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724018701.0 + "updated_at": 1723630209.0 }, { "config_readme": null, "data_format": 2, - "description": "Repository to generate the input data files used for the MEIHAWAI model", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp75b8fk3c/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "scarlatti-nz/MEIHAWAI-data", + "description": "PacBio Jasmine pipeline, penalized regression, and DMR identification", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpup7dp332/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "aliciasillers/Preliminary-CpG-Data-Analysis", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp75b8fk3c/Snakefile\", line 6, in \u003cmodule\u003e\n output_directory = config[\"output_dir\"]\n ~~~~~~^^^^^^^^^^^^^^^\n\nKeyError: \u0027output_dir\u0027\n\n", + "linting": "Lints for rule pbmm2 (line 18, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cpgtools (line 44, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1724018619.0 + "updated_at": 1723591308.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/rules/assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpytc_unr4/workflow/Snakefile\": SyntaxError: L42: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/rules/analysis.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zeyak/rescue", + "description": "Deep mutational scanning of the MERS-CoV and PDF-2180 receptor-binding domains", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp2b6mul21/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 351)\n[INFO] In file \"/tmp/tmp2b6mul21/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "tstarrlab/MERS-PDF2180-RBD_DMS", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpytc_unr4/workflow/rules/assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc (line 1, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule meryl (line 67, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 100, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 136, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 167, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 198, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 2, /tmp/tmpytc_unr4/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 30, /tmp/tmpytc_unr4/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 58, /tmp/tmpytc_unr4/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cdhit (line 194, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "TabError in file \u003cstring\u003e, line 351:\ninconsistent use of tabs and spaces in indentation:\n \tconfig[\u0027codon_variant_table_file_MERS_rpk\u0027],\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1723982118.0 + "updated_at": 1723589726.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpr64def82/workflow/Snakefile\": SyntaxError: L42: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpr64def82/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpr64def82/workflow/rules/assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr64def82/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr64def82/workflow/rules/analysis.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zeyak/GenoDiploBasic_2", + "description": "Benchmark for the AI LLM integration project", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpmumhq60x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "xwiki-contrib/ai-llm-benchmark", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpr64def82/workflow/rules/assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc (line 1, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule meryl (line 67, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 100, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 136, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 167, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 198, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 2, /tmp/tmpr64def82/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 30, /tmp/tmpr64def82/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 58, /tmp/tmpr64def82/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cdhit (line 194, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Lints for rule download (line 47, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_french (line 64, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_german (line 91, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index (line 118, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule split (line 140, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule collect (line 167, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule eval_summary (line 202, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_text_generation (line 234, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_rag_qa (line 265, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_plots (line 300, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule report (line 333, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_model_outputs_report (line 370, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule calculate_average_power (line 403, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule archive (line 431, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 465, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TASKS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable SNAKEOUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable REPORTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_SUMMARIZATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_TEXT_GENERATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_QA_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 47, "topics": [], - "updated_at": 1723981093.0 + "updated_at": 1723575430.0 }, { "config_readme": null, "data_format": 2, - "description": "Overview of IMAP - Integrated Microbiome Analysis Pipelines", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpdr29dksq/workflow/Snakefile\": Keyword \"input\" at line 14 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdr29dksq/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "tmbuza/imap-project-overview", + "description": "WIP HIBF benchmarks", + "formatting": null, + "full_name": "seqan/hibf_benchmarks", "latest_release": null, - "linting": "Lints for rule generate_rulegraph (line 32, /tmp/tmpdr29dksq/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule project_tree (line 62, /tmp/tmpdr29dksq/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule snakemake_report (line 90, /tmp/tmpdr29dksq/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule render_bs4_book (line 107, /tmp/tmpdr29dksq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for rule plot_landingpage (line 42, /tmp/tmpjpma0sez/workflow/rules/plot.smk):\n * Param HTML_DIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 6, "topics": [], - "updated_at": 1723885717.0 + "updated_at": 1723547496.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake-ified Alignment for ONT Data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/sv_call.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/Snakefile\": Keyword \"input\" at line 17 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/qc_alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/cleanup.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/phasing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/alignment.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mgaleyuw/alignment_snake", - "latest_release": "0.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/sv_call.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/common.smk\", line 4, in \u003cmodule\u003e\n samples = pd.read_table(config[\"samples\"], sep=\"\\t\").set_index(\u0027SampleID\u0027)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027config/missingVariant_config.tsv\u0027\n\n", + "description": "Remove and Quantify Organism Spike Reads from Sequencing Data", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpkzm451zl/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mskcc-microbiome/spikequant", + "latest_release": null, + "linting": "/tmp/tmpkzm451zl/workflow/Snakefile:689: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n/tmp/tmpkzm451zl/workflow/Snakefile:715: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpkzm451zl/workflow/Snakefile\", line 19, in \u003cmodule\u003e\n #mapper = \"minimap2-sr\"\n ^^^^^^^^^^^^^^^^^\n\nAssertionError: spiketable is a required config argument!\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1723842992.0 + "updated_at": 1723506913.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/rules/analysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpp121nj2z/workflow/Snakefile\": SyntaxError: L42: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/rules/assembly.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zeyak/GenoDiploBasic", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/recomb.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/octomom.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "A1um/mixed-experiment-workflow", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpp121nj2z/workflow/rules/assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc (line 1, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule meryl (line 67, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 100, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 136, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 167, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 198, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 2, /tmp/tmpp121nj2z/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 30, /tmp/tmpp121nj2z/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 58, /tmp/tmpp121nj2z/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cdhit (line 194, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/recomb.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\", line 9, in \u003cmodule\u003e\n samples = pd.read_json(config[\"sample_sheet\"], orient=\"records\") # noqa: F821\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 791, in read_json\n json_reader = JsonReader(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 904, in __init__\n data = self._get_data_from_filepath(filepath_or_buffer)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 960, in _get_data_from_filepath\n raise FileNotFoundError(f\"File {filepath_or_buffer} does not exist\")\n\nFileNotFoundError: File ./config/workflow.json does not exist\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4160,16 +4255,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723814371.0 + "updated_at": 1723498924.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpn9mx7s4y/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "simonmoulds/india-crop-atlas", + "description": "Testing snakemake", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpljqu2g_d/workflow/rules/map2db.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpljqu2g_d/workflow/rules/concatenate_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpljqu2g_d/workflow/Snakefile\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "cmc-aau/snakemake_project_template", "latest_release": null, - "linting": null, + "linting": "Lints for snakefile /tmp/tmpljqu2g_d/workflow/rules/concatenate_fastq.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule concatenate_fastq (line 9, /tmp/tmpljqu2g_d/workflow/rules/concatenate_fastq.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": { "desc": null, "flags": null @@ -4184,16 +4279,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723811684.0 + "updated_at": 1723456148.0 }, { "config_readme": null, "data_format": 2, - "description": "Bash script and basic structure to install and run a snakemake workflow", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbwtkk4sn/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "jmoldon/run_snakemake", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/04_left_trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/06_select_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/13_snpEff.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/11_annovar_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_fa_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_bam_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/12_annovar_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/07_filter_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/08_filter_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/05_select_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/02_combine_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_picard_dict.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/01_haplotype_caller.smk\": Formatted content is different from original\n[INFO] 17 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "DariaKIL/WES_Cardiomyopathy", "latest_release": null, - "linting": "Lints for rule hello (line 12, /tmp/tmpbwtkk4sn/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Lints for snakefile /tmp/tmpebsle3xl/Snakefile:\n * Absolute path \"/mnt/IMBG-NGS-Analysys/StudentsWork\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/reference\" in line 18:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/hs37d5\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 31:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 32:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 38:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 40:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_fa_index.smk\" in line 50:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_bam_index.smk\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_picard_dict.smk\" in line 52:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/01_haplotype_caller.smk\" in line 53:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/02_combine_gvcf.smk\" in line 54:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/03_genotype_gvcf.smk\" in line 55:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/04_left_trim.smk\" in line 56:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/05_select_snp.smk\" in line 57:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/06_select_indel.smk\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/07_filter_snp.smk\" in line 59:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/08_filter_indel.smk\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/09_bcftools_norm_snp.smk\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/10_bcftools_norm_ind.smk\" in line 62:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/11_annovar_snp.smk\" in line 63:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/12_annovar_ind.smk\" in line 64:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/13_snpEff.smk\" in line 65:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 18:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 33:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 38:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 40:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 42:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 50:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 51:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 52:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 53:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 55:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 59:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 60:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 61:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 62:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 64:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_fa_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_bam_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_picard_dict.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/04_left_trim.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/05_select_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/06_select_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/07_filter_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/08_filter_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/11_annovar_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/12_annovar_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/13_snpEff.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule fa_index (line 5, /tmp/tmpebsle3xl/rules/00_fa_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bam_index (line 5, /tmp/tmpebsle3xl/rules/00_bam_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule picard_dict (line 5, /tmp/tmpebsle3xl/rules/00_picard_dict.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule haplotype_caller (line 5, /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_gvcf (line 5, /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genotype_gvcf (line 5, /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable ref from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule left_trim (line 5, /tmp/tmpebsle3xl/rules/04_left_trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_snp (line 5, /tmp/tmpebsle3xl/rules/05_select_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_indel (line 5, /tmp/tmpebsle3xl/rules/06_select_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule snp_filter (line 5, /tmp/tmpebsle3xl/rules/07_filter_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule indel_filter (line 5, /tmp/tmpebsle3xl/rules/08_filter_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_snp (line 5, /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_ind (line 5, /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule anovar_snp (line 5, /tmp/tmpebsle3xl/rules/11_annovar_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule anovar_ind (line 5, /tmp/tmpebsle3xl/rules/12_annovar_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule snpEff_snp (line 5, /tmp/tmpebsle3xl/rules/13_snpEff.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4201,16 +4296,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723801249.0 + "updated_at": 1723453165.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr25x1sr_/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "margotl9/SimmsLab_BradyrhizobiumPDS", + "formatting": null, + "full_name": "bjoernellens1/pypsa-eur-project", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpr25x1sr_/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 28:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk:\n * Path composition with \u0027+\u0027 in line 22:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 82:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 83:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 86:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 88:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule prodigal (line 22, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule defenseFinder (line 57, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir_sp is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule analyze_PDS (line 94, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule padloc_db (line 134, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule padloc (line 159, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplwxdek0h/Snakefile\", line 13, in \u003cmodule\u003e\n from scripts._helpers import path_provider, copy_default_files, get_scenarios, get_rdir\n\n File \"/tmp/tmplwxdek0h/scripts/_helpers.py\", line 23, in \u003cmodule\u003e\n from tqdm import tqdm\n\nModuleNotFoundError: No module named \u0027tqdm\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4218,152 +4313,192 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1723761676.0 + "updated_at": 1723384817.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake workflow for Whole Genome analysis with minION", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\#\u0027\n[DEBUG] In file \"/tmp/tmp_mylcuqi/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "lisosome/minION_snakemake", - "latest_release": null, - "linting": "/tmp/tmp_mylcuqi/Snakefile:70: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n \"ont-guppy-gpu/6.5.7\",\n/tmp/tmp_mylcuqi/Snakefile:86: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n export CUDA_VISIBLE_DEVICES=0\n/tmp/tmp_mylcuqi/Snakefile:203: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n resources:\n/tmp/tmp_mylcuqi/Snakefile:241: SyntaxWarning: invalid escape sequence \u0027\\;\u0027\n/tmp/tmp_mylcuqi/Snakefile:294: SyntaxWarning: invalid escape sequence \u0027\\#\u0027\n/tmp/tmp_mylcuqi/Snakefile:303: SyntaxWarning: invalid escape sequence \u0027\\#\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp_mylcuqi/Snakefile\", line 4, in \u003cmodule\u003e\n raw_data = config[\"paths\"][\"rawdata\"] # path of the folder containing the data transferred from the minION\n ^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027paths\u0027\n\n", + "description": "Snakemake workflow to map PacBio HiFi reads back to an assembly and check for misassemblies at specific regions via NucFlag.", + "formatting": null, + "full_name": "logsdon-lab/Snakemake-NucFlag", + "latest_release": "v0.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/rules/common.smk\", line 37, in get_sample_assemblies_and_reads\n for sm in config[\"samples\"]:\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027samples\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1724849960.0 + "updated_at": 1723304315.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/0.0_angsd_pipeline.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/2.0_downsampling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/1.0_landscape_modeling.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "zjnolen/polyommatini-landcover-diversity", - "latest_release": "v1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/Snakefile\", line 10, in \u003cmodule\u003e\n include: \"rules/0.0_angsd_pipeline.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpoig1vdtu/zjnolen-polyommatini-landcover-diversity-0416606/workflow/rules/0.0_angsd_pipeline.smk\", line 15, in \u003cmodule\u003e\n use rule all from angsd as angsd_all\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 2147, in decorate\n module.use_rules(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/modules.py\", line 104, in use_rules\n self.workflow.include(snakefile, overwrite_default_target=True)\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"https://:ghs_00HNn0swOh4G4RhVL3lARFbuHBWzOJ0b5Fl6@raw.githubusercontent.com/zjnolen/PopGLen/v0.2.0/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n from dataclasses import dataclass, field\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"https://:ghs_00HNn0swOh4G4RhVL3lARFbuHBWzOJ0b5Fl6@raw.githubusercontent.com/zjnolen/PopGLen/v0.2.0/workflow/rules/common.smk\", line 95, in \u003cmodule\u003e\n from snakemake.wrapper import wrapper\n ^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027reference\u0027\n\n", + "description": "next step after recount-pump in the monorail pipeline", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj8zjb2fc/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "langmead-lab/recount-unify", + "latest_release": null, + "linting": "need to pass values for \u0027gene_rejoin_mapping\u0027 and \u0027exon_rejoin_mapping\u0027 and \u0027sample_ids_file\u0027 and \u0027num_samples\u0027 for the initial rejoining part of the pipeline!\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 5, "topics": [], - "updated_at": 1724838425.0 + "updated_at": 1723235817.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 64 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 144 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"input\" at line 180 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Keyword \"shell\" at line 194 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/repeat_region_spanning.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/variables.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/input.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile\": \n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/read_orientation.smk\": Keyword \"shell\" at line 80 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/read_orientation.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/alleles.smk\": Keyword \"shell\" at line 32 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/rules/alleles.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "kilpert/FAME3_analyses", - "latest_release": "v0.2", - "linting": "/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile:189: SyntaxWarning: invalid escape sequence \u0027\\w\u0027\n \n/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile:190: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n \nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdyce992t/kilpert-FAME3_analyses-cfe7be8/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n from Bio.Seq import Seq\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/demand.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/model.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/wind-and-solar.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/doc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/biofuels.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n[DEBUG] In file \"/tmp/tmp22brxynr/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/transmission.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/nuclear.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/hydro.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/shapes.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "calliope-project/euro-calliope-modular", + "latest_release": null, + "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\n/tmp/tmp22brxynr/Snakefile:50: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \n/tmp/tmp22brxynr/Snakefile:114: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \"techs/supply/open-field-solar-and-wind-onshore.yaml\",\nLints for snakefile /tmp/tmp22brxynr/Snakefile:\n * Absolute path \"/\" if config[\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 89:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 100:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/biofuels.smk:\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/model.smk:\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/transmission.smk:\n * Path composition with \u0027+\u0027 in line 26:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule units (line 1, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule units_without_shape (line 29, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_potentials (line 9, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule potentials (line 40, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_capacity_factors_wind_and_solar (line 92, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule area_to_capacity_limits (line 123, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_onshore_wind_and_solar (line 161, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_eez (line 210, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eez (line 241, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule shared_coast (line 287, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_offshore (line 326, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_biofuel_potentials_and_costs (line 3, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule preprocess_biofuel_potentials_and_cost (line 34, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuels (line 73, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuel_tech_module (line 123, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_units (line 17, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_hydro_generation_data (line 69, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_pumped_hydro_data (line 102, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_runoff_data (line 135, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_basins_database (line 172, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_stations_database (line 205, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_basins_database (line 238, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_stations_database (line 269, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_basins (line 309, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_hydro_stations (line 345, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_m3 (line 382, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_mwh (line 417, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_hydro_capacities (line 457, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_capacity_factors_hydro (line 488, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule data_hydro (line 100, /tmp/tmp22brxynr/./rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_raw_load (line 4, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load_national (line 35, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load (line 71, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database_zipped (line 1, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database (line 32, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule nuclear_regional_capacity (line 60, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model_input_locations (line 1, /tmp/tmp22brxynr/./rules/model.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_entsoe_tyndp_zip (line 4, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule entsoe_tyndp_xlsx (line 35, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_entsoe_tyndp_tech_module (line 70, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_linked_neighbours_tech_module (line 110, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_with_location_specific_data (line 91, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_location_specific_data (line 134, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_specific_data (line 147, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule auxiliary_files (line 180, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model (line 213, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dag (line 290, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clean (line 311, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 3, "topics": [], - "updated_at": 1724832178.0 + "updated_at": 1723213764.0 }, { "config_readme": null, "data_format": 2, - "description": "Workflow for massive analysis of internet images", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[WARNING] In file \"/tmp/tmp63i3npu6/Snakefile\": Keyword \"input\" at line 46 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp63i3npu6/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "eamonnbell-dur/maoii-workflow", + "description": "A Snakemake pipeline for copy number variant calling without normal tissue samples", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mutect2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mask_ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bowtie2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/bcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/umi_mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bwa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/qc_map.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": InvalidPython: Black error:\n```\nCannot parse: 54:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": \n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"shell\" at line 160 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"params\" at line 316 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/purecn.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/trimming_fastqc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "pedricolino/cnakepit", "latest_release": null, - "linting": "/tmp/tmp63i3npu6/Snakefile:6: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n regionid=\"\\d+\"\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp63i3npu6/Snakefile\", line 3, in \u003cmodule\u003e\n HTTP = HTTPRemoteProvider()\n ^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/remote/__init__.py\", line 8, in __init__\n raise NotImplementedError(\n\nNotImplementedError: Remote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzqunecdj/workflow/Snakefile\", line 30, in \u003cmodule\u003e\n samples = read_sample(config[\u0027data\u0027][\u0027samples_in_directory\u0027])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027resources/data/sample_sheet.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724827560.0 + "subscribers_count": 1, + "topics": [ + "bioinformatics", + "bwa", + "cna", + "cnv", + "cnvkit", + "conda", + "copynumbervariation", + "mutect2", + "panels", + "purecn", + "sequencing-data", + "snakemake", + "targeted-sequencing" + ], + "updated_at": 1723212951.0 }, { - "config_readme": null, + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "Dataprocessing project for converting the FAST-GBS pipeline to a snakemake pipeline.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpngi0u1el/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Kyreria/Dataprocessing_FAST-GBS", + "description": "Snakemake workflow to call denovo dna variants on a RIL population", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9m5bzqwx/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Bioinflows-Bioversity-CIAT/denovo-dna-variant-calling", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpngi0u1el/workflow/Snakefile\", line 38, in \u003cmodule\u003e\n include: \"Rules/Trimming.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpngi0u1el/workflow/Rules/Fasta.smk\", line 26, in \u003cmodule\u003e\n message:\n \n\n File \"/tmp/tmpngi0u1el/workflow/Rules/Fasta.smk\", line 14, in get_new_demultiplex_file_names\n return [f\"{data_dir}/demultiplexed/{sample}_R{read}.fastq\" for read in [1,2] for sample in get_sample_names_from_barcodes()]\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/tmp/tmpngi0u1el/workflow/Snakefile\", line 30, in get_sample_names_from_barcodes\n split_line = line.strip().split(\" \")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/students/2023-2024/Thema11/dhaandrikman_snakemake/data/barcodes/barcodes.txt\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 0, "topics": [], - "updated_at": 1724810573.0 + "updated_at": 1723209947.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral Configuration\u003c/h1\u003e\u003ca id=\"user-content-general-configuration\" class=\"anchor\" aria-label=\"Permalink: General Configuration\" href=\"#general-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eOutput folders\u003c/h2\u003e\u003ca id=\"user-content-output-folders\" class=\"anchor\" aria-label=\"Permalink: Output folders\" href=\"#output-folders\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBy default, this workflow stores the files obtained, parsed and aggregated into three different folders (\u003ccode\u003edownloaded/\u003c/code\u003e, \u003ccode\u003eparsed/\u003c/code\u003e \u003ccode\u003eaggregated/\u003c/code\u003e) in the working directory. This behavior can be changed with the entries \u003ccode\u003edownloaded_mriot_dir:\u003c/code\u003e, \u003ccode\u003eparsed_mriot_dir:\u003c/code\u003e and \u003ccode\u003eaggregated_mriot_dir:\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eFiles corresponding to a specific MRIOT will be stored in a subfolder of the corresponding name. For instance, Exiobase 3 (in ixi system) for year 1995 aggregated to 74 sectors will be stored under \u003ccode\u003eparsed/exiobase3_ixi/exiobase3_ixi_1995_74_sectors.pkl\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSector aggregation files\u003c/h2\u003e\u003ca id=\"user-content-sector-aggregation-files\" class=\"anchor\" aria-label=\"Permalink: Sector aggregation files\" href=\"#sector-aggregation-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow looks for aggregation files in the \u003ccode\u003eaggregation_csv_dir:\u003c/code\u003e (\u003ccode\u003econfig/aggregation_files\u003c/code\u003e) by default.\u003c/p\u003e\n\u003cp\u003eSome existing aggregation are included in the repository, and new ones can be added. If you think an aggregation file you designed would be a valuable contribution, don\u0027t hesitate to pull-request it !\u003c/p\u003e\n\u003cp\u003eThe folder structure follows the same as for outputs, for instance, the file used to aggregate Exiobase 3 to 74 sectors is looked under \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_74_sectors.csv\u003c/code\u003e\u003c/p\u003e\n\u003cp\u003eFiles should be in csv format, with a first column \u003ccode\u003esector\u003c/code\u003e with all the original sectors of the MRIOT, and \u003ccode\u003egroup\u003c/code\u003e and \u003ccode\u003ename\u003c/code\u003e columns with the new ID and names to map the original sectors too.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eCommon aggregation\u003c/h2\u003e\u003ca id=\"user-content-common-aggregation\" class=\"anchor\" aria-label=\"Permalink: Common aggregation\" href=\"#common-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAs an additional way to aggregate different MRIOTs into a common one, this workflow also embarks a \u003ccode\u003econfig/aggregation_files/sectors_common_aggreg.ods\u003c/code\u003e file for this purpose.\u003c/p\u003e\n\u003cp\u003eThe sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e of the file defines the sector to aggregate to via \u003ccode\u003egroup_id\u003c/code\u003e and \u003ccode\u003esector_name\u003c/code\u003e columns. The following sheets, \u003ccode\u003e\u0026lt;mriot_name\u0026gt;_to_common_aggreg\u003c/code\u003e, have \u003ccode\u003eoriginal sector\u003c/code\u003e, \u003ccode\u003eto_id\u003c/code\u003e and a \u003ccode\u003enew sector\u003c/code\u003e columns auto computed from \u003ccode\u003eto_id\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eAsking the workflow to build \u003ccode\u003eaggregated/icio2021/icio2021_2003_common_aggreg.pkl\u003c/code\u003e, for instance, will aggregate \u003ccode\u003eicio2021_2003_full.pkl\u003c/code\u003e to the sectors defined in the sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e based on the correspondence in \u003ccode\u003eicio2021_to_common_aggreg\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eDisclaimer: This work is still under progress and still requires to be streamlined.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eParameters aggregation\u003c/h2\u003e\u003ca id=\"user-content-parameters-aggregation\" class=\"anchor\" aria-label=\"Permalink: Parameters aggregation\" href=\"#parameters-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow also allows to build sector parameters files for the \u003ccode\u003eBoARIO\u003c/code\u003e model.\nWe provide a \u003ccode\u003econfig/mriot_params/exiobase3_ixi_full_sectors.csv\u003c/code\u003e \"master\" file that contains values we used with the model and this MRIOT, and from which similar files can be obtained for the other MRIOT, using \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_to_other_mrio_sectors.ods\u003c/code\u003e.\u003c/p\u003e\n", "data_format": 2, - "description": "Materials for organization data dictionary", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpks5nstct/CT-Data-Haven-dictionary-build-5905514/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 10:6: conda:\n```\n\n[INFO] In file \"/tmp/tmpks5nstct/CT-Data-Haven-dictionary-build-5905514/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "CT-Data-Haven/dictionary-build", - "latest_release": "v0.2.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpks5nstct/CT-Data-Haven-dictionary-build-5905514/Snakefile\", line 1, in \u003cmodule\u003e\n from dotenv import load_dotenv\n\nModuleNotFoundError: No module named \u0027dotenv\u0027\n\n", - "mandatory_flags": [], + "description": "Pipelines to parse and aggregate MRIOT data for BoARIO", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/mrio_treatments.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/sectors_config.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "spjuhel/BoARIO-MRIOT-Tools", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpfciba8yw/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n from boario_tools.regex_patterns import (\n\nModuleNotFoundError: No module named \u0027boario_tools\u0027\n\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, "report": false, - "software_stack_deployment": null, - "standardized": false, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 3, + "subscribers_count": 1, "topics": [], - "updated_at": 1724802397.0 + "updated_at": 1723205425.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9xzo805v/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "DariaKIL/Glioblastoma_mutations", - "latest_release": null, - "linting": "Lints for rule split_vcf (line 33, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fix_GERP_notation (line 58, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule to_tsv_main (line 83, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule to_vcf_VEP (line 108, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule header_to_main (line 133, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule header_to_VEP (line 158, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_tsv (line 182, /tmp/tmp9xzo805v/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "description": "Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s). ", + "formatting": null, + "full_name": "pmenzel/score-assemblies-MIT", + "latest_release": "v1.2", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1724798308.0 + "topics": [ + "bacterial-genome-analysis", + "bioinformatics-pipeline", + "nanopore-sequencing", + "snakemake" + ], + "updated_at": 1723619591.0 }, { "config_readme": null, "data_format": 2, - "description": "Pipeline to analyze DNA sequencing data with legacy compatibility for the Pool lab\u0027s Drosophila Genome Nexus data.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/fas1k.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpnvu0aj6j/Snakefile\": EmptyContextError: L364: rule has no keywords attached to it.\n[DEBUG] In file \"/tmp/tmpnvu0aj6j/Snakefile\": \n[ERROR] In file \"/tmp/tmpnvu0aj6j/rules/genome_indexing.smk\": EmptyContextError: L2: rule has no keywords attached to it.\n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/genome_indexing.smk\": \n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpnvu0aj6j/rules/qc.smk\": Formatted content is different from original\n[INFO] 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "JamieCFreeman/DGN_compatible", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpnvu0aj6j/Snakefile:\n * Absolute path \"/round1/alt_ref/\u0027, wildcards.sample, \" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/round1/alt_ref/\u0027, wildcards.sample, \" in line 49:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/opt/bioscript/stampy/stampy.py\" in line 191:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpnvu0aj6j/rules/genome_indexing.smk:\n * Absolute path \"/opt/bioscript/stampy/stampy.py\" in line 59:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpnvu0aj6j/rules/fas1k.smk:\n * Absolute path \"/home/jamie/FAS1K_utils\" in line 75:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 3:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule calc_fas1k_het (line 1, /tmp/tmpnvu0aj6j/rules/stats.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule multiqc (line 33, /tmp/tmpnvu0aj6j/rules/qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule round1_index_ok (line 2, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule round2_index_ok (line 28, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all_round2_index_ok (line 54, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_index (line 76, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ref_fai (line 97, /tmp/tmpnvu0aj6j/rules/genome_indexing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prep_indel_shift (line 1, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule run_indel_shift (line 28, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fas (line 66, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule indel_mask_bed (line 106, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule add_fas_header (line 143, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule mask_around_indels (line 167, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule wrap_fas1k (line 196, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mv_fas1k (line 223, /tmp/tmpnvu0aj6j/rules/fas1k.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule test (line 163, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_aln_1 (line 187, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_aln_2 (line 218, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_sampe (line 249, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule aln_flagstat (line 278, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bwa_mem (line 298, /tmp/tmpnvu0aj6j/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule flagstat (line 333, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sam2bam (line 390, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule stampy_flagstat (line 411, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule qfilter_bam (line 432, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_bam (line 454, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mark_dups (line 479, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule add_RG (line 516, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule dup_bam_bai (line 541, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gz_vcf (line 715, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_vcf (line 785, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tgz_alt_ref (line 941, /tmp/tmpnvu0aj6j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "description": "Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.", + "formatting": null, + "full_name": "pmenzel/ont-assembly-snake-MIT", + "latest_release": "v1.4", + "linting": "Lints for snakefile /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 28:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 67:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule filtlong (line 227, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMB (line 272, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongPC (line 318, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMBql (line 363, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule canu (line 918, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable target_genome_size from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, "subscribers_count": 1, - "topics": [], - "updated_at": 1724797409.0 + "topics": [ + "bacterial-genome-analysis", + "bioinformatics", + "bioinformatics-pipeline", + "nanopore-sequencing", + "snakemake", + "snakemake-workflow" + ], + "updated_at": 1723619513.0 }, { "config_readme": null, "data_format": 2, - "description": "Repository for my Advanced dataprocessing school project. A pipeline made with snakemake", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/reference_files.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/fasta.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/feature_counts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/visualization.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsatfeeb4/workflow/rules/alignment.smk\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "SibrenReekers/Snakemake", + "description": "A snakemake-based workflow for converting Illumina\u0027s bcl files to fastq files with the option of further downstream analysis (using FastQC, STAR+RSeQC, cutadapt) and encryption via gocryptfs", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": Keyword \"input\" at line 135 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": InvalidPython: Black error:\n```\nCannot parse: 143:4: log:\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 226 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"output\" at line 379 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/bcl2fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qcShort.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp690v5jwz/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:6: needs to be here for the snakemake workflow catalogue\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/Snakefile\": \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 95 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 114 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": NoParametersError: L170: In input definition.\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc_pe.smk\": Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "WestGermanGenomeCenter/bcl2fastq2_Pipeline", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpsatfeeb4/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n include: \"rules/alignment.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpsatfeeb4/workflow/rules/fasta.smk\", line 56, in \u003cmodule\u003e\n\nKeyError: \u0027mem_mb\u0027\n\n", + "linting": "SyntaxError in file /tmp/tmp690v5jwz/Snakefile, line 1:\ninvalid syntax:\nneeds to be here for the snakemake workflow catalogue\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4371,16 +4506,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724790650.0 + "updated_at": 1723118553.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": null, - "full_name": "tauqeerrumaney/RSE_2", + "description": "Mapping of RNAseq reads to sequences obtained from CryoEM in Toxoplasma gondii", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Keyword \"input\" at line 362 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "glaParaBio/cryoem-mitoribosome-rnaseq", "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmp3p9pjll8/config/config.yaml).\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdpo1e4ok/Snakefile\", line 7, in \u003cmodule\u003e\n TGMITO = os.path.basename(config[\u0027tgmito\u0027])\n ^^^^^^^^^^^^\n\nKeyError: \u0027tgmito\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4388,33 +4523,40 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724776328.0 + "updated_at": 1723114523.0 }, { - "config_readme": null, + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "Lecture on Advertising Attribution Models for Digital and Social Media Strategies at Tilburg U", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpu7x0jbic/rules/renv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpu7x0jbic/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "deer-marketing-lab/dsms-lecture-ad-attribution", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp81j129ms/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mdondrup/test", "latest_release": null, - "linting": "Lints for rule build_html (line 16, /tmp/tmpu7x0jbic/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule build_pdf (line 46, /tmp/tmpu7x0jbic/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable run_r from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable log_all from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule clean (line 89, /tmp/tmpu7x0jbic/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_install (line 10, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable runR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule renv_consent (line 22, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_init (line 34, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_snap (line 46, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule renv_restore (line 58, /tmp/tmpu7x0jbic/rules/renv.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 0, + "subscribers_count": 1, "topics": [], - "updated_at": 1724775155.0 + "updated_at": 1724322240.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk\": Keyword \"output\" at line 6 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpr17ecgo_/workflow/Snakefile\": SyntaxError: L26: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/4_sequence_level.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zeyak/barkhanus", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw\" in line 3:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/{process}/nanopore.fastq.gz\" in line 16:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases/{db}\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 74:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 101:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 133:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc_before_trimming (line 1, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule setup_nr_db (line 66, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule blastn (line 87, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule makeblastdb (line 122, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outname is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule blastn_EST (line 160, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule meryl (line 224, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 257, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 293, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 324, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 355, /tmp/tmpr17ecgo_/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 1, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule glimmerhmm_ (line 29, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule augustus (line 85, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule V3_busco_geneset (line 118, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_transcriptome (line 152, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_plot (line 187, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 214, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 259, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eggnogmapper (line 294, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule interproscan (line 328, /tmp/tmpr17ecgo_/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpr17ecgo_/workflow/rules/3_genome_level.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "description": "Snakemake workflow for mining Marchantia polymorpha DNA sequences for viruses. ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/megan_meganizer.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/fastq_gunzip.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/megan_export.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/megahit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/rules/diamond.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpo4h407o4/LanaVogrinec-snakemake-marchantia-5357222/workflow/Snakefile\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "LanaVogrinec/snakemake-marchantia", + "latest_release": "v.1.0.0", + "linting": null, "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4422,92 +4564,93 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724769923.0 + "updated_at": 1724320101.0 }, { "config_readme": null, "data_format": 2, - "description": "Simulation of long-read sequencing data with structural variations in human genomes", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpauhlru5d/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "villena-francis/visor-simulations", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpauhlru5d/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule generate_bed (line 102, /tmp/tmpauhlru5d/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable GENOME_FILE from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule visor_laser_tumour (line 153, /tmp/tmpauhlru5d/workflow/Snakefile):\n * Shell command directly uses variable COVERAGE from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule visor_laser_normal (line 228, /tmp/tmpauhlru5d/workflow/Snakefile):\n * Shell command directly uses variable COVERAGE from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "description": "Snakemake workflow for bulk RNA sequencing with pytximport.", + "formatting": null, + "full_name": "complextissue/snakemake-bulk-rna-seq-workflow", + "latest_release": "Initial", + "linting": "WorkflowError:\nError validating row 0 of data frame.\nValidationError: 1 is not of type \u0027string\u0027\n\nFailed validating \u0027type\u0027 in schema[\u0027properties\u0027][\u0027sample_id\u0027]:\n {\u0027type\u0027: \u0027string\u0027, \u0027description\u0027: \u0027Unique identifier for the sample\u0027}\n\nOn instance[\u0027sample_id\u0027]:\n 1\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1724765812.0 + "updated_at": 1724319910.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eWorkflow config\u003c/h2\u003e\u003ca id=\"user-content-workflow-config\" class=\"anchor\" aria-label=\"Permalink: Workflow config\" href=\"#workflow-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires configuration by modification of \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\nFollow the explanations provided as comments in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample \u0026amp; unit config\u003c/h2\u003e\u003ca id=\"user-content-sample--unit-config\" class=\"anchor\" aria-label=\"Permalink: Sample \u0026amp; unit config\" href=\"#sample--unit-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration of samples and units is specified as tab-separated value (\u003ccode\u003e.tsv\u003c/code\u003e) files.\nEach \u003ccode\u003e.tsv\u003c/code\u003e requires specific columns (see below), but extra columns may be present (however, will not be used).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-samplestsv\" class=\"anchor\" aria-label=\"Permalink: samples.tsv\" href=\"#samplestsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the sample sheet is \u003ccode\u003econfig/samples.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e requires only one column named \u003ccode\u003esample\u003c/code\u003e, which contains the desired names of the samples.\nSample names must be unique, corresponding to a physical sample.\nBiological and technical replicates should be specified as separate samples.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-unitstsv\" class=\"anchor\" aria-label=\"Permalink: units.tsv\" href=\"#unitstsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the unit sheet is \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e requires four columns, named \u003ccode\u003esample\u003c/code\u003e, \u003ccode\u003eunit\u003c/code\u003e, \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e.\nEach row of the units sheet corresponds to a single sequencing unit.\nTherefore, for each sample specified in \u003ccode\u003esamples.tsv\u003c/code\u003e, one or more sequencing units should be present.\n\u003ccode\u003eunit\u003c/code\u003e values must be unique within each sample.\nA common example of an experiment with multiple sequencing units is a sample split across several runs/lanes.\u003c/p\u003e\n\u003cp\u003eFor each unit, the respective path to \u003ccode\u003eFASTQ\u003c/code\u003e files must be specified in the \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e columns.\nBoth columns must exist, however, the \u003ccode\u003efq2\u003c/code\u003e column may be left empty in the case of single-end sequencing experiments.\nThis is how one specifies whether single- or paired-end rules are run by the workflow.\u003c/p\u003e\n", "data_format": 2, - "description": "\ud83e\uddec\ud83d\udd0dCNV analysis and outcome prediction in Ultra-High-Risk and First Episode Psychosis individuals \ud83e\ude7a\ud83e\udde0", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiod6la1s/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zhukovanadezhda/cnv-psychosis", - "latest_release": null, - "linting": "Lints for rule all (line 5, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule produce_pathogenic_file (line 13, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule execute_notebooks (line 25, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_classifycnv (line 42, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_cnv_database (line 55, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_brain_database (line 66, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_cytobands (line 75, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule annotate_vcf (line 86, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule map_to_cytobands (line 97, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule define_brain_genes (line 109, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule identify_rare_cnv (line 121, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule filter_cnv (line 133, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_initial_stat_per_individual (line 144, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_genetic_and_clinical (line 154, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule exclude_pathogenic (line 167, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_updated_stat_per_individual (line 178, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule final_merge_with_clinical (line 188, /tmp/tmpiod6la1s/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], + "description": "Snakemake implementation of the GATK best-practices workflow for RNA-seq short variant discovery", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 12 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "baerlachlan/smk-rnaseq-gatk-variants", + "latest_release": "v1.0.3", + "linting": "Lints for rule genome_get (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule genome_index (line 26, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule genome_dict (line 53, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotation_get (line 80, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule star_index (line 105, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule known_variants_get (line 134, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule known_variants_index (line 164, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule gtf_to_bed (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/intervals.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bed_to_intervals (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/intervals.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_raw (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_trim (line 29, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_align (line 57, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_se (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_pe (line 30, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_md5 (line 64, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule align (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule align_md5 (line 31, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule assign_read_groups (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assign_read_groups_index (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule assign_read_groups_md5 (line 50, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule group_umis_se (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule group_umis_pe (line 52, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule group_umis_md5 (line 105, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule mark_duplicates (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/mark_duplicates.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mark_duplicates_umi (line 24, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/mark_duplicates.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule mark_duplicates_md5 (line 52, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/mark_duplicates.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule split_n_cigar_reads (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/split_n_cigar_reads.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule split_n_cigar_reads_md5 (line 26, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/split_n_cigar_reads.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bqsr_firstpass (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/bqsr.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bqsr_apply (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/bqsr.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bqsr_apply_md5 (line 60, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/bqsr.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule variation_call (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_combine (line 36, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_genotype (line 62, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_select (line 88, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_filter (line 119, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_cleanup (line 157, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule variation_gvcf_md5 (line 188, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule variation_vcf_md5 (line 217, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/variation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": null, "report": false, - "software_stack_deployment": null, - "standardized": false, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, "stargazers_count": 0, "subscribers_count": 1, - "topics": [ - "cnv", - "cnv-analysis", - "outcome-prediction", - "psychosis", - "wgs" - ], - "updated_at": 1725813013.0 + "topics": [], + "updated_at": 1724293620.0 }, { - "config_readme": null, + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eWorkflow config\u003c/h2\u003e\u003ca id=\"user-content-workflow-config\" class=\"anchor\" aria-label=\"Permalink: Workflow config\" href=\"#workflow-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires configuration by modification of \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\nFollow the explanations provided as comments in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample \u0026amp; unit config\u003c/h2\u003e\u003ca id=\"user-content-sample--unit-config\" class=\"anchor\" aria-label=\"Permalink: Sample \u0026amp; unit config\" href=\"#sample--unit-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration of samples and units is specified as tab-separated value (\u003ccode\u003e.tsv\u003c/code\u003e) files.\nEach \u003ccode\u003e.tsv\u003c/code\u003e requires specific columns (see below), but extra columns may be present (however, will not be used).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-samplestsv\" class=\"anchor\" aria-label=\"Permalink: samples.tsv\" href=\"#samplestsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the sample sheet is \u003ccode\u003econfig/samples.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e requires only one column named \u003ccode\u003esample\u003c/code\u003e, which contains the desired names of the samples.\nSample names must be unique, corresponding to a physical sample.\nBiological and technical replicates should be specified as separate samples.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-unitstsv\" class=\"anchor\" aria-label=\"Permalink: units.tsv\" href=\"#unitstsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the unit sheet is \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e requires four columns, named \u003ccode\u003esample\u003c/code\u003e, \u003ccode\u003eunit\u003c/code\u003e, \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e.\nEach row of the units sheet corresponds to a single sequencing unit.\nTherefore, for each sample specified in \u003ccode\u003esamples.tsv\u003c/code\u003e, one or more sequencing units should be present.\n\u003ccode\u003eunit\u003c/code\u003e values must be unique within each sample.\nA common example of an experiment with multiple sequencing units is a sample split across several runs/lanes.\u003c/p\u003e\n\u003cp\u003eFor each unit, the respective path to \u003ccode\u003eFASTQ\u003c/code\u003e files must be specified in the \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e columns.\nBoth columns must exist, however, the \u003ccode\u003efq2\u003c/code\u003e column may be left empty in the case of single-end sequencing experiments.\nThis is how one specifies whether single- or paired-end rules are run by the workflow.\u003c/p\u003e\n", "data_format": 2, - "description": "A workflow to train a convolutional neural network with SLiM outputs", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/sweep_stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/extract_log_data.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/stratified_sampling.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp1re72tuf/workflow/rules/create_image.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 4)\n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/create_image.smk\": \n[WARNING] In file \"/tmp/tmp1re72tuf/workflow/rules/slim.smk\": Keyword \"output\" at line 102 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/slim.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp1re72tuf/workflow/Snakefile\": Keyword \"input\" at line 14 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1re72tuf/workflow/rules/fit_cnn.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "milesroberts-123/selection-demography-cnn", - "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", - "mandatory_flags": [], + "description": "Snakemake workflow for generating gene-level counts from RNA-seq data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 7 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "baerlachlan/smk-rnaseq-star-featurecounts", + "latest_release": "v1.1.2", + "linting": "Lints for rule genome_get (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule annotation_get (line 26, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule star_index (line 51, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/refs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_raw (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_trim (line 29, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastqc_align (line 57, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_se (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_pe (line 30, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule trim_md5 (line 64, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/merge.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_md5 (line 27, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/merge.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule align (line 1, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule align_md5 (line 31, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule count_s0 (line 2, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/count.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule count_s1 (line 37, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/count.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule count_s2 (line 72, /tmp/tmp5fho7a7j/baerlachlan-smk-rnaseq-star-featurecounts-8c11dc6/workflow/rules/count.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": null, "report": false, - "software_stack_deployment": null, - "standardized": false, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1724702227.0 + "updated_at": 1724291750.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpt_50h4ge/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 14)\n[INFO] In file \"/tmp/tmpt_50h4ge/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "cjfiscus/Kmer-it", - "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 14:\ninconsistent use of tabs and spaces in indentation:\n\t expand(\"results/cn_ests/{id}.txt\", id=all_ids)\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "description": "Here be dragons.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/cohorts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/utility.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/site.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/gwss.smk\": NoParametersError: L61: In params definition.\n[INFO] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/gwss.smk\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/rules/gwss.smk\": 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "anopheles-genomic-surveillance/selection-atlas", + "latest_release": "v0.0.1", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbdveq03h/anopheles-genomic-surveillance-selection-atlas-0589b15/workflow/Snakefile\", line 2, in \u003cmodule\u003e\n import geopandas as gpd\n\nModuleNotFoundError: No module named \u0027geopandas\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1724697796.0 + "updated_at": 1725379785.0 }, { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003einput_dir\u003c/code\u003e: The input folder is expected to contain a subfolder for each sampleID/barcode, then all fastq files in each subfolder are concatenated and the folder name is used as sample ID downstream. This is usually the \"fastq_pass\" folder from nanopore sequencing and basecalling output\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eoutput_dir\u003c/code\u003e: Output directory with the final results\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003etmp_dir\u003c/code\u003e: Directory for temporary files\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003elog_dir\u003c/code\u003e: Directory for log files for all rules\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003edb_fasta\u003c/code\u003e: Database for minimap2 in fasta file format. Each sequence header must only contain an ID matching the taxonomy file below, nothing else.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003edb_tax\u003c/code\u003e: 2-column TSV file with corresponding taxonomy for each sequence in the above fasta file. The first column is for the sequence IDs, the second a semi-colon separated taxonomy string.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eminalignlen\u003c/code\u003e: Minimum alignment length for the mapping. Any alignments shorter than this threshold will be filtered\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eminIDfrac\u003c/code\u003e: Minimum identity threshold of each mapping (value must be between \u003ccode\u003e0.0-1.0\u003c/code\u003e). Any alignments with an identity lower than this threshold will be filtered.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003efiltlong_args\u003c/code\u003e: Arguments passed on to the \u003ccode\u003efiltlong\u003c/code\u003e command for pre-filtering reads\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003emax_threads\u003c/code\u003e: Max number of threads for any rule\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eHave a look in the \u003ccode\u003e.test\u003c/code\u003e directory for example files.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eDatabase files\u003c/h2\u003e\u003ca id=\"user-content-database-files\" class=\"anchor\" aria-label=\"Permalink: Database files\" href=\"#database-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIf you want to use the SILVA database, you can use \u003ca href=\"https://github.com/KasperSkytte/bioscripts/blob/main/extract_qiimetax.R\"\u003ethis R script\u003c/a\u003e to create the two requires database files. For the MiDAS database the files can be downloaded directly from \u003ca href=\"https://midasfieldguide.org/guide/downloads\" rel=\"nofollow\"\u003edownload section\u003c/a\u003e on the website.\u003c/p\u003e\n", + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, - "description": "Snakemake workflow to process 16S nanopore amplicon sequences (of any length) and produce an abundance table including taxonomy", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/05-mapping_overview.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/04-map2db.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/03-checksum_fq_headers.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/02-qfilter.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/01-cat_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/rules/06-abund_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/Snakefile\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "cmc-aau/nanopore_16Samp", - "latest_release": "v2.0.5", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp16k5p49e/cmc-aau-nanopore_16Samp-9978980/workflow/Snakefile\", line 17, in \u003cmodule\u003e\n ]\n \n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027nanopore_run_xyz123/fastq_pass\u0027\n\n", - "mandatory_flags": null, - "report": false, + "description": "Tree sequence workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmperkt4kl2/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "percyfal/tswf-smk", + "latest_release": null, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, "software_stack_deployment": { "conda": true, "singularity": false, @@ -4515,52 +4658,35 @@ var data = }, "standardized": true, "stargazers_count": 0, - "subscribers_count": 3, - "topics": [], - "updated_at": 1724682622.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "This pipeline uses repeatmasker, repeatmodeler, and the TREP database (https://trep-db.uzh.ch/) to annotate and mask transposable elements (TEs) in a wheat genome assembly.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj65z628m/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mattrwillman/wheat-te-annotation", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpj65z628m/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n GENOTYPE = config[\u0027GENOTYPE\u0027]\n ~~~~~~^^^^^^^^^^^^^\n\nKeyError: \u0027GENOTYPE\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724681984.0 + "updated_at": 1724259444.0 }, { "config_readme": null, "data_format": 2, - "description": "The repository contains scripts for wheat genome assembly of PacBio CCS reads.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpb_m2zqad/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mattrwillman/wheat-assembly", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpb_m2zqad/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n GENOTYPE = config[\u0027GENOTYPE\u0027]\n ~~~~~~^^^^^^^^^^^^^\n\nKeyError: \u0027GENOTYPE\u0027\n\n", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/bcftools.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\{\u0027\n[DEBUG] In file \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/filter_vcf.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "hydra-genetics/filtering", + "latest_release": "v1.0.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpc741xxpx/hydra-genetics-filtering-fb7cef2/workflow/rules/common.smk\", line 10, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 4, "topics": [], - "updated_at": 1724681636.0 + "updated_at": 1724242954.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Keyword \"input\" at line 34 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Keyword \"input\" at line 166 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Keyword \"output\" at line 424 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp2zf9x_5g/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "imallona/rhapsodist", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpio56hnnd/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "srinzema/viralfind", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp2zf9x_5g/Snakefile\", line 32, in \u003cmodule\u003e\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n\n File \"\u003cfrozen os\u003e\", line 225, in makedirs\n\nPermissionError: [Errno 13] Permission denied: \u0027/home/imallona\u0027\n\n", + "linting": "SyntaxError in file /tmp/tmpio56hnnd/Snakefile, line 516:\ninvalid syntax:\n\tshell ( , bench_record=bench_record, bench_iteration=bench_iteration\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4568,50 +4694,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724677895.0 + "updated_at": 1724230991.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmph1ig95i3/workflow/rules/qc.smk\": Keyword \"params\" at line 39 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmph1ig95i3/workflow/rules/qc.smk\": Keyword \"shell\" at line 48 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmph1ig95i3/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmph1ig95i3/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 19:0: \u003cline number missing in source\u003e\n```\n\n[INFO] In file \"/tmp/tmph1ig95i3/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmph1ig95i3/workflow/Snakefile\": 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "kilpert/minion_basecalling", + "description": "Analysis of a multi-mutant, barcoded influenza H3 library in the A/HongKong/45/2019 background.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp46xl89ss/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "dms-vep/flu_h3_hk19_dms", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmph1ig95i3/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmph1ig95i3/workflow/rules/qc.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule folder_nanoplot (line 54, /tmp/tmph1ig95i3/workflow/rules/qc.smk):\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule run_multiqc (line 109, /tmp/tmph1ig95i3/workflow/rules/qc.smk):\n * Param indir_pycoqc is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param indir_nanoplot is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule guppy_basecaller_available_workflows (line 255, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule guppy_basecaller (line 280, /tmp/tmph1ig95i3/workflow/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule guppy_basecaller_fastq (line 339, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastq_sequencing_summary (line 393, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastq (line 430, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastq_md5 (line 458, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastq_overview (line 492, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param indir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastq_flowcell_stats_figures (line 532, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule fastq_fastqc (line 566, /tmp/tmph1ig95i3/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "WorkflowError:\nFailed to open source file /tmp/tmp46xl89ss/dms-vep-pipeline/pipeline.smk\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/tmp/tmp46xl89ss/dms-vep-pipeline/pipeline.smk\u0027\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 4, "topics": [], - "updated_at": 1724676010.0 + "updated_at": 1724175546.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": null, - "full_name": "fneum/import-benefits", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6f7oe7t3/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6f7oe7t3/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6f7oe7t3/workflow/rules/picard.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ikarls/simple_pipeline", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp40w9k1ic/workflow/Snakefile\", line 5, in \u003cmodule\u003e\n shell:\n \n\nKeyError: \u0027remote\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6f7oe7t3/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6f7oe7t3/workflow/rules/common.smk\", line 15, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 1, "topics": [], - "updated_at": 1724665636.0 + "updated_at": 1724152053.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpyxqaszb4/workflow/Snakefile\": SyntaxError: \u003cfunction line_nb at 0x7fb2d3744b80\u003eNewline expected after keyword \u0027onstart\u0027\n[DEBUG] In file \"/tmp/tmpyxqaszb4/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpyxqaszb4/workflow/rules/setup.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mdondrup/admixture_workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp7sa742oj/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "LET19/snakemake-template", "latest_release": null, - "linting": "SyntaxError in file /tmp/tmpyxqaszb4/workflow/Snakefile, line 24:\ninvalid syntax:\n print (\"The workflow will re-try these jobs up to 5 times\")\n\n", + "linting": null, "mandatory_flags": { "desc": null, "flags": null @@ -4626,16 +4752,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724596081.0 + "updated_at": 1724118252.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": null, - "full_name": "Pierre-Alexandre35/weather_pipeline", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp9p9mnt6s/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 183:7: params:\n```\n\n[INFO] In file \"/tmp/tmp9p9mnt6s/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "ebp-nor/GenomeAnnotation", "latest_release": null, - "linting": "Lints for rule get_weather (line 1, /tmp/tmpm_lavqm5/workflow/rules/get_weather.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9p9mnt6s/workflow/Snakefile\", line 51, in \u003cmodule\u003e\n expand(\"galba/busco_galba_{lineage}\", lineage=config[\"busco_lineage\"]),\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027prefix\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4643,16 +4769,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724528043.0 + "updated_at": 1724071470.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp5ju0r58g/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_short-read-assembly", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp49jsbt49/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "scarlatti-nz/MEIHAWAI", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5ju0r58g/workflow/Snakefile\", line 14, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \"short-read-assembly\")\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "linting": "Lints for snakefile /tmp/tmp49jsbt49/Snakefile:\n * Absolute path \"/plots/initial_land_use.tif\" in line 25:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/agents_25.arrow\" in line 31:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/plots/initial_land_use.tif\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{grid_cell}/complete.txt\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/agents_25.arrow\" in line 45:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/{grid_cell}/complete.txt\" in line 54:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 25:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 31:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 45:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule cleanup (line 25, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule plots (line 41, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable verbosePlots from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule join (line 63, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule main (line 88, /tmp/tmp49jsbt49/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable data_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable output_dir from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable run_id from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4660,33 +4786,33 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724522800.0 + "updated_at": 1724018701.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmpfuhf1bjf/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_gene-catalog", + "description": "Repository to generate the input data files used for the MEIHAWAI model", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp75b8fk3c/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "scarlatti-nz/MEIHAWAI-data", "latest_release": null, - "linting": "/tmp/tmpfuhf1bjf/workflow/Snakefile:339: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n/tmp/tmpfuhf1bjf/workflow/Snakefile:349: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpfuhf1bjf/workflow/Snakefile\", line 12, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027gene_catalog\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp75b8fk3c/Snakefile\", line 6, in \u003cmodule\u003e\n output_directory = config[\"output_dir\"]\n ~~~~~~^^^^^^^^^^^^^^^\n\nKeyError: \u0027output_dir\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 2, + "subscribers_count": 0, "topics": [], - "updated_at": 1724521396.0 + "updated_at": 1724018619.0 }, { "config_readme": null, "data_format": 2, - "description": "example snakemake workflow for the 2024 SAGC workflow workshop", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/rules/report.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/rules/preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpddufb8g3/workflow/Snakefile\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "beardymcjohnface/snakemake-example-workflow-2024", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/rules/assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpytc_unr4/workflow/Snakefile\": SyntaxError: L42: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpytc_unr4/workflow/rules/analysis.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zeyak/rescue", "latest_release": null, - "linting": "Lints for rule minimap (line 3, /tmp/tmpddufb8g3/workflow/rules/mapping.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_alignment (line 51, /tmp/tmpddufb8g3/workflow/rules/mapping.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule fastp (line 3, /tmp/tmpddufb8g3/workflow/rules/preprocessing.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule flagstat (line 3, /tmp/tmpddufb8g3/workflow/rules/report.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule multiqc (line 30, /tmp/tmpddufb8g3/workflow/rules/report.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param qcdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": "Lints for snakefile /tmp/tmpytc_unr4/workflow/rules/assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc (line 1, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule meryl (line 67, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 100, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 136, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 167, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 198, /tmp/tmpytc_unr4/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 2, /tmp/tmpytc_unr4/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 30, /tmp/tmpytc_unr4/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 58, /tmp/tmpytc_unr4/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cdhit (line 194, /tmp/tmpytc_unr4/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4694,16 +4820,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724480463.0 + "updated_at": 1723982118.0 }, { "config_readme": null, "data_format": 2, - "description": "Snakemake port of https://github.com/fedorrik/HumAS-HMMER_for_AnVIL/tree/main.", - "formatting": null, - "full_name": "logsdon-lab/Snakemake-HumAS-HMMER", + "description": null, + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpr64def82/workflow/Snakefile\": SyntaxError: L42: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpr64def82/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpr64def82/workflow/rules/assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr64def82/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr64def82/workflow/rules/analysis.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zeyak/GenoDiploBasic_2", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp5hgnrheo/workflow/Snakefile\", line 27, in \u003cmodule\u003e\n hmm=config[\"model\"],\n ^\n\nKeyError: \u0027input_dir\u0027\n\n", + "linting": "Lints for snakefile /tmp/tmpr64def82/workflow/rules/assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc (line 1, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule meryl (line 67, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 100, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 136, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 167, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 198, /tmp/tmpr64def82/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 2, /tmp/tmpr64def82/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 30, /tmp/tmpr64def82/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 58, /tmp/tmpr64def82/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cdhit (line 194, /tmp/tmpr64def82/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4711,16 +4837,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724473258.0 + "updated_at": 1723981093.0 }, { "config_readme": null, "data_format": 2, - "description": "Pipeline for Somatic Variant Calling with WES and WGS data", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmppkvj6rza/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 10)\n[DEBUG] In file \"/tmp/tmppkvj6rza/Snakefile\": \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/pon.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmppkvj6rza/rules/preprocessing.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "JeBinLEE/ngs-pipeline", + "description": "Overview of IMAP - Integrated Microbiome Analysis Pipelines", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpdr29dksq/workflow/Snakefile\": Keyword \"input\" at line 14 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdr29dksq/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "tmbuza/imap-project-overview", "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 10:\ninconsistent use of tabs and spaces in indentation:\n\t\"qc/depths.csv\",\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "linting": "Lints for rule generate_rulegraph (line 32, /tmp/tmpdr29dksq/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule project_tree (line 62, /tmp/tmpdr29dksq/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule snakemake_report (line 90, /tmp/tmpdr29dksq/workflow/Snakefile):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule render_bs4_book (line 107, /tmp/tmpdr29dksq/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4728,74 +4854,50 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724431394.0 + "updated_at": 1723885717.0 }, { "config_readme": null, "data_format": 2, - "description": "A snakemake workflow to produce mode-resolved INS intensities in incoherent approximation", - "formatting": null, - "full_name": "ajjackson/abins-mode-intensities", - "latest_release": null, - "linting": "Lints for rule get_all_intensities (line 21, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule get_reference (line 61, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule write_modes (line 101, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule write_highlights (line 135, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule bin_and_broaden (line 169, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_modes (line 204, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_reference (line 238, /tmp/tmpzvwoy4om/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "description": "Snakemake-ified Alignment for ONT Data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/sv_call.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/Snakefile\": Keyword \"input\" at line 17 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/qc_alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/cleanup.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/phasing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/alignment.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mgaleyuw/alignment_snake", + "latest_release": "0.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/sv_call.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpyn42poo_/mgaleyuw-alignment_snake-3c6684a/workflow/rules/common.smk\", line 4, in \u003cmodule\u003e\n samples = pd.read_table(config[\"samples\"], sep=\"\\t\").set_index(\u0027SampleID\u0027)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027config/missingVariant_config.tsv\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 1, + "subscribers_count": 2, "topics": [], - "updated_at": 1724427780.0 + "updated_at": 1723842992.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/rules/ncbi_blast.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 8 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "vdclab/sORTholog", - "latest_release": "0.6.2", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/Snakefile\", line 85, in \u003cmodule\u003e\n include: \"rules/hmmer.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzf7mwqq8/vdclab-sORTholog-6ba30c1/workflow/rules/common.smk\", line 245, in \u003cmodule\u003e\n seed_table = pd.read_table(seed_file, dtype=seed_dtypes)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1405, in read_table\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027path/to/seeds.tsv\u0027\n\n", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/rules/analysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/rules/annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpp121nj2z/workflow/Snakefile\": SyntaxError: L42: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmpp121nj2z/workflow/rules/assembly.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zeyak/GenoDiploBasic", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmpp121nj2z/workflow/rules/assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc (line 1, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule meryl (line 67, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 100, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 136, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 167, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 198, /tmp/tmpp121nj2z/workflow/rules/assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 2, /tmp/tmpp121nj2z/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 30, /tmp/tmpp121nj2z/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp (line 58, /tmp/tmpp121nj2z/workflow/rules/annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_database_repeatmodeler (line 2, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmodeler (line 40, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_name is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule repeatmasker (line 74, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan (line 105, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule tRNAscan_cov (line 137, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule barrnap (line 168, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cdhit (line 194, /tmp/tmpp121nj2z/workflow/rules/analysis.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 0, - "subscribers_count": 3, - "topics": [], - "updated_at": 1724425769.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpcysasrw2/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "alzel/refseq_pipeline", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpcysasrw2/workflow/Snakefile:\n * Absolute path \"/\" + genome + f\" in line 21:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data\" in line 109:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data\" in line 129:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Deprecated singularity directive used for container definition in line 110.:\n Use the container directive instead (it is agnostic of the underlying\n container runtime).\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_genomic (line 78, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download_gff (line 105, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule gunzip (line 131, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_parts (line 199, /tmp/tmpcysasrw2/workflow/Snakefile):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule filter_fasta (line 247, /tmp/tmpcysasrw2/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724422964.0 + "updated_at": 1723814371.0 }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp9cqhnd78/workflow/Snakefile\": Keyword \"output\" at line 137 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp9cqhnd78/workflow/Snakefile\": Keyword \"shell\" at line 151 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp9cqhnd78/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mdondrup/admixture_simulation", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpn9mx7s4y/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "simonmoulds/india-crop-atlas", "latest_release": null, - "linting": "Lints for rule setup (line 49, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule build_model (line 77, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule subsample_recode (line 107, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule make_new_clusterfile (line 180, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule treemix_input (line 230, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule TreeMix_bootstrap_{wildcards.model}_{wildcards.migrations}_{wildcards.replicate} (line 262, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule merge_replicates_{wildcards.model}_{wildcards.migrations} (line 344, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule OptM (line 384, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param folder is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule plot_trees (line 444, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable rule from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule consensus (line 529, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule final_tree_from_consensus (line 597, /tmp/tmp9cqhnd78/workflow/Snakefile):\n * Param prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "linting": null, "mandatory_flags": { "desc": null, "flags": null @@ -4810,33 +4912,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724420390.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6wwq7z5b/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[INFO] 1 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "kenji-yt/snake-GENESPACE", - "latest_release": null, - "linting": "Make sure there is a config.yaml file in /tmp/tmp6wwq7z5b or specify one with the --configfile commandline parameter.\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724411185.0 + "updated_at": 1723811684.0 }, { "config_readme": null, "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk\": Keyword \"output\" at line 6 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp7dl9bldo/workflow/Snakefile\": SyntaxError: L22: Unrecognised keyword \u0027expand\u0027 in rule definition\n[DEBUG] In file \"/tmp/tmp7dl9bldo/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zeyak/GenoDiplo", + "description": "Bash script and basic structure to install and run a snakemake workflow", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbwtkk4sn/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "jmoldon/run_snakemake", "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk:\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw\" in line 3:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/{process}/nanopore.fastq.gz\" in line 16:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 30:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/databases/{db}\" in line 46:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 74:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/EST/S_barkhanus_cloneMiner_cDNA_library.fasta\" in line 101:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/data/zeynep/barkhanus_data/DNA/raw/{long_read}.fastq.gz\" in line 133:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for rule fastqc_before_trimming (line 1, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule flye (line 33, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule setup_nr_db (line 66, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule blastn (line 87, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule makeblastdb (line 122, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outname is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule blastn_EST (line 160, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param db_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule meryl (line 224, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule winnowmap (line 257, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule quast (line 293, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule multiqc (line 324, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_coverage_cont (line 355, /tmp/tmp7dl9bldo/workflow/rules/1_assembly.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule prodigal (line 1, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule glimmerhmm_ (line 29, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule augustus (line 85, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule V3_busco_geneset (line 118, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_transcriptome (line 152, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule busco_plot (line 187, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule make_diamond_db (line 214, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule diamond_blastp_ (line 259, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eggnogmapper (line 294, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param outdir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule interproscan (line 328, /tmp/tmp7dl9bldo/workflow/rules/2_annotation.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "linting": "Lints for rule hello (line 12, /tmp/tmpbwtkk4sn/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4844,84 +4929,16 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724406283.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A snakemake workflow for amplicon sequencing ", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/rules/qc-notebooks.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/rules/analysis.smk\": Formatted content is different from original\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n[INFO] 6 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "sanjaynagi/AmpSeeker", - "latest_release": "v0.3.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpr60bckfs/sanjaynagi-AmpSeeker-d49fb6f/workflow/Snakefile\", line 17, in \u003cmodule\u003e\n metadata = pd.read_csv(config[\"metadata\"], sep=\",\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027config/metadata.tsv\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 4, - "topics": [ - "amplicon-sequencing", - "gene-drive", - "genomic-surveillance", - "illumina", - "insecticide-resistance", - "snakemake-workflow" - ], - "updated_at": 1724405875.0 + "updated_at": 1723801249.0 }, { "config_readme": null, "data_format": 2, "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/convert_pdf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/summary_report.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/results.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/dotnet.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/create_background_file.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/sample_order_for_multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/bcftools.smk\": Formatted content is different from original\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "clinical-genomics-uppsala/pickett_bcr_abl_pipeline", - "latest_release": "v0.2.2", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpap2yglyq/clinical-genomics-uppsala-pickett_bcr_abl_pipeline-947d149/workflow/rules/common.smk\", line 16, in \u003cmodule\u003e\n from hydra_genetics.utils.misc import replace_dict_variables\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724400847.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A repository for efficient population genomic analysis using Snakemake workflow.", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp58ll2v5d/Snakefile\": SyntaxError: L125: Unrecognised keyword \u0027expand\u0027 in rule definition\n[INFO] In file \"/tmp/tmp58ll2v5d/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "meeranhussain/Population_genomic_analysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr25x1sr_/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "margotl9/SimmsLab_BradyrhizobiumPDS", "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp58ll2v5d/Snakefile\", line 13, in \u003cmodule\u003e\n fasta_path = config[\"fasta_path\"]\n ~~~~~~^^^^^^^^^^^^^^^\n\nKeyError: \u0027fasta_path\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "genome-analysis", - "ngs", - "ngs-analysis", - "population", - "population-genomics", - "snakemake-workflow", - "variant-calling", - "whole", - "rprogramming" - ], - "updated_at": 1724388998.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Align almost any kind of RNA-seq data", - "formatting": null, - "full_name": "isaacvock/THE_Aligner", - "latest_release": "v1.0.0", - "linting": null, + "linting": "Lints for snakefile /tmp/tmpr25x1sr_/workflow/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 28:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk:\n * Path composition with \u0027+\u0027 in line 22:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 82:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 83:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 86:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 88:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule prodigal (line 22, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule defenseFinder (line 57, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir_sp is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule analyze_PDS (line 94, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule padloc_db (line 134, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule padloc (line 159, /tmp/tmpr25x1sr_/workflow/rules/01_phage_defense.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param out_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, @@ -4929,7 +4946,7 @@ var data = "stargazers_count": 0, "subscribers_count": 1, "topics": [], - "updated_at": 1724360758.0 + "updated_at": 1723761676.0 }, { "config_readme": null, @@ -4948,23 +4965,6 @@ var data = "topics": [], "updated_at": 1724355682.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\": Keyword \"output\" at line 50 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\": Keyword \"input\" at line 71 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "radio1988/ccount", - "latest_release": "v0.2", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n\n File \"/tmp/tmpbkmc5a5q/radio1988-ccount-e6da0e3/workflow/scripts/ccount/snake/get_samples.py\", line 42, in get_samples\n SAMPLES=os.listdir(DATA_DIR)\n ^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027data/\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1725552375.0 - }, { "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n fair_fastqc_multiqc:\n # Optional parameters for multiqc\n multiqc: --module fastqc --zip-data-dir --verbose --no-megaqc-upload --no-ansi --force\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_fastqc_multiqc/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Path to downstream fastq file, leave empty in case of Single ended library.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_fastqc_multiqc/blob/main/workflow/schemas/samples.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release\nhomo_sapiens,GRCh38,105\nmus_musculus,GRCm38,99\nmus_musculus,GRCm39,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_fastqc_multiqc/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eNote:\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", "data_format": 2, @@ -36559,6 +36559,153 @@ var data = "topics": [], "updated_at": 1614368088.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow for assembling transcript models from RNA-seq reads", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpheqx_j05/workflow/Snakefile\": Keyword \"input\" at line 29 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/transdecoder.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/stringtie.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/starindex.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpheqx_j05/workflow/rules/starindex_wannots.smk\": InvalidPython: Black error:\n```\nCannot parse: 2:35: genome = open(genomefasta , \"r\"])\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/starindex_wannots.smk\": \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/ncrnainclude.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/star.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "harvardinformatics/AnnotationRNAseqAssembly", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpheqx_j05/workflow/Snakefile\", line 76, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpheqx_j05/workflow/rules/starindex.smk\", line 32, in \u003cmodule\u003e\n\n File \"/tmp/tmpheqx_j05/workflow/rules/starindex.smk\", line 2, in get_star_SAindexNbases\n genome = open(config[\"genome\"],\"r\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027data/genome/headercleaned_GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 2, + "topics": [], + "updated_at": 1724844187.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/trim_map_preprocess.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/cnv.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/ffpe.smk\": NoParametersError: L4: In input definition.\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/ffpe.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/somatic_snps.paired.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/somatic_snps.common.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/somatic_snps.tumor_only.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/gatk_vqsr.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/germline.smk\": Keyword \"input\" at line 56 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/germline.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/nidap.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/qc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "CCBR/XAVIER", + "latest_release": "v3.1.0", + "linting": "/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/Snakefile:47: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \"(?\u003c!\\.recal)\\.bam$\": \".input.bam\",\n/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/Snakefile:48: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \"\\.recal\\.bam$\": \".input.bam\"\nWorkflowError:\nWorkflow defines configfile config.json but it is not present or accessible (full checked path: /tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/config.json).\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 4, + "topics": [], + "updated_at": 1724785339.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Analysis for Variant-FlowFISH experiments", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/bowtie2.smk\": NoParametersError: L6: In input definition.\n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/bowtie2.smk\": \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/make_count_tables.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/plots.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/estimate_effect_sizes.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/crispresso2.smk\": Keyword \"output\" at line 41 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/crispresso2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "EngreitzLab/variant-flowfish", + "latest_release": "v0.0.1-alpha", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/common.smk\", line 171, in \u003cmodule\u003e\n keyCols = config[\u0027experiment_keycols\u0027].split(\u0027,\u0027)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027experiment_keycols\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 6, + "topics": [], + "updated_at": 1724781765.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp66ut_ios/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp66ut_ios/rules/scz_analysis.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "jmp448/hdcQTL", + "latest_release": null, + "linting": "TabError in file \u003cstring\u003e, line 124:\ninconsistent use of tabs and spaces in indentation:\n\t output:\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 2, + "topics": [], + "updated_at": 1724708022.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Repository practice project in EEAD-CSIC", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpfmrs4ud4/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "carmenmiravete/barley_variant_calling", + "latest_release": null, + "linting": "WorkflowError:\nConfig file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation.\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724663377.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmphvzy65v8/Snakefile\": Keyword \"input\" at line 43 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmphvzy65v8/Snakefile\": Keyword \"input\" at line 88 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmphvzy65v8/Snakefile\": Keyword \"output\" at line 646 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmphvzy65v8/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "imallona/rock_roi_method", + "latest_release": null, + "linting": "Lints for rule simulate_genome (line 26, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simulate_gtf (line 179, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simulate_fastqs (line 205, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule simulate_fastqs_from_a_cell (line 266, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule index (line 60, /tmp/tmphvzy65v8/Snakefile):\n * Param processing_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule prepare_whitelists (line 130, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule align_wta (line 156, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param index_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_tso_whitelist_from_wta_filtered (line 267, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule align_tso (line 311, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param index_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule subset_gtf_for_custom_counting (line 427, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule subset_chromosomes_for_custom_counting (line 471, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule add_readgroups_to_bam (line 544, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule split_by_chr (line 731, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dedup_by_cb_umi_and_gx_and_start (line 776, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_deduped_bams (line 876, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule create_deduped_coverage_tracks_all_filtered_in_cbs (line 922, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule retrieve_genome_sizes (line 1006, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ready_for_sce (line 1042, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_bam (line 1109, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule install_r_deps (line 1147, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param working_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param log_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_sce_multi_all (line 1192, /tmp/tmphvzy65v8/Snakefile):\n * Param multimodal_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param working_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule render_descriptive_report (line 1262, /tmp/tmphvzy65v8/Snakefile):\n * Param multimodal_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param working_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_mapping_report (line 1341, /tmp/tmphvzy65v8/Snakefile):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 3, + "topics": [], + "updated_at": 1724658894.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Short read taxonomy", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpbb99ecvd/workflow/Snakefile\": Keyword \"output\" at line 366 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpbb99ecvd/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_short-read-taxonomy", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbb99ecvd/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027short-read-taxonomy\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724523414.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "A rapid pipeline for targeted ONT monkeypox sequencing", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/map.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/visualize.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/tree.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 5 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "OpenOmics/mpox-seek", + "latest_release": "v0.2.0", + "linting": "WorkflowError:\nWorkflow defines configfile config.json but it is not present or accessible (full checked path: /tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/config.json).\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [ + "conda", + "mamba", + "monkeypox", + "mpox", + "oxford-nanopore", + "phylogenetics", + "pipeline", + "singularity", + "snakemake", + "rapid" + ], + "updated_at": 1724358633.0 + }, { "config_readme": null, "data_format": 2, @@ -37596,153 +37743,6 @@ var data = "topics": [], "updated_at": 1723819098.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow for assembling transcript models from RNA-seq reads", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpheqx_j05/workflow/Snakefile\": Keyword \"input\" at line 29 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/transdecoder.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/stringtie.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/starindex.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpheqx_j05/workflow/rules/starindex_wannots.smk\": InvalidPython: Black error:\n```\nCannot parse: 2:35: genome = open(genomefasta , \"r\"])\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/starindex_wannots.smk\": \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/ncrnainclude.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpheqx_j05/workflow/rules/star.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "harvardinformatics/AnnotationRNAseqAssembly", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpheqx_j05/workflow/Snakefile\", line 76, in \u003cmodule\u003e\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpheqx_j05/workflow/rules/starindex.smk\", line 32, in \u003cmodule\u003e\n\n File \"/tmp/tmpheqx_j05/workflow/rules/starindex.smk\", line 2, in get_star_SAindexNbases\n genome = open(config[\"genome\"],\"r\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027data/genome/headercleaned_GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724844187.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/trim_map_preprocess.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/cnv.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/ffpe.smk\": NoParametersError: L4: In input definition.\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/ffpe.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/somatic_snps.paired.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/somatic_snps.common.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\y\u0027\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/somatic_snps.tumor_only.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/gatk_vqsr.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/germline.smk\": Keyword \"input\" at line 56 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/germline.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/nidap.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/rules/qc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "CCBR/XAVIER", - "latest_release": "v3.1.0", - "linting": "/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/Snakefile:47: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \"(?\u003c!\\.recal)\\.bam$\": \".input.bam\",\n/tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/workflow/Snakefile:48: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n \"\\.recal\\.bam$\": \".input.bam\"\nWorkflowError:\nWorkflow defines configfile config.json but it is not present or accessible (full checked path: /tmp/tmp78jl5ut4/CCBR-XAVIER-d2362c4/config.json).\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 4, - "topics": [], - "updated_at": 1724785339.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Analysis for Variant-FlowFISH experiments", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/bowtie2.smk\": NoParametersError: L6: In input definition.\n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/bowtie2.smk\": \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/make_count_tables.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/plots.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/estimate_effect_sizes.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/crispresso2.smk\": Keyword \"output\" at line 41 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/crispresso2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "EngreitzLab/variant-flowfish", - "latest_release": "v0.0.1-alpha", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpxtyjv8fy/EngreitzLab-variant-flowfish-61e49f7/workflow/rules/common.smk\", line 171, in \u003cmodule\u003e\n keyCols = config[\u0027experiment_keycols\u0027].split(\u0027,\u0027)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027experiment_keycols\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 6, - "topics": [], - "updated_at": 1724781765.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp66ut_ios/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp66ut_ios/rules/scz_analysis.smk\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "jmp448/hdcQTL", - "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 124:\ninconsistent use of tabs and spaces in indentation:\n\t output:\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724708022.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Repository practice project in EEAD-CSIC", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpfmrs4ud4/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "carmenmiravete/barley_variant_calling", - "latest_release": null, - "linting": "WorkflowError:\nConfig file is not valid JSON or YAML. In case of YAML, make sure to not mix whitespace and tab indentation.\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724663377.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmphvzy65v8/Snakefile\": Keyword \"input\" at line 43 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmphvzy65v8/Snakefile\": Keyword \"input\" at line 88 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmphvzy65v8/Snakefile\": Keyword \"output\" at line 646 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmphvzy65v8/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "imallona/rock_roi_method", - "latest_release": null, - "linting": "Lints for rule simulate_genome (line 26, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simulate_gtf (line 179, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simulate_fastqs (line 205, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule simulate_fastqs_from_a_cell (line 266, /tmp/tmphvzy65v8/src/simulate.snmk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule index (line 60, /tmp/tmphvzy65v8/Snakefile):\n * Param processing_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule prepare_whitelists (line 130, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule align_wta (line 156, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param index_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_tso_whitelist_from_wta_filtered (line 267, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule align_tso (line 311, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param index_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule subset_gtf_for_custom_counting (line 427, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule subset_chromosomes_for_custom_counting (line 471, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule add_readgroups_to_bam (line 544, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule split_by_chr (line 731, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dedup_by_cb_umi_and_gx_and_start (line 776, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_deduped_bams (line 876, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule create_deduped_coverage_tracks_all_filtered_in_cbs (line 922, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule retrieve_genome_sizes (line 1006, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ready_for_sce (line 1042, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule index_bam (line 1109, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule install_r_deps (line 1147, /tmp/tmphvzy65v8/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param working_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param log_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_sce_multi_all (line 1192, /tmp/tmphvzy65v8/Snakefile):\n * Param multimodal_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param working_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule render_descriptive_report (line 1262, /tmp/tmphvzy65v8/Snakefile):\n * Param multimodal_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param working_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule generate_mapping_report (line 1341, /tmp/tmphvzy65v8/Snakefile):\n * Param path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 3, - "topics": [], - "updated_at": 1724658894.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Short read taxonomy", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpbb99ecvd/workflow/Snakefile\": Keyword \"output\" at line 366 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpbb99ecvd/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_short-read-taxonomy", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbb99ecvd/workflow/Snakefile\", line 13, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027short-read-taxonomy\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724523414.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A rapid pipeline for targeted ONT monkeypox sequencing", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/map.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/visualize.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/workflow/rules/tree.smk\": Formatted content is different from original\n[DEBUG] \n[INFO] 5 file(s) would be changed \ud83d\ude2c\n[INFO] 1 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "OpenOmics/mpox-seek", - "latest_release": "v0.2.0", - "linting": "WorkflowError:\nWorkflow defines configfile config.json but it is not present or accessible (full checked path: /tmp/tmpd15857f3/OpenOmics-mpox-seek-4476c68/config.json).\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [ - "conda", - "mamba", - "monkeypox", - "mpox", - "oxford-nanopore", - "phylogenetics", - "pipeline", - "singularity", - "snakemake", - "rapid" - ], - "updated_at": 1724358633.0 - }, { "config_readme": null, "data_format": 2, @@ -43357,6 +43357,93 @@ var data = "topics": [], "updated_at": 1551028733.0 }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "simonlabcode/bam2bakR", + "latest_release": "v3.0.2", + "linting": "Lints for rule sort_filter (line 87, /tmp/tmpu3heb5ug/simonlabcode-bam2bakR-4fdd5ef/workflow/rules/bam2bakr.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 2, + "topics": [], + "updated_at": 1724852276.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/force-call-vcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/archive.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp6sul25g9/workflow/rules/angsd-ready-bams.smk\": Keyword \"shell\" at line 64 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp6sul25g9/workflow/rules/angsd-ready-bams.smk\": Keyword \"shell\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/angsd-ready-bams.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n\u003cunknown\u003e:3: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:5: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/destination-rules.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/downsample.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/bqsr.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/hardfilter.smk\": Formatted content is different from original\n[INFO] 14 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "eriqande/mega-non-model-wgs-snakeflow", + "latest_release": null, + "linting": "WorkflowError:\nError validating config file.\nValidationError: \u0027units\u0027 is a required property\n\nFailed validating \u0027required\u0027 in schema:\n {\u0027$schema\u0027: \u0027http://json-schema.org/draft-04/schema#\u0027,\n \u0027description\u0027: \u0027snakemake configuration file\u0027,\n \u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027units\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027chromosomes\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027scaffold_groups\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027scatter_intervals_file\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027bqsr_rounds\u0027: {\u0027type\u0027: \u0027integer\u0027},\n \u0027bqsr_maf\u0027: {\u0027type\u0027: \u0027number\u0027},\n \u0027bqsr_qual\u0027: {\u0027type\u0027: \u0027number\u0027},\n \u0027bqsr_qd\u0027: {\u0027type\u0027: \u0027number\u0027},\n \u0027maf_cutoffs\u0027: {\u0027type\u0027: \u0027array\u0027},\n \u0027ref\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027species_name\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027genome_version_name\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027genome_url\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027gff_or_gtf_url\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027species_name\u0027,\n \u0027genome_version_name\u0027,\n \u0027genome_url\u0027,\n \u0027gff_or_gtf_url\u0027]},\n \u0027filtering\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027vqsr\u0027: {\u0027type\u0027: \u0027boolean\u0027},\n \u0027hard\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027snvs\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027indels\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027snvs\u0027,\n \u0027indels\u0027]}},\n \u0027required\u0027: [\u0027vqsr\u0027, \u0027hard\u0027]},\n \u0027processing\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027remove-duplicates\u0027: {\u0027type\u0027: \u0027boolean\u0027},\n \u0027restrict-regions\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027region-padding\u0027: {\u0027type\u0027: \u0027integer\u0027}},\n \u0027required\u0027: [\u0027remove-duplicates\u0027]},\n \u0027params\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027gatk\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027HaplotypeCaller\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027BaseRecalibrator\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027GenotypeGVCFs\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027VariantRecalibrator\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027HaplotypeCaller\u0027,\n \u0027BaseRecalibrator\u0027,\n \u0027GenotypeGVCFs\u0027,\n \u0027VariantRecalibrator\u0027]},\n \u0027picard\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027MarkDuplicates\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027MarkDuplicates\u0027]}},\n \u0027required\u0027: [\u0027gatk\u0027, \u0027picard\u0027]}},\n \u0027required\u0027: [\u0027units\u0027,\n \u0027ref\u0027,\n \u0027filtering\u0027,\n \u0027processing\u0027,\n \u0027params\u0027,\n \u0027chromosomes\u0027,\n \u0027scaffold_groups\u0027,\n \u0027scatter_intervals_file\u0027,\n \u0027bqsr_rounds\u0027,\n \u0027bqsr_maf\u0027,\n \u0027bqsr_qual\u0027,\n \u0027bqsr_qd\u0027,\n \u0027maf_cutoffs\u0027]}\n\nOn instance:\n {}\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 3, + "topics": [ + "noaa-omics-software" + ], + "updated_at": 1724797617.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/seurat_preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/helper_functions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/counts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/larry_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/create_cellranger_libraries.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "dfernandezperez/cloneRanger", + "latest_release": "v0.1.0", + "linting": "Lints for rule clean_names (line 2, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clean_names_atac (line 24, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_lanes (line 45, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_lanes_atac (line 95, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move_gex_fq (line 138, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move_cellhash_fq (line 174, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move_atac_fq (line 210, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_library (line 1, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/create_cellranger_libraries.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724750087.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqafpeqys/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_binning", + "latest_release": null, + "linting": "/tmp/tmpqafpeqys/workflow/utils.py:172: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n CONTIG_PART_EXPR = re.compile(\"(.*)\\.concoct_part_([0-9]*)\")\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpqafpeqys/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n from utils import Workflow_Dirs, ingest_samples, cut_up_fasta, make_concoct_table, split_concoct_output, get_dastool_unbinned\n\n File \"/tmp/tmpqafpeqys/workflow/utils.py\", line 113, in \u003cmodule\u003e\n from Bio import SeqIO\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724520771.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpus6d579j/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "open-energy-transition/heat-demand-peaks", + "latest_release": null, + "linting": "localrules directive specifies rules that are not present in the Snakefile:\n\tall\n\nLints for rule plot_total_cost (line 25, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_capacity_expansion (line 73, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_electricity_bill (line 116, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_electricity_for_heat (line 146, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_heat_saving (line 211, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_electricity_generation (line 267, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_curtailment (line 311, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_hydrogen_production (line 360, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_heat_tech_ratio (line 415, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_COP (line 459, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_co2_level (line 481, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_DSR (line 509, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_historic_generation (line 558, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_heat_pump (line 570, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_infra_saving (line 613, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_transmission_congestion (line 668, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_res_share (line 710, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule set_capacity (line 886, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule moderate_retrofitting (line 930, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule improve_cops_after_renovation (line 973, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724418320.0 + }, { "config_readme": null, "data_format": 2, @@ -44153,93 +44240,6 @@ var data = "topics": [], "updated_at": 1724052866.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/force-call-vcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/archive.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp6sul25g9/workflow/rules/angsd-ready-bams.smk\": Keyword \"shell\" at line 64 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp6sul25g9/workflow/rules/angsd-ready-bams.smk\": Keyword \"shell\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/angsd-ready-bams.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n\u003cunknown\u003e:3: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n\u003cunknown\u003e:5: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/destination-rules.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/calling.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/downsample.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/bqsr.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6sul25g9/workflow/rules/hardfilter.smk\": Formatted content is different from original\n[INFO] 14 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "eriqande/mega-non-model-wgs-snakeflow", - "latest_release": null, - "linting": "WorkflowError:\nError validating config file.\nValidationError: \u0027units\u0027 is a required property\n\nFailed validating \u0027required\u0027 in schema:\n {\u0027$schema\u0027: \u0027http://json-schema.org/draft-04/schema#\u0027,\n \u0027description\u0027: \u0027snakemake configuration file\u0027,\n \u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027units\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027chromosomes\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027scaffold_groups\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027scatter_intervals_file\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027bqsr_rounds\u0027: {\u0027type\u0027: \u0027integer\u0027},\n \u0027bqsr_maf\u0027: {\u0027type\u0027: \u0027number\u0027},\n \u0027bqsr_qual\u0027: {\u0027type\u0027: \u0027number\u0027},\n \u0027bqsr_qd\u0027: {\u0027type\u0027: \u0027number\u0027},\n \u0027maf_cutoffs\u0027: {\u0027type\u0027: \u0027array\u0027},\n \u0027ref\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027species_name\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027genome_version_name\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027genome_url\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027gff_or_gtf_url\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027species_name\u0027,\n \u0027genome_version_name\u0027,\n \u0027genome_url\u0027,\n \u0027gff_or_gtf_url\u0027]},\n \u0027filtering\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027vqsr\u0027: {\u0027type\u0027: \u0027boolean\u0027},\n \u0027hard\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027snvs\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027indels\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027snvs\u0027,\n \u0027indels\u0027]}},\n \u0027required\u0027: [\u0027vqsr\u0027, \u0027hard\u0027]},\n \u0027processing\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027remove-duplicates\u0027: {\u0027type\u0027: \u0027boolean\u0027},\n \u0027restrict-regions\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027region-padding\u0027: {\u0027type\u0027: \u0027integer\u0027}},\n \u0027required\u0027: [\u0027remove-duplicates\u0027]},\n \u0027params\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027gatk\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027HaplotypeCaller\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027BaseRecalibrator\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027GenotypeGVCFs\u0027: {\u0027type\u0027: \u0027string\u0027},\n \u0027VariantRecalibrator\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027HaplotypeCaller\u0027,\n \u0027BaseRecalibrator\u0027,\n \u0027GenotypeGVCFs\u0027,\n \u0027VariantRecalibrator\u0027]},\n \u0027picard\u0027: {\u0027type\u0027: \u0027object\u0027,\n \u0027properties\u0027: {\u0027MarkDuplicates\u0027: {\u0027type\u0027: \u0027string\u0027}},\n \u0027required\u0027: [\u0027MarkDuplicates\u0027]}},\n \u0027required\u0027: [\u0027gatk\u0027, \u0027picard\u0027]}},\n \u0027required\u0027: [\u0027units\u0027,\n \u0027ref\u0027,\n \u0027filtering\u0027,\n \u0027processing\u0027,\n \u0027params\u0027,\n \u0027chromosomes\u0027,\n \u0027scaffold_groups\u0027,\n \u0027scatter_intervals_file\u0027,\n \u0027bqsr_rounds\u0027,\n \u0027bqsr_maf\u0027,\n \u0027bqsr_qual\u0027,\n \u0027bqsr_qd\u0027,\n \u0027maf_cutoffs\u0027]}\n\nOn instance:\n {}\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 3, - "topics": [ - "noaa-omics-software" - ], - "updated_at": 1724797617.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/seurat_preprocessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/helper_functions.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/counts.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/larry_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/create_cellranger_libraries.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "dfernandezperez/cloneRanger", - "latest_release": "v0.1.0", - "linting": "Lints for rule clean_names (line 2, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clean_names_atac (line 24, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule merge_lanes (line 45, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_lanes_atac (line 95, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move_gex_fq (line 138, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move_cellhash_fq (line 174, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule move_atac_fq (line 210, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/prepare_fastqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule create_library (line 1, /tmp/tmpwj44bwkm/dfernandezperez-cloneRanger-b851a5e/workflow/rules/create_cellranger_libraries.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724750087.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqafpeqys/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_binning", - "latest_release": null, - "linting": "/tmp/tmpqafpeqys/workflow/utils.py:172: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n CONTIG_PART_EXPR = re.compile(\"(.*)\\.concoct_part_([0-9]*)\")\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpqafpeqys/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n from utils import Workflow_Dirs, ingest_samples, cut_up_fasta, make_concoct_table, split_concoct_output, get_dastool_unbinned\n\n File \"/tmp/tmpqafpeqys/workflow/utils.py\", line 113, in \u003cmodule\u003e\n from Bio import SeqIO\n\nModuleNotFoundError: No module named \u0027Bio\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724520771.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpus6d579j/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "open-energy-transition/heat-demand-peaks", - "latest_release": null, - "linting": "localrules directive specifies rules that are not present in the Snakefile:\n\tall\n\nLints for rule plot_total_cost (line 25, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_capacity_expansion (line 73, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_electricity_bill (line 116, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_electricity_for_heat (line 146, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_heat_saving (line 211, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_electricity_generation (line 267, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_curtailment (line 311, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_hydrogen_production (line 360, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_heat_tech_ratio (line 415, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_COP (line 459, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_co2_level (line 481, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_DSR (line 509, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_historic_generation (line 558, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_heat_pump (line 570, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_infra_saving (line 613, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_transmission_congestion (line 668, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule get_res_share (line 710, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule set_capacity (line 886, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule moderate_retrofitting (line 930, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule improve_cops_after_renovation (line 973, /tmp/tmpus6d579j/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724418320.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "simonlabcode/bam2bakR", - "latest_release": "v3.0.2", - "linting": "Lints for rule sort_filter (line 87, /tmp/tmpu3heb5ug/simonlabcode-bam2bakR-4fdd5ef/workflow/rules/bam2bakr.smk):\n * Shell command directly uses variable config from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724852276.0 - }, { "config_readme": null, "data_format": 2, @@ -46893,6 +46893,36 @@ var data = ], "updated_at": 1617804426.0 }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eRunning the workflow\u003c/h2\u003e\u003ca id=\"user-content-running-the-workflow\" class=\"anchor\" aria-label=\"Permalink: Running the workflow\" href=\"#running-the-workflow\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eInput data\u003c/h3\u003e\u003ca id=\"user-content-input-data\" class=\"anchor\" aria-label=\"Permalink: Input data\" href=\"#input-data\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires the following input:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eAn NCBI Refseq ID, e.g. \u003ccode\u003eGCF_000006945.2\u003c/code\u003e. Find your genome assembly and corresponding ID on \u003ca href=\"https://www.ncbi.nlm.nih.gov/data-hub/genome/\" rel=\"nofollow\"\u003eNCBI genomes\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eOR use a custom pair of \u003ccode\u003e*.fasta\u003c/code\u003e file and \u003ccode\u003e*.gff\u003c/code\u003e file that describe the genome of choice\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eImportant requirements when using custom \u003ccode\u003e*.fasta\u003c/code\u003e and \u003ccode\u003e*.gff\u003c/code\u003e files:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003e*.gff\u003c/code\u003e genome annotation must have the same chromosome/region name as the \u003ccode\u003e*.fasta\u003c/code\u003e file (example: \u003ccode\u003eNC_003197.2\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003e*.gff\u003c/code\u003e genome annotation must have \u003ccode\u003egene\u003c/code\u003e and \u003ccode\u003eCDS\u003c/code\u003e type annotation that is automatically parsed to extract transcripts\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003e*.gff\u003c/code\u003e genome annotation must have additional qualifiers \u003ccode\u003eName=...\u003c/code\u003e, \u003ccode\u003eID=...\u003c/code\u003e, and \u003ccode\u003eParent=...\u003c/code\u003e for \u003ccode\u003eCDS\u003c/code\u003es\u003c/li\u003e\n\u003cli\u003eall chromosomes/regions in the \u003ccode\u003e*.gff\u003c/code\u003e genome annotation must be present in the \u003ccode\u003e*.fasta\u003c/code\u003e sequence\u003c/li\u003e\n\u003cli\u003ebut not all sequences in the \u003ccode\u003e*.fasta\u003c/code\u003e file need to have annotated genes in the \u003ccode\u003e*.gff\u003c/code\u003e file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eStarting the workflow\u003c/h3\u003e\u003ca id=\"user-content-starting-the-workflow\" class=\"anchor\" aria-label=\"Permalink: Starting the workflow\" href=\"#starting-the-workflow\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo run the workflow from command line, change the working directory.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003ecd /path/to/snakemake-crispr-guides\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eAdjust the global and module-specific options in the default config file \u003ccode\u003econfig/config.yml\u003c/code\u003e.\nBefore running the entire workflow, you can perform a dry run using:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --dry-run\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eTo run the complete workflow with test files using \u003cstrong\u003e\u003ccode\u003econda\u003c/code\u003e\u003c/strong\u003e, execute the following command. The definition of the number of compute cores is mandatory.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --cores 10 --use-conda\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eTo run the workflow with \u003cstrong\u003e\u003ccode\u003esingularity\u003c/code\u003e\u003c/strong\u003e, run:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --cores 10 --use-singularity --use-conda\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eTo supply a custom config file and/or use options that override the defaults, run the workflow like this:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --cores 10 --use-conda \\\n --configfile \u0027config/my_config.yml\u0027 \\\n --config \\\n option=\u0027input\u0027\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eParameters\u003c/h3\u003e\u003ca id=\"user-content-parameters\" class=\"anchor\" aria-label=\"Permalink: Parameters\" href=\"#parameters\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis table lists all parameters that can be used to run the workflow.\u003c/p\u003e\n\u003ctable\u003e\n\u003cthead\u003e\n\u003ctr\u003e\n\u003cth\u003eparameter\u003c/th\u003e\n\u003cth\u003etype\u003c/th\u003e\n\u003cth\u003edetails\u003c/th\u003e\n\u003cth\u003edefault\u003c/th\u003e\n\u003c/tr\u003e\n\u003c/thead\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd\u003eGET_GENOME\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003edatabase\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eone of \u003ccode\u003encbi\u003c/code\u003e, \u003ccode\u003emanual\u003c/code\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003encbi\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eassembly\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eRefSeq ID\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eGCF_000006945.2\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efasta\u003c/td\u003e\n\u003ctd\u003epath\u003c/td\u003e\n\u003ctd\u003eoptional input\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003egff\u003c/td\u003e\n\u003ctd\u003epath\u003c/td\u003e\n\u003ctd\u003eoptional input\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003egff_source_type\u003c/td\u003e\n\u003ctd\u003elist\u003c/td\u003e\n\u003ctd\u003eallowed source types in GFF file\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e\u0027RefSeq\u0027: \u0027gene\u0027, ...\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eDESIGN_GUIDES\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etarget_region\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003euse subset of regions for testing\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[\"NC_003277.2\"]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etarget_type\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003especify targets for guide design (see below)\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[\"target\", \"intergenic\", \"ntc\"]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etss_window\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003eupstream/downstream window around TSS\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[0, 500]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etiling_window\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003ewindow size for intergenic regions\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e1000\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etiling_min_dist\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emin distance between TSS and intergenic region\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e0\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ecircular\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eis the genome circular?\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eFalse\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ecanonical\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eonly canonical PAM sites are included\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eTrue\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003estrands\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003etarget \u003ccode\u003ecoding\u003c/code\u003e, \u003ccode\u003etemplate\u003c/code\u003e or \u003ccode\u003eboth\u003c/code\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eboth\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003espacer_length\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003edesired length of guides\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e20\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eguide_aligner\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eone of \u003ccode\u003ebiostrings\u003c/code\u003e, \u003ccode\u003ebowtie\u003c/code\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003ebiostrings\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ecrispr_enzyme\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eCRISPR enzyme ID\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eSpCas9\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003escore_methods\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003esee \u003cem\u003ecrisprScore\u003c/em\u003e package\u003c/td\u003e\n\u003ctd\u003edefault scores are listed below\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003escore_weights\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003eopt. weights when calculating mean score\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[1, 1, 1, 1, 1, 1]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003erestriction_sites\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003esequences to omit in entire guide\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ebad_seeds\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003esequences to omit in seed region\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[\"ACCCA\", \"ATACT\", \"TGGAA\"]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eno_target_controls\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003enumber of non targeting guides (neg. controls)\u003c/td\u003e\n\u003ctd\u003e100\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eFILTER_GUIDES\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_best_per_gene\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emax number of guides to return per gene\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e10\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_best_per_tile\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emax number of guides to return per ig/tile\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e10\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_score_threshold\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emean score to use as lower limit\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_multi_targets\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eremove guides that perfectly match \u0026gt;1 target\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eTrue\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_rna\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eremove guides that target e.g. rRNA or tRNA\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eTrue\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003egc_content_range\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003erange of allowed GC content\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[30, 70]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efiveprime_linker\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eoptionally add 5\u0027 linker to each guide\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ethreeprime_linker\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eoptionally add 3\u0027 linker to each guide\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eexport_as_gff\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eexport result table also as \u003ccode\u003e.gff\u003c/code\u003e file\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eFalse\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eREPORT\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eshow_examples\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003enumber of genes to show guide position\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e10\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eTarget type\u003c/h3\u003e\u003ca id=\"user-content-target-type\" class=\"anchor\" aria-label=\"Permalink: Target type\" href=\"#target-type\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eOne of the most important options is to specify the \u003cem\u003etype of target\u003c/em\u003e with the \u003ccode\u003etarget_type\u003c/code\u003e parameter. The pipeline can generate up to three different types of guide RNAs:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eguides for \u003cstrong\u003etargets\u003c/strong\u003e - these are typically genes, promoters or other annotated genetic elements determined from the supplied GFF file. The pipeline will try to find the best guides by position and score targeting the defined window around the start of the gene/feature (parameter \u003ccode\u003etss_window\u003c/code\u003e). The number of guides is specified with \u003ccode\u003efilter_best_per_gene\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003eguides for \u003cstrong\u003eintergenic regions\u003c/strong\u003e - for non-annotated regions (or in the absence of any targets), the pipeline attempts to design guide RNAs using a \u0027tiling\u0027 approach. This means that the supplied genome is subdivided into \u0027tiles\u0027 (bins) of width \u003ccode\u003etiling_window\u003c/code\u003e, and the best guide RNAs per window are selected. The number of guides is specified with \u003ccode\u003efilter_best_per_tile\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003eguides \u003cstrong\u003enot targeting anything\u003c/strong\u003e - this type of guide RNAs is most useful as negative control, in order to gauge the effect of the genetic background on mutant selection without targeting a gene. These guides are random nucleotide sequences with the same length as the target guide RNAs. The no-target control guides are named \u003ccode\u003eNTC_\u0026lt;number\u0026gt;\u003c/code\u003e and exported in a separate table (\u003ccode\u003eresults/filter_guides/guideRNAs_ntc.csv\u003c/code\u003e). Some very reduced checks are done for these guides, such as off-target binding. mMst on-target checks are omitted for these guides as they have no defined binding site, strand, or other typical guide properties.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eOff-target scores\u003c/h3\u003e\u003ca id=\"user-content-off-target-scores\" class=\"anchor\" aria-label=\"Permalink: Off-target scores\" href=\"#off-target-scores\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe pipeline maps each guide RNA to the target genome and -by default- counts the number of alternative alignments with 1, 2, 3, or 4 mismatches. All guide RNAs that map to any other position including up to 4 allowed mismatches are removed.\nAn exception to this rule is made for guides that perfectly match multiple targets when the \u003ccode\u003efilter_multi_targets\u003c/code\u003e is set to \u003ccode\u003eFalse\u003c/code\u003e (default: \u003ccode\u003eTrue\u003c/code\u003e). The reasoning behind this rule is that genomes often contain duplicated genes/targets, and the default but sometimes undesired behavior is to remove all guides targeting the two or more duplicates. If set to \u003ccode\u003eFalse\u003c/code\u003e, these guides will not be removed and duplicated genes will be targeted even if they are located at different sites.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eOn-target scores\u003c/h3\u003e\u003ca id=\"user-content-on-target-scores\" class=\"anchor\" aria-label=\"Permalink: On-target scores\" href=\"#on-target-scores\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe list of available on-target scores in the \u003ca href=\"https://github.com/crisprVerse/crisprScore\"\u003eR crisprScore package\u003c/a\u003e is larger than the different scores included by default. It is important to note that the computation of some scores does not necessarily make sense for the design of every CRISPR library. For example, several scores were obtained from analysis of Cas9 cutting efficiency in human cell lines. For such scores it is questionable if they are useful for the design of a different type of library, for example a dCas9 CRISPR inhibition library for bacteria.\u003c/p\u003e\n\u003cp\u003eAnother good reason to exclude some scores are the computational resources they require. Particularly deep learning-derived scores are calculated by machine learning models that require both a lot of extra resources in terms of disk space (downloaded and installed \u003cem\u003evia\u003c/em\u003e \u003ccode\u003ebasilisk\u003c/code\u003e and \u003ccode\u003econda\u003c/code\u003e environments) and processing power (orders of magnitude longer computation time).\u003c/p\u003e\n\u003cp\u003eUsers can look up all available scores on the \u003ca href=\"https://github.com/crisprVerse/crisprScore\"\u003eR crisprScore github page\u003c/a\u003e and decide which ones should be included. In addition, the default behavior of the pipeline is to compute an average score and select the top N guides based on it. The average score is the \u003cem\u003eweighted mean\u003c/em\u003e of all single scores and the \u003ccode\u003escore_weights\u003c/code\u003e can be defined in the \u003ccode\u003econfig/config.yml\u003c/code\u003e file. If a score should be excluded from the ranking, it\u0027s weight can simply be set to zero.\u003c/p\u003e\n\u003cp\u003eThe default scores are:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eruleset1\u003c/code\u003e, \u003ccode\u003eruleset3\u003c/code\u003e, \u003ccode\u003ecrisprater\u003c/code\u003e, and \u003ccode\u003ecrisprscan\u003c/code\u003e from the \u003ccode\u003ecrisprScore\u003c/code\u003e package\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003etssdist\u003c/code\u003e as an additional score representing the relative distance to the promoter. Only relevant for CRISRPi repression\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003egenrich\u003c/code\u003e as an additional score representing the \u003ccode\u003eG\u003c/code\u003e enrichment in the -4 to -14 nt region of a spacer (\u003ca href=\"https://www.biorxiv.org/content/10.1101/2023.02.13.528328v1\" rel=\"nofollow\"\u003eMiao \u0026amp; Jahn et al., 2023\u003c/a\u003e). Only relevant for CRISPRi repression\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eStrand specificity\u003c/h3\u003e\u003ca id=\"user-content-strand-specificity\" class=\"anchor\" aria-label=\"Permalink: Strand specificity\" href=\"#strand-specificity\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe strand specificity is important for some CRISPR applications. In contrast to the \u003ccode\u003ecrisprDesign\u003c/code\u003e package, functions were added to allow the design of guide RNAs that target either both strands, or just the coding (non-template) strand, or the template strand. This can be defined with the \u003ccode\u003estrands\u003c/code\u003e parameter in the config file.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eFor CRISPRi (inhibition) experiments, the literature recommends to target the \u003cstrong\u003ecoding strand for the CDS\u003c/strong\u003e or \u003cstrong\u003eboth strands for the promoter\u003c/strong\u003e (\u003ca href=\"http://dx.doi.org/10.1038/nprot.2013.132\" rel=\"nofollow\"\u003eLarson et al., Nat Prot, 2013\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003ethis pipeline will automatically filter guides for the chosen strand\u003c/li\u003e\n\u003cli\u003efor example, if only guides for the coding (non-template) strand are desired, genes on the \"+\" strand will be targeted with reverse-complement guides (\"-\"), and genes on the \"-\" strand with \"+\" guides.\u003c/li\u003e\n\u003c/ul\u003e\n", + "data_format": 2, + "description": "A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.", + "formatting": null, + "full_name": "MPUSP/snakemake-crispr-guides", + "latest_release": "v1.2.0", + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": true + }, + "standardized": true, + "stargazers_count": 3, + "subscribers_count": 0, + "topics": [ + "bioinformatics-pipeline", + "crispr", + "crispr-design", + "guide-rna-library", + "python3", + "r-markdown", + "snakemake", + "workflow" + ], + "updated_at": 1724662792.0 + }, { "config_readme": null, "data_format": 2, @@ -47401,36 +47431,6 @@ var data = "topics": [], "updated_at": 1724078847.0 }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eRunning the workflow\u003c/h2\u003e\u003ca id=\"user-content-running-the-workflow\" class=\"anchor\" aria-label=\"Permalink: Running the workflow\" href=\"#running-the-workflow\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eInput data\u003c/h3\u003e\u003ca id=\"user-content-input-data\" class=\"anchor\" aria-label=\"Permalink: Input data\" href=\"#input-data\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires the following input:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eAn NCBI Refseq ID, e.g. \u003ccode\u003eGCF_000006945.2\u003c/code\u003e. Find your genome assembly and corresponding ID on \u003ca href=\"https://www.ncbi.nlm.nih.gov/data-hub/genome/\" rel=\"nofollow\"\u003eNCBI genomes\u003c/a\u003e\n\u003c/li\u003e\n\u003cli\u003eOR use a custom pair of \u003ccode\u003e*.fasta\u003c/code\u003e file and \u003ccode\u003e*.gff\u003c/code\u003e file that describe the genome of choice\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eImportant requirements when using custom \u003ccode\u003e*.fasta\u003c/code\u003e and \u003ccode\u003e*.gff\u003c/code\u003e files:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003e*.gff\u003c/code\u003e genome annotation must have the same chromosome/region name as the \u003ccode\u003e*.fasta\u003c/code\u003e file (example: \u003ccode\u003eNC_003197.2\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003e*.gff\u003c/code\u003e genome annotation must have \u003ccode\u003egene\u003c/code\u003e and \u003ccode\u003eCDS\u003c/code\u003e type annotation that is automatically parsed to extract transcripts\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003e*.gff\u003c/code\u003e genome annotation must have additional qualifiers \u003ccode\u003eName=...\u003c/code\u003e, \u003ccode\u003eID=...\u003c/code\u003e, and \u003ccode\u003eParent=...\u003c/code\u003e for \u003ccode\u003eCDS\u003c/code\u003es\u003c/li\u003e\n\u003cli\u003eall chromosomes/regions in the \u003ccode\u003e*.gff\u003c/code\u003e genome annotation must be present in the \u003ccode\u003e*.fasta\u003c/code\u003e sequence\u003c/li\u003e\n\u003cli\u003ebut not all sequences in the \u003ccode\u003e*.fasta\u003c/code\u003e file need to have annotated genes in the \u003ccode\u003e*.gff\u003c/code\u003e file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eStarting the workflow\u003c/h3\u003e\u003ca id=\"user-content-starting-the-workflow\" class=\"anchor\" aria-label=\"Permalink: Starting the workflow\" href=\"#starting-the-workflow\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo run the workflow from command line, change the working directory.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003ecd /path/to/snakemake-crispr-guides\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eAdjust the global and module-specific options in the default config file \u003ccode\u003econfig/config.yml\u003c/code\u003e.\nBefore running the entire workflow, you can perform a dry run using:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --dry-run\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eTo run the complete workflow with test files using \u003cstrong\u003e\u003ccode\u003econda\u003c/code\u003e\u003c/strong\u003e, execute the following command. The definition of the number of compute cores is mandatory.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --cores 10 --use-conda\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eTo run the workflow with \u003cstrong\u003e\u003ccode\u003esingularity\u003c/code\u003e\u003c/strong\u003e, run:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --cores 10 --use-singularity --use-conda\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eTo supply a custom config file and/or use options that override the defaults, run the workflow like this:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esnakemake --cores 10 --use-conda \\\n --configfile \u0027config/my_config.yml\u0027 \\\n --config \\\n option=\u0027input\u0027\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eParameters\u003c/h3\u003e\u003ca id=\"user-content-parameters\" class=\"anchor\" aria-label=\"Permalink: Parameters\" href=\"#parameters\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis table lists all parameters that can be used to run the workflow.\u003c/p\u003e\n\u003ctable\u003e\n\u003cthead\u003e\n\u003ctr\u003e\n\u003cth\u003eparameter\u003c/th\u003e\n\u003cth\u003etype\u003c/th\u003e\n\u003cth\u003edetails\u003c/th\u003e\n\u003cth\u003edefault\u003c/th\u003e\n\u003c/tr\u003e\n\u003c/thead\u003e\n\u003ctbody\u003e\n\u003ctr\u003e\n\u003ctd\u003eGET_GENOME\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003edatabase\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eone of \u003ccode\u003encbi\u003c/code\u003e, \u003ccode\u003emanual\u003c/code\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003encbi\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eassembly\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eRefSeq ID\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eGCF_000006945.2\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efasta\u003c/td\u003e\n\u003ctd\u003epath\u003c/td\u003e\n\u003ctd\u003eoptional input\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003egff\u003c/td\u003e\n\u003ctd\u003epath\u003c/td\u003e\n\u003ctd\u003eoptional input\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003egff_source_type\u003c/td\u003e\n\u003ctd\u003elist\u003c/td\u003e\n\u003ctd\u003eallowed source types in GFF file\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e\u0027RefSeq\u0027: \u0027gene\u0027, ...\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eDESIGN_GUIDES\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etarget_region\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003euse subset of regions for testing\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[\"NC_003277.2\"]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etarget_type\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003especify targets for guide design (see below)\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[\"target\", \"intergenic\", \"ntc\"]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etss_window\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003eupstream/downstream window around TSS\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[0, 500]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etiling_window\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003ewindow size for intergenic regions\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e1000\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003etiling_min_dist\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emin distance between TSS and intergenic region\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e0\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ecircular\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eis the genome circular?\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eFalse\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ecanonical\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eonly canonical PAM sites are included\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eTrue\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003estrands\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003etarget \u003ccode\u003ecoding\u003c/code\u003e, \u003ccode\u003etemplate\u003c/code\u003e or \u003ccode\u003eboth\u003c/code\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eboth\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003espacer_length\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003edesired length of guides\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e20\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eguide_aligner\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eone of \u003ccode\u003ebiostrings\u003c/code\u003e, \u003ccode\u003ebowtie\u003c/code\u003e\n\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003ebiostrings\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ecrispr_enzyme\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eCRISPR enzyme ID\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eSpCas9\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003escore_methods\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003esee \u003cem\u003ecrisprScore\u003c/em\u003e package\u003c/td\u003e\n\u003ctd\u003edefault scores are listed below\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003escore_weights\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003eopt. weights when calculating mean score\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[1, 1, 1, 1, 1, 1]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003erestriction_sites\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003esequences to omit in entire guide\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ebad_seeds\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003esequences to omit in seed region\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[\"ACCCA\", \"ATACT\", \"TGGAA\"]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eno_target_controls\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003enumber of non targeting guides (neg. controls)\u003c/td\u003e\n\u003ctd\u003e100\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eFILTER_GUIDES\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_best_per_gene\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emax number of guides to return per gene\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e10\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_best_per_tile\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emax number of guides to return per ig/tile\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e10\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_score_threshold\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003emean score to use as lower limit\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_multi_targets\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eremove guides that perfectly match \u0026gt;1 target\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eTrue\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efilter_rna\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eremove guides that target e.g. rRNA or tRNA\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eTrue\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003egc_content_range\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003erange of allowed GC content\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e[30, 70]\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003efiveprime_linker\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eoptionally add 5\u0027 linker to each guide\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003ethreeprime_linker\u003c/td\u003e\n\u003ctd\u003estring\u003c/td\u003e\n\u003ctd\u003eoptionally add 3\u0027 linker to each guide\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eNull\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eexport_as_gff\u003c/td\u003e\n\u003ctd\u003elogical\u003c/td\u003e\n\u003ctd\u003eexport result table also as \u003ccode\u003e.gff\u003c/code\u003e file\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003eFalse\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eREPORT\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003ctd\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003ctr\u003e\n\u003ctd\u003eshow_examples\u003c/td\u003e\n\u003ctd\u003enumeric\u003c/td\u003e\n\u003ctd\u003enumber of genes to show guide position\u003c/td\u003e\n\u003ctd\u003e\u003ccode\u003e10\u003c/code\u003e\u003c/td\u003e\n\u003c/tr\u003e\n\u003c/tbody\u003e\n\u003c/table\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eTarget type\u003c/h3\u003e\u003ca id=\"user-content-target-type\" class=\"anchor\" aria-label=\"Permalink: Target type\" href=\"#target-type\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eOne of the most important options is to specify the \u003cem\u003etype of target\u003c/em\u003e with the \u003ccode\u003etarget_type\u003c/code\u003e parameter. The pipeline can generate up to three different types of guide RNAs:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003eguides for \u003cstrong\u003etargets\u003c/strong\u003e - these are typically genes, promoters or other annotated genetic elements determined from the supplied GFF file. The pipeline will try to find the best guides by position and score targeting the defined window around the start of the gene/feature (parameter \u003ccode\u003etss_window\u003c/code\u003e). The number of guides is specified with \u003ccode\u003efilter_best_per_gene\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003eguides for \u003cstrong\u003eintergenic regions\u003c/strong\u003e - for non-annotated regions (or in the absence of any targets), the pipeline attempts to design guide RNAs using a \u0027tiling\u0027 approach. This means that the supplied genome is subdivided into \u0027tiles\u0027 (bins) of width \u003ccode\u003etiling_window\u003c/code\u003e, and the best guide RNAs per window are selected. The number of guides is specified with \u003ccode\u003efilter_best_per_tile\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003eguides \u003cstrong\u003enot targeting anything\u003c/strong\u003e - this type of guide RNAs is most useful as negative control, in order to gauge the effect of the genetic background on mutant selection without targeting a gene. These guides are random nucleotide sequences with the same length as the target guide RNAs. The no-target control guides are named \u003ccode\u003eNTC_\u0026lt;number\u0026gt;\u003c/code\u003e and exported in a separate table (\u003ccode\u003eresults/filter_guides/guideRNAs_ntc.csv\u003c/code\u003e). Some very reduced checks are done for these guides, such as off-target binding. mMst on-target checks are omitted for these guides as they have no defined binding site, strand, or other typical guide properties.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eOff-target scores\u003c/h3\u003e\u003ca id=\"user-content-off-target-scores\" class=\"anchor\" aria-label=\"Permalink: Off-target scores\" href=\"#off-target-scores\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe pipeline maps each guide RNA to the target genome and -by default- counts the number of alternative alignments with 1, 2, 3, or 4 mismatches. All guide RNAs that map to any other position including up to 4 allowed mismatches are removed.\nAn exception to this rule is made for guides that perfectly match multiple targets when the \u003ccode\u003efilter_multi_targets\u003c/code\u003e is set to \u003ccode\u003eFalse\u003c/code\u003e (default: \u003ccode\u003eTrue\u003c/code\u003e). The reasoning behind this rule is that genomes often contain duplicated genes/targets, and the default but sometimes undesired behavior is to remove all guides targeting the two or more duplicates. If set to \u003ccode\u003eFalse\u003c/code\u003e, these guides will not be removed and duplicated genes will be targeted even if they are located at different sites.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eOn-target scores\u003c/h3\u003e\u003ca id=\"user-content-on-target-scores\" class=\"anchor\" aria-label=\"Permalink: On-target scores\" href=\"#on-target-scores\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe list of available on-target scores in the \u003ca href=\"https://github.com/crisprVerse/crisprScore\"\u003eR crisprScore package\u003c/a\u003e is larger than the different scores included by default. It is important to note that the computation of some scores does not necessarily make sense for the design of every CRISPR library. For example, several scores were obtained from analysis of Cas9 cutting efficiency in human cell lines. For such scores it is questionable if they are useful for the design of a different type of library, for example a dCas9 CRISPR inhibition library for bacteria.\u003c/p\u003e\n\u003cp\u003eAnother good reason to exclude some scores are the computational resources they require. Particularly deep learning-derived scores are calculated by machine learning models that require both a lot of extra resources in terms of disk space (downloaded and installed \u003cem\u003evia\u003c/em\u003e \u003ccode\u003ebasilisk\u003c/code\u003e and \u003ccode\u003econda\u003c/code\u003e environments) and processing power (orders of magnitude longer computation time).\u003c/p\u003e\n\u003cp\u003eUsers can look up all available scores on the \u003ca href=\"https://github.com/crisprVerse/crisprScore\"\u003eR crisprScore github page\u003c/a\u003e and decide which ones should be included. In addition, the default behavior of the pipeline is to compute an average score and select the top N guides based on it. The average score is the \u003cem\u003eweighted mean\u003c/em\u003e of all single scores and the \u003ccode\u003escore_weights\u003c/code\u003e can be defined in the \u003ccode\u003econfig/config.yml\u003c/code\u003e file. If a score should be excluded from the ranking, it\u0027s weight can simply be set to zero.\u003c/p\u003e\n\u003cp\u003eThe default scores are:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eruleset1\u003c/code\u003e, \u003ccode\u003eruleset3\u003c/code\u003e, \u003ccode\u003ecrisprater\u003c/code\u003e, and \u003ccode\u003ecrisprscan\u003c/code\u003e from the \u003ccode\u003ecrisprScore\u003c/code\u003e package\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003etssdist\u003c/code\u003e as an additional score representing the relative distance to the promoter. Only relevant for CRISRPi repression\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003egenrich\u003c/code\u003e as an additional score representing the \u003ccode\u003eG\u003c/code\u003e enrichment in the -4 to -14 nt region of a spacer (\u003ca href=\"https://www.biorxiv.org/content/10.1101/2023.02.13.528328v1\" rel=\"nofollow\"\u003eMiao \u0026amp; Jahn et al., 2023\u003c/a\u003e). Only relevant for CRISPRi repression\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eStrand specificity\u003c/h3\u003e\u003ca id=\"user-content-strand-specificity\" class=\"anchor\" aria-label=\"Permalink: Strand specificity\" href=\"#strand-specificity\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe strand specificity is important for some CRISPR applications. In contrast to the \u003ccode\u003ecrisprDesign\u003c/code\u003e package, functions were added to allow the design of guide RNAs that target either both strands, or just the coding (non-template) strand, or the template strand. This can be defined with the \u003ccode\u003estrands\u003c/code\u003e parameter in the config file.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eFor CRISPRi (inhibition) experiments, the literature recommends to target the \u003cstrong\u003ecoding strand for the CDS\u003c/strong\u003e or \u003cstrong\u003eboth strands for the promoter\u003c/strong\u003e (\u003ca href=\"http://dx.doi.org/10.1038/nprot.2013.132\" rel=\"nofollow\"\u003eLarson et al., Nat Prot, 2013\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003ethis pipeline will automatically filter guides for the chosen strand\u003c/li\u003e\n\u003cli\u003efor example, if only guides for the coding (non-template) strand are desired, genes on the \"+\" strand will be targeted with reverse-complement guides (\"-\"), and genes on the \"-\" strand with \"+\" guides.\u003c/li\u003e\n\u003c/ul\u003e\n", - "data_format": 2, - "description": "A Snakemake workflow for the design of small guide RNAs (sgRNAs) for CRISPR applications.", - "formatting": null, - "full_name": "MPUSP/snakemake-crispr-guides", - "latest_release": "v1.2.0", - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": true - }, - "standardized": true, - "stargazers_count": 3, - "subscribers_count": 0, - "topics": [ - "bioinformatics-pipeline", - "crispr", - "crispr-design", - "guide-rna-library", - "python3", - "r-markdown", - "snakemake", - "workflow" - ], - "updated_at": 1724662792.0 - }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration options\u003c/h1\u003e\u003ca id=\"user-content-configuration-options\" class=\"anchor\" aria-label=\"Permalink: Configuration options\" href=\"#configuration-options\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003edefrabb uses two configuration files\u003c/p\u003e\n\u003cp\u003eSee \u003ccode\u003eschema/analyses-schema.yml\u003c/code\u003e and \u003ccode\u003eschema/resources-schema.yml\u003c/code\u003e for detailed descriptions and field formats requirements.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eresource.yaml\u003c/h2\u003e\u003ca id=\"user-content-resourceyaml\" class=\"anchor\" aria-label=\"Permalink: resource.yaml\" href=\"#resourceyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eused to define:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eparameters, threads, and memory for compute intensive steps\u003c/li\u003e\n\u003cli\u003eurls for remote files: diploid assemblies, genome reference files, stratifications, and callsets used to evaluate draft benchmark\u003c/li\u003e\n\u003cli\u003eexclusion sets and how they are applied\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eAnalyses Tables\u003c/h2\u003e\u003ca id=\"user-content-analyses-tables\" class=\"anchor\" aria-label=\"Permalink: Analyses Tables\" href=\"#analyses-tables\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eProvides run specific configurations\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003einput diploid assembly\u003c/li\u003e\n\u003cli\u003eversion of reference genome\u003c/li\u003e\n\u003cli\u003eassembly-based variant caller and parameters\u003c/li\u003e\n\u003cli\u003evcf and bed processing including what exclusions to use\u003c/li\u003e\n\u003cli\u003ebenchmarking method and comparison callset used for initial evaluation\u003c/li\u003e\n\u003c/ul\u003e\n", "data_format": 2, @@ -48995,6 +48995,46 @@ var data = "topics": [], "updated_at": 1616871931.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ac1513/MAGqual", + "latest_release": "v.0.3.0", + "linting": "Lints for snakefile /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule bakta_db (line 51, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule bakta (line 109, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule checkm_db (line 160, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule checkm (line 216, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule seqkit (line 272, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule high_mags (line 308, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param out_loc is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule report_gen (line 361, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 1, + "topics": [ + "metagenomic-analysis", + "metagenomic-pipeline", + "metagenomics", + "snakemake", + "snakemake-pipeline" + ], + "updated_at": 1724849292.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpa7c4q4jc/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_short-read-quality-control", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpa7c4q4jc/workflow/Snakefile\", line 14, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027short_read_qc\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 3, + "topics": [], + "updated_at": 1724523776.0 + }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eCNVand Configuration Instructions\u003c/h1\u003e\u003ca id=\"user-content-cnvand-configuration-instructions\" class=\"anchor\" aria-label=\"Permalink: CNVand Configuration Instructions\" href=\"#cnvand-configuration-instructions\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration File\u003c/h2\u003e\u003ca id=\"user-content-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Configuration File\" href=\"#configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration file (\u003ccode\u003econfig/config.yaml\u003c/code\u003e) contains various settings that the CNVand pipeline requires. Below is an example of a typical configuration file along with an explanation of each parameter.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eExample Configuration File\u003c/h3\u003e\u003ca id=\"user-content-example-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Example Configuration File\" href=\"#example-configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Samplesheet\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003econfig/samplesheet.tsv\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Output directory\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eoutdir\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eoutput/\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Reference data\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eref\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003egenome\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eworkflow/resources/Homo_sapiens_assembly38.fasta \u003c/span\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e Take care you\u0027re using the same reference in your full workflow\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003etarget_bed\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e.tests/integration/input/target.bed\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eantitarget_bed\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e.tests/integration/input/antitarget.bed\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Toolkit parameter settings\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eparams\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003ecnvkit\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etarget_coverage\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-q 20\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eantitarget_coverage\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-q 20\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ereference\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ecall\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eploidy\u003c/span\u003e: \u003cspan class=\"pl-c1\"\u003e2\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003ebintest\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003ebreaks\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003egenemetrics\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003escatter\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003ey_min\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-2.5\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003eexport_vcf\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003esegment\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eannotsv\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eannotations\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eworkflow/data/annotations/\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e Annotations to be downloaded externally - see README.md for more details\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eParameter Explanations\u003c/h3\u003e\u003ca id=\"user-content-parameter-explanations\" class=\"anchor\" aria-label=\"Permalink: Parameter Explanations\" href=\"#parameter-explanations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSamplesheet\u003c/h4\u003e\u003ca id=\"user-content-samplesheet\" class=\"anchor\" aria-label=\"Permalink: Samplesheet\" href=\"#samplesheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003esamples\u003c/strong\u003e: Path to the samplesheet file that contains information about the samples to be processed. This should be set to \u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eOutput Directory\u003c/h4\u003e\u003ca id=\"user-content-output-directory\" class=\"anchor\" aria-label=\"Permalink: Output Directory\" href=\"#output-directory\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eoutdir\u003c/strong\u003e: Path to the directory where the output files will be stored. This is set to \u003ccode\u003eoutput/\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eReference Data\u003c/h4\u003e\u003ca id=\"user-content-reference-data\" class=\"anchor\" aria-label=\"Permalink: Reference Data\" href=\"#reference-data\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eref\u003c/strong\u003e:\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003egenome\u003c/strong\u003e: Path to the reference genome file. Ensure that the reference genome used here is consistent throughout your workflow. Example: \u003ccode\u003eworkflow/resources/Homo_sapiens_assembly38.fasta\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003etarget_bed\u003c/strong\u003e: Path to the target BED file. Example: \u003ccode\u003e.tests/integration/input/target.bed\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eantitarget_bed\u003c/strong\u003e: Path to the antitarget BED file. Example: \u003ccode\u003e.tests/integration/input/antitarget.bed\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eToolkit Parameter Settings\u003c/h4\u003e\u003ca id=\"user-content-toolkit-parameter-settings\" class=\"anchor\" aria-label=\"Permalink: Toolkit Parameter Settings\" href=\"#toolkit-parameter-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eparams\u003c/strong\u003e:\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003ecnvkit\u003c/strong\u003e: Parameters for CNVkit tools.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003etarget_coverage\u003c/strong\u003e: Additional parameters for target coverage calculations. Example: \u003ccode\u003e-q 20\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eantitarget_coverage\u003c/strong\u003e: Additional parameters for antitarget coverage calculations. Example: \u003ccode\u003e-q 20\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ereference\u003c/strong\u003e: Additional parameters for reference generation.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ecall\u003c/strong\u003e: Parameters for CNV calling.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eploidy\u003c/strong\u003e: Ploidy level to be used. Example: \u003ccode\u003e2\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for the call step.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebintest\u003c/strong\u003e: Additional parameters for bin testing.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebreaks\u003c/strong\u003e: Additional parameters for breakpoints detection.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003egenemetrics\u003c/strong\u003e: Additional parameters for gene metrics calculation.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003escatter\u003c/strong\u003e: Parameters for scatter plot generation.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003ey_min\u003c/strong\u003e: Minimum y-axis value for scatter plots. Example: \u003ccode\u003e-2.5\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for scatter plots.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eexport_vcf\u003c/strong\u003e: Additional parameters for VCF export.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003esegment\u003c/strong\u003e: Additional parameters for segmentation.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eannotsv\u003c/strong\u003e: Parameters for AnnotSV tool.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eannotations\u003c/strong\u003e: Path to the directory containing annotation files. Example: \u003ccode\u003eworkflow/data/annotations/\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for AnnotSV.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSamplesheet\u003c/h2\u003e\u003ca id=\"user-content-samplesheet-1\" class=\"anchor\" aria-label=\"Permalink: Samplesheet\" href=\"#samplesheet-1\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe samplesheet (\u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e) contains information about the samples to be processed by the CNVand pipeline. It includes the sample name, path to the BAM file, and path to the VCF file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eExample Samplesheet\u003c/h3\u003e\u003ca id=\"user-content-example-samplesheet\" class=\"anchor\" aria-label=\"Permalink: Example Samplesheet\" href=\"#example-samplesheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-generic-db\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c1\"\u003esample bam_path vcf_path\u003c/span\u003e\n\u003cspan class=\"pl-c1\"\u003eM24352 .tests/integration/input/M24352_CHR21.bam .tests/integration/input/M24352_CHR21.vcf.gz\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eColumn Explanations\u003c/h3\u003e\u003ca id=\"user-content-column-explanations\" class=\"anchor\" aria-label=\"Permalink: Column Explanations\" href=\"#column-explanations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003esample\u003c/strong\u003e: Unique identifier for the sample. Example: \u003ccode\u003eM24352\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebam_path\u003c/strong\u003e: Path to the BAM file for the sample. Example: \u003ccode\u003e.tests/integration/input/M24352_CHR21.bam\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003evcf_path\u003c/strong\u003e: Path to the VCF file for the sample. Example: \u003ccode\u003e.tests/integration/input/M24352_CHR21.vcf.gz\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSummary\u003c/h2\u003e\u003ca id=\"user-content-summary\" class=\"anchor\" aria-label=\"Permalink: Summary\" href=\"#summary\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cstrong\u003eConfiguration File\u003c/strong\u003e: Ensure all paths and parameters are correctly set in the \u003ccode\u003econfig/config.yaml\u003c/code\u003e file.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eSamplesheet\u003c/strong\u003e: Ensure the \u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e file contains accurate paths to the BAM and VCF files for each sample.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eBy following these instructions, you will set up the CNVand pipeline correctly, ensuring accurate CNV analysis and annotation.\u003c/p\u003e\n", "data_format": 2, @@ -49234,46 +49274,6 @@ var data = "topics": [], "updated_at": 1724313234.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ac1513/MAGqual", - "latest_release": "v.0.3.0", - "linting": "Lints for snakefile /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule bakta_db (line 51, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule bakta (line 109, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule checkm_db (line 160, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule checkm (line 216, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule seqkit (line 272, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule high_mags (line 308, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param out_loc is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule report_gen (line 361, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 1, - "topics": [ - "metagenomic-analysis", - "metagenomic-pipeline", - "metagenomics", - "snakemake", - "snakemake-pipeline" - ], - "updated_at": 1724849292.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpa7c4q4jc/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_short-read-quality-control", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpa7c4q4jc/workflow/Snakefile\", line 14, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027short_read_qc\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 3, - "topics": [], - "updated_at": 1724523776.0 - }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral Settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General Settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIn the \u003ca href=\"./\"\u003e\u003ccode\u003econfig\u003c/code\u003e\u003c/a\u003e directory, you will find template configuration files\nfor this pipeline. For your run, you\u0027ll need to edit \u003ccode\u003esamples.tsv\u003c/code\u003e,\n\u003ccode\u003eunits.tsv\u003c/code\u003e, and \u003ccode\u003econfig.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSamples list\u003c/h2\u003e\u003ca id=\"user-content-samples-list\" class=\"anchor\" aria-label=\"Permalink: Samples list\" href=\"#samples-list\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAll your samples should be listed in \u003ccode\u003esamples.tsv\u003c/code\u003e. Samples preceded with a \u003ccode\u003e#\u003c/code\u003e\nwill not be included, this can be useful if you want to exclude a sample after\nquality checking.\u003c/p\u003e\n\u003cp\u003eEach sample must have four columns filled in the sample sheet. The columns are\ntab separated:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample\u003c/code\u003e - The name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003epopulation\u003c/code\u003e - The populations you will group your samples into. These are\nthe groups that population level stats are calculated on.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003etime\u003c/code\u003e - This should be either \u003ccode\u003emodern\u003c/code\u003e or \u003ccode\u003ehistorical\u003c/code\u003e, the only thing this\nwill affect is whether or not your bam files will be corrected for\npost-mortem damage or not.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edepth\u003c/code\u003e - This is only used for depth filtering. Extreme levels (both high\nand low) will be calculated for each group you put here as well as the\ndataset as a whole, and all will be filtered out for all analyses. Any string\ncan be used for this. If all samples are sequenced to roughly similar depths,\nall can have the same value. If some are low coverage, and some higher,\nsimply using \u0027low\u0027 and \u0027high\u0027 on the corresponding samples is sufficient.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe values in the sample list will end up in filenames, so ensure that they are\nonly characters permitted in filenames on your system.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eUnits list\u003c/h2\u003e\u003ca id=\"user-content-units-list\" class=\"anchor\" aria-label=\"Permalink: Units list\" href=\"#units-list\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAll your raw data will be pointed to in \u003ccode\u003eunits.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eEach sample must have five columns filled in the units sheet. The columns are\ntab separated:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample\u003c/code\u003e - The sample name, same as in \u003ccode\u003esamples.tsv\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eunit\u003c/code\u003e - This is used to fill out the \u003ccode\u003eID\u003c/code\u003e read group in the bam file. It\nmust be unique to each read group, so the same sample shouldn\u0027t have the\nsame unit for more than one sequencing run. A good format might be\n\u003ccode\u003esequencer_barcode.lane\u003c/code\u003e. Optical duplicates will be removed within units.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elib\u003c/code\u003e - This is used to fill out the \u003ccode\u003eLB\u003c/code\u003e read group. This should be a unique\nidentifier for each sample library. Sequencing runs from the same library,\nbut different runs, will have the same value in \u003ccode\u003elib\u003c/code\u003e, but different in\n\u003ccode\u003eunit\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eplatform\u003c/code\u003e - This is used to fill out the \u003ccode\u003ePL\u003c/code\u003e read group. Put what you\u0027d\nwant there. Usually \u003ccode\u003eILLUMINA\u003c/code\u003e for Illumina platforms.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e - The absolute or relative paths from the working directory\nto the raw fastq files for the sample. Currently the pipeline only supports\npaired-end sequencing, single end may be added down the line.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration file\u003c/h2\u003e\u003ca id=\"user-content-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Configuration file\" href=\"#configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e contains the configuration for the workflow, this is where you\nwill put what analyses, filters, and options you want. Below I describe the\nconfiguration options. The \u003ca href=\"config.yaml\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/a\u003e in this repository\nserves as a template, but includes some \u0027default\u0027 parameters that may be good\nstarting points for some users. If \u003ccode\u003e--configfile\u003c/code\u003e is not specified in the\nsnakemake command, the workflow will default to \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eConfiguration options\u003c/h3\u003e\u003ca id=\"user-content-configuration-options\" class=\"anchor\" aria-label=\"Permalink: Configuration options\" href=\"#configuration-options\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eDataset Configuration\u003c/h4\u003e\u003ca id=\"user-content-dataset-configuration\" class=\"anchor\" aria-label=\"Permalink: Dataset Configuration\" href=\"#dataset-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eRequired configuration of the \u0027dataset\u0027.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples:\u003c/code\u003e An absolute or relative path from the working directory to the\n\u003ccode\u003esamples.tsv\u003c/code\u003e file.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eunits:\u003c/code\u003e An absolute or relative path from the working directory to the\n\u003ccode\u003eunits.tsv\u003c/code\u003e file.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edataset:\u003c/code\u003e A name for this dataset run - essentially, an identifier for a\nbatch of samples to be analysed together with the same configuration.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eHere, dataset means a set of samples and configurations that the workflow will\nbe run with. Each dataset should have its own \u003ccode\u003esamples.tsv\u003c/code\u003e and \u003ccode\u003econfig.yaml\u003c/code\u003e,\nbut the same \u003ccode\u003eunits.tsv\u003c/code\u003e can be used for multiple if you prefer. Essentially,\nwhat the dataset identifier does is keeps your outputs organized into projects,\nso that the same BAM files can be used in multiple datasets without having to\nbe remade.\u003c/p\u003e\n\u003cp\u003eSo, say you have \u003ccode\u003edataset1_samples.tsv\u003c/code\u003e and \u003ccode\u003edataset2_samples.tsv\u003c/code\u003e, with\ncorresponding \u003ccode\u003edataset1_config.tsv\u003c/code\u003e and \u003ccode\u003edataset2_config.yaml\u003c/code\u003e. The sample\nfiles contain different samples, though some are shared between the datasets.\nThe workflow for dataset1 can be run, and then dataset2 can be run. When\ndataset2 runs, it map new samples, but won\u0027t re-map samples processed in\ndataset1. Each will perform downstream analyses independently with their sample\nset and configuration files, storing these results in dataset specific folders.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eReference Configuration\u003c/h4\u003e\u003ca id=\"user-content-reference-configuration\" class=\"anchor\" aria-label=\"Permalink: Reference Configuration\" href=\"#reference-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eRequired configuration of the reference.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003echunk_size:\u003c/code\u003e A size in bp (integer). Your reference will be analyzed in\n\u0027chunks\u0027 of contigs of this size to parallelize processing. This size should\nbe larger than the largest contig in your genome. A larger number means fewer\njobs that run longer. A smaller number means more jobs that run shorter. The\nbest fit will depend on the reference and the compute resources you have\navailable. Leaving this blank will not divide the reference up into chunks\n(but this isn\u0027t optimized yet, so it will do a couple unnecessary steps).\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003ereference:\u003c/code\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003ename:\u003c/code\u003e A name for your reference genome, will go in the file names.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efasta:\u003c/code\u003e A path to the reference fasta file (currently only supports\nuncompressed fasta files)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emito:\u003c/code\u003e Mitochondrial contig name(s), will be removed from analysis. Should\nbe listed within brackets []\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003esex-linked:\u003c/code\u003e Sex-linked contig name(s), will be removed from analysis.\nShould be listed within brackets []\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eexclude:\u003c/code\u003e Additional contig name(s) to exclude from analysis. Should be\nlisted within brackets []\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emin_size:\u003c/code\u003e A size in bp (integer). All contigs below this size will be\nexcluded from analysis.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eReference genomes should be uncompressed, and contig names should be clear and\nconcise. Currently, there are some issues parsing contig names with\nunderscores, so please change these in your reference before running the\npipeline. Alphanumeric characters, as well as \u003ccode\u003e.\u003c/code\u003e in contig names have been\ntested to work so far, other symbols have not been tested.\u003c/p\u003e\n\u003cp\u003ePotentially the ability to use bgzipped genomes will be added, I just need to\ncheck that it works with all underlying tools. Currently, it will for sure not\nwork, as calculating chunks is hard-coded to work on an uncompressed genome.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSample Set Configuration\u003c/h4\u003e\u003ca id=\"user-content-sample-set-configuration\" class=\"anchor\" aria-label=\"Permalink: Sample Set Configuration\" href=\"#sample-set-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis will exclude individuals from analysis that are listed in the sample list.\nThis may be useful if you run the workflow and find a poor quality sample, and\nwant to re-run without it. Or if you have relatives in the dataset and you want\nto exclude them where necessary.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eexclude_ind:\u003c/code\u003e Sample name(s) that will be excluded from the workflow. Should\nbe a list in [].\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eexcl_pca-admix:\u003c/code\u003e Sample name(s) that will be excluded \u003cem\u003eonly\u003c/em\u003e from PCA and\nAdmixture analyses. Useful for close relatives that violate the assumptions\nof these analyses, but that you want in others. Should be a list in [].\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eAnalysis Selection\u003c/h4\u003e\u003ca id=\"user-content-analysis-selection\" class=\"anchor\" aria-label=\"Permalink: Analysis Selection\" href=\"#analysis-selection\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eHere, you will define which analyses you will perform. It is useful to start\nwith only a few, and add more in subsequent workflow runs, just to ensure you\ncatch errors before you use compute time running all analyses. Most are set\nwith (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e) or a value, described below. Modifications to the\nsettings for each analysis are set in the next section.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003epopulations:\u003c/code\u003e A list of populations found in your sample list to limit\npopulation analyses to. Might be useful if you want to perform individual\nanalyses on some samples but not include them in any population level\nanalyses\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eanalyses:\u003c/code\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003egenmap:\u003c/code\u003e Filter out sites with low mappability estimated by Genmap\n(\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erepeatmasker:\u003c/code\u003e (NOTE: Only one of the three options should be filled/true)\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003elocal_lib:\u003c/code\u003e Filter repeats by masking with an already made library you\nhave locally. Should be file path.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edfam_lib:\u003c/code\u003e Filter repeats using a library available from dfam. Should be\na taxonomic group name.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild_lib:\u003c/code\u003e Use RepeatModeler to build a library of repeats from the\nreference itself, then filter them from analysis (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e).\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eextreme_depth:\u003c/code\u003e Filter out sites with extremely high or low global\nsequencing depth (\u003ccode\u003e[lower, upper]\u003c/code\u003e). The value of \u003ccode\u003elower\u003c/code\u003e (float) will be\nmultiplied by the median global depth to create a lower global depth\nthreshold, and \u003ccode\u003eupper\u003c/code\u003e will do the same to creat an upper threshold. This\nis done for all samples, as well as separately for depth groupings defined\nin samples file.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edataset_missing_data:\u003c/code\u003e A floating point value between 0 and 1. Sites with\ndata for fewer than this proportion of individuals across the whole dataset\nwill be filtered out.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003epopulation_missing_data:\u003c/code\u003e A floating point value between 0 and 1. Sites\nwith data for fewer than this proportion of individuals in any population\nwill be filtered out for all populations.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003equalimap:\u003c/code\u003e Perform Qualimap bamqc on bam files for general quality stats\n(\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edamageprofiler:\u003c/code\u003e Estimate post-mortem DNA damage on historical samples\nwith Damageprofiler (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e) NOTE: This just adds the addition of\nDamageprofiler to the already default output of MapDamage. DNA damage will\nalways be estimated and rescaled by MapDamage for samples marked as\n\u0027historical\u0027\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eestimate_ld:\u003c/code\u003e Estimate pairwise linkage disquilibrium between sites with\nngsLD for each popualation and the whole dataset. Note, only set this if\nyou want to generate the LD estimates for use in downstream analyses\noutside this workflow. Other analyses within this workflow that require LD\nestimates (LD decay/pruning) will function properly regardless of the\nsetting here. (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eld_decay:\u003c/code\u003e Use ngsLD to plot LD decay curves for each population and for\nthe dataset as a whole (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003epca_pcangsd:\u003c/code\u003e Perform Principal Component Analysis with PCAngsd\n(\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eadmix_ngsadmix:\u003c/code\u003e Perform admixture analysis with NGSadmix (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelatedness:\u003c/code\u003e Can be performed multiple ways, set any combination of the\nthree options below. Note, that I\u0027ve mostly incorporated these with the\nR0/R1/KING kinship methods in Waples et al. 2019, \u003cem\u003eMol. Ecol.\u003c/em\u003e in mind.\nThese methods differ slightly from how they implement this method, and will\ngive slightly more/less accurate estimates of kinship depending on your\nreference\u0027s relationship to your samples. \u003ccode\u003eibsrelate_ibs\u003c/code\u003e uses the\nprobabilities of all possible genotypes, so should be the most accurate\nregardless, but can use a lot of memory and take a long time with many\nsamples. \u003ccode\u003eibsrelate_sfs\u003c/code\u003e is a bit more efficient, as it does things in a\npairwise fashion in parallel, but may be biased if the segregating alleles\nin your populations are not represented in the reference. \u003ccode\u003engsrelate\u003c/code\u003e uses\nseveral methods, one of which is similar to \u003ccode\u003eibsrelate_sfs\u003c/code\u003e, but may be\nless accurate due to incorporating in less data. In my experience,\nNGSrelate is suitable to identify up to third degree relatives in the\ndataset, but only if the exact relationship can be somewhat uncertain (i.e.\nyou don\u0027t need to know the difference between, say, parent/offspring and\nfull sibling pairs, or between second degree and third degree relatives).\nIBSrelate_sfs can get you greater accuracy, but may erroneously inflate\nkinship if your datset has many alleles not represented in your reference.\nIf you notice, for instance, a large number of third degree relatives\n(KING ~0.03 - 0.07) in your dataset that is not expected, it may be worth\ntrying the IBS based method (\u003ccode\u003eibsrelate_ibs\u003c/code\u003e).\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003engsrelate:\u003c/code\u003e Co-estimate inbreeding and pairwise relatedness with\nNGSrelate (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eibsrelate_ibs:\u003c/code\u003e Estimate pairwise relatedness with the IBS based method\nfrom Waples et al. 2019, \u003cem\u003eMol. Ecol.\u003c/em\u003e. This can use a lot of memory, as\nit has genotype likelihoods for all sites from all samples loaded into\nmemory, so it is done per \u0027chunk\u0027, which still takes a lot of time and\nmemory. (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eibsrelate_sfs:\u003c/code\u003e Estimate pairwise relatedness with the SFS based method\nfrom Waples et al. 2019, \u003cem\u003eMol. Ecol.\u003c/em\u003e. Enabling this can greatly increase\nthe time needed to build the workflow DAG if you have many samples. As a\nform of this method is implemented in NGSrelate, it may be more\nefficient to only enable that. (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ethetas_angsd:\u003c/code\u003e Estimate pi, theta, and Tajima\u0027s D for each population in\nwindows across the genome using ANGSD (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eheterozygosity_angsd:\u003c/code\u003e Estimate individual genome-wide heterozygosity\nusing ANGSD (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efst_angsd:\u003c/code\u003e Estimate pairwise $F_{ST}$ using ANGSD. Set one or both of the\nbelow options. Estimates both globally and in windows across the genome.\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003epopulations:\u003c/code\u003e Pairwise $F_{ST}$ is calculated between all possible\npopulation pairs (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eindividuals:\u003c/code\u003e Pairwise $F_{ST}$ is calculated between all possible\npopulation pairs. NOTE: This can be really intensive on the DAG building\nprocess, so I don\u0027t recommend enabling unless you\u0027re certain you want\nthis (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003einbreeding_ngsf-hmm:\u003c/code\u003e Estimates inbreeding coefficients and runs of\nhomozygosity using ngsF-HMM. Output is converted into an inbreeding measure\n$F_ROH$, which describes the proportion of the genome in runs of\nhomozygosity over a certain length. (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eibs_matrix:\u003c/code\u003e Estimate pairwise identity by state distance between all\nsamples using ANGSD. (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eFilter Sets\u003c/h4\u003e\u003ca id=\"user-content-filter-sets\" class=\"anchor\" aria-label=\"Permalink: Filter Sets\" href=\"#filter-sets\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBy default, this workflow will perform all analyses requested in the above\nsection on all sites that pass the filters set in the above section. These\noutputs will contain \u003ccode\u003eallsites-filts\u003c/code\u003e in the filename and in the report.\nHowever, many times, it is useful to perform an analysis on different subsets\nof sites, for instance, to compare results for genic vs. intergenic regions,\nneutral sites, exons vs. introns, etc. Here, users can set an arbitrary number\nof additional filters using BED files. For each BED file supplied, the contents\nwill be intersected with the sites passing the filters set in the above\nsection, and all analyses will be performed additionally using those sites.\u003c/p\u003e\n\u003cp\u003eFor instance, given a BED file containing putatively neutral sites, one could\nset the following:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003efilter_beds\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eneutral-sites\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eresources/neutral_sites.bed\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIn this case, for each requested analysis, in addition to the \u003ccode\u003eallsites-filts\u003c/code\u003e\noutput, a \u003ccode\u003eneutral-filts\u003c/code\u003e (named after the key assigned to the BED file in\n\u003ccode\u003econfig.yaml\u003c/code\u003e) output will also be generated, containing the results for sites\nwithin the specified BED file that passed any set filters.\u003c/p\u003e\n\u003cp\u003eMore than one BED file can be set, up to an arbitrary number:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-ent\"\u003efilter_beds\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eneutral\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eresources/neutral_sites.bed\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eintergenic\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eresources/intergenic_sites.bed\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eintrons\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eresources/introns.bed\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIt may also sometimes be desireable to skip analyses on \u003ccode\u003eallsites-filts\u003c/code\u003e, say\nif you are trying to only generate diversity estimates or generate SFS for a\nset of neutral sites you supply. To skip running any analyses for\n\u003ccode\u003eallsites-filts\u003c/code\u003e and only perform them for the BED files you supply, you can\nset \u003ccode\u003eonly_filter_beds: true\u003c/code\u003e in the config file. This may also be useful in the\nevent you have a set of already filtered sites, and want to run the workflow on\nthose, ignoring any of the built in filter options by setting them to \u003ccode\u003efalse\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSoftware Configuration\u003c/h4\u003e\u003ca id=\"user-content-software-configuration\" class=\"anchor\" aria-label=\"Permalink: Software Configuration\" href=\"#software-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThese are software specific settings that can be user configured in the\nworkflow. If you are missing a configurable setting you need, open up an issue\nor a pull request and I\u0027ll gladly put it in.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003emapQ:\u003c/code\u003e Phred-scaled mapping quality filter. Reads below this threshold will\nbe filtered out. (integer)\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003ebaseQ:\u003c/code\u003e Phred-scaled base quality filter. Reads below this threshold will be\nfiltered out. (integer)\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003ccode\u003eparams:\u003c/code\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003egenmap:\u003c/code\u003e Parameters for mappability analysis, see \u003ca href=\"https://github.com/cpockrandt/genmap/\"\u003eGenMap\u0027s documentation\u003c/a\u003e\nfor more details.\n\u003cul\u003e\n\u003cli\u003e\u003ccode\u003eK:\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003e\u003ccode\u003eE:\u003c/code\u003e\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emap_thresh:\u003c/code\u003e A threshold mappability score. Sites with a mappability\nscore below this threshold are filtered out if GenMap is enabled.\n(integer/float, 0-1)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efastp:\u003c/code\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eextra:\u003c/code\u003e Additional options to pass to fastp trimming. (string)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003epicard:\u003c/code\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eMarkDuplicates:\u003c/code\u003e Additional options to pass to Picard MarkDuplicates.\n\u003ccode\u003e--REMOVE_DUPLICATES true\u003c/code\u003e is recommended. (string)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eangsd:\u003c/code\u003e General options in ANGSD, relevant doc pages are linked\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003egl_model:\u003c/code\u003e Genotype likelihood model to use in calculation\n(\u003ccode\u003e-GL\u003c/code\u003e option in ANGSD, \u003ca href=\"http://www.popgen.dk/angsd/index.php/Genotype_Likelihoods\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emaxdepth:\u003c/code\u003e When calculating individual depth, sites with depth higher\nthan this will be binned to this value. Should be fine for most to leave\nat \u003ccode\u003e1000\u003c/code\u003e. (integer, \u003ca href=\"http://www.popgen.dk/angsd/index.php/Depth\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eextra:\u003c/code\u003e Additional options to pass to ANGSD during genotype likelihood\ncalculation. This is primarily useful for adding BAM input filters. Note\nthat \u003ccode\u003e--remove_bads\u003c/code\u003e and \u003ccode\u003e-only_proper_pairs\u003c/code\u003e are enabled by default, so\nthey only need to be included if you want to turn them off. I\u0027ve also\nfound that for some datasets, \u003ccode\u003e-C 50\u003c/code\u003e and \u003ccode\u003e-baq 1\u003c/code\u003e can create a strong\nrelationship between sample depth and detected diversity, effectively\nremoving the benefits of ANGSD for low/variable depth data. I recommend\nthat these aren\u0027t included unless you know you need them, and even then,\nI\u0027d recommend plotting \u003ccode\u003eheterozygosity ~ sample depth\u003c/code\u003e to ensure there is\nnot any relationship. Since the workflow uses bwa to map, \u003ccode\u003e-uniqueOnly 1\u003c/code\u003e\ndoesn\u0027t do anything if your minimum mapping quality is \u0026gt; 0. Don\u0027t put\nmapping and base quality thresholds here either, it will use the ones\ndefined above automatically. Although historical samples will have DNA\ndamaged assessed and to some extent, corrected, it may be useful to put\n\u003ccode\u003e-noTrans 1\u003c/code\u003e or \u003ccode\u003e-trim INT\u003c/code\u003e here if you\u0027re interested in stricter filters\nfor degraded DNA. (string, \u003ca href=\"http://www.popgen.dk/angsd/index.php/Input#BAM.2FCRAM\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003esnp_pval:\u003c/code\u003e The p-value to use for calling SNPs (float, \u003ca href=\"http://www.popgen.dk/angsd/index.php/SNP_calling\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emin_maf:\u003c/code\u003e The minimum minor allele frequency required to call a SNP.\n(float, \u003ca href=\"http://www.popgen.dk/angsd/index.php/Allele_Frequencies\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003engsld:\u003c/code\u003e Settings for ngsLD (\u003ca href=\"https://github.com/fgvieira/ngsLD\"\u003edocs\u003c/a\u003e)\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003emax_kb_dist_est-ld:\u003c/code\u003e For the LD estimates generated when setting\n\u003ccode\u003eestimate_ld: true\u003c/code\u003e above, set the maximum distance between sites in kb\nthat LD will be estimated for (\u003ccode\u003e--max_kb_dist\u003c/code\u003e in ngsLD, integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emax_kb_dist_decay:\u003c/code\u003e The same as \u003ccode\u003emax_kb_dist_est-ld:\u003c/code\u003e, but used when\nestimating LD decay when setting \u003ccode\u003eld_decay: true\u003c/code\u003e above (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emax_kb_dist_pruning:\u003c/code\u003e The same as \u003ccode\u003emax_kb_dist_est-ld:\u003c/code\u003e, but used when\nlinkage pruning SNPs as inputs for PCA, Admix, and Inbreeding analyses.\nAny positions above this distance will be assumed to be in linkage\nequilibrium during the pruning process (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ernd_sample_est-ld:\u003c/code\u003e For the LD estimates generated when setting\n\u003ccode\u003eestimate_ld: true\u003c/code\u003e above, randomly sample this proportion of pairwise\nlinkage estimates rather than estimating all (\u003ccode\u003e--rnd_sample\u003c/code\u003e in ngsLD,\nfloat)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ernd_sample_decay:\u003c/code\u003e The same as \u003ccode\u003ernd_sample_est-ld:\u003c/code\u003e, but used when\nestimating LD decay when setting \u003ccode\u003eld_decay: true\u003c/code\u003e above (float)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efit_LDdecay_extra:\u003c/code\u003e Additional plotting arguments to pass to\n\u003ccode\u003efit_LDdecay.R\u003c/code\u003e when estimating LD decay (string)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efit_LDdecay_n_correction:\u003c/code\u003e When estimating LD decay, should the sample\nsize corrected r^2 model be used? (\u003ccode\u003etrue\u003c/code\u003e/\u003ccode\u003efalse\u003c/code\u003e, \u003ccode\u003etrue\u003c/code\u003e is the\nequivalent of passing a sample size to \u003ccode\u003efit_LDdecay.R\u003c/code\u003e in ngsLD using\n\u003ccode\u003e--n_ind\u003c/code\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003epruning_min-weight:\u003c/code\u003e The minimum r^2 to assume two positions are in\nlinkage disequilibrium when pruning (float)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erealSFS:\u003c/code\u003e Settings for realSFS\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efold:\u003c/code\u003e Whether or not to fold the produced SFS (0 or 1, \u003ca href=\"http://www.popgen.dk/angsd/index.php/SFS_Estimation\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\n\u003cstrong\u003eNOTE:\u003c/strong\u003e I have not implemented the use of an ancestral reference into\nthis workflow, so this should always be set to 1 until I implement this.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003esfsboot:\u003c/code\u003e Doesn\u0027t work now, but when it does it will produce this many\nbootstrapped SFS per population and population pair (integer)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efst:\u003c/code\u003e Settings for $F_{ST}$ calculation in ANGSD\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003ewhichFst:\u003c/code\u003e Determines which $F_{ST}$ estimator is used by ANGSD. With 0\nbeing the default Reynolds 1983 and 1 being the Bhatia 2013 estimator.\nThe latter is preferable for small or uneven sample sizes\n(0 or 1, \u003ca href=\"http://www.popgen.dk/angsd/index.php/Fst\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ewin_size:\u003c/code\u003e Window size in bp for sliding window analysis (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ewin_step:\u003c/code\u003e Window step size in bp for sliding window analysis (integer)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ethetas:\u003c/code\u003e Settings for pi, theta, and Tajima\u0027s D estimation\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003ewin_size:\u003c/code\u003e Window size in bp for sliding window analysis (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ewin_step:\u003c/code\u003e Window step size in bp for sliding window analysis (integer)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003engsadmix:\u003c/code\u003e Settings for admixture analysis with NGSadmix. This analysis is\nperformed for a set of K groupings, and each K has several replicates\nperformed. Replicates will continue until a set of N highest likelihood\nreplicates converge, or the number of replicates reaches an upper threshold\nset here. Defaults for \u003ccode\u003ereps\u003c/code\u003e, \u003ccode\u003eminreps\u003c/code\u003e, \u003ccode\u003ethresh\u003c/code\u003e, and \u003ccode\u003econv\u003c/code\u003e can be left\nas default for most.\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003ekvalues:\u003c/code\u003e A list of values of K to fit the data to (list of integers)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ereps:\u003c/code\u003e The maximum number of replicates to perform per K (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eminreps:\u003c/code\u003e The minimum number of replicates to perform, even if\nreplicates have converged (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ethresh:\u003c/code\u003e The convergence threshold - the top replicates must all be\nwithin this value of log-likelihood units to consider the run converged\n(integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003econv:\u003c/code\u003e The number of top replicates to include in convergence\nassessment. (integer)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eextra:\u003c/code\u003e Additional arguments to pass to NGSadmix (for instance,\nincreasing \u003ccode\u003e-maxiter\u003c/code\u003e). (string, \u003ca href=\"http://www.popgen.dk/software/index.php/NgsAdmix\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eibs:\u003c/code\u003e Settings for identity by state calculation with ANGSD\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003e-doIBS:\u003c/code\u003e Whether to use a random (1) or consensus (2) base in IBS\ndistance calculation (\u003ca href=\"http://www.popgen.dk/angsd/index.php/PCA_MDS\" rel=\"nofollow\"\u003edocs\u003c/a\u003e)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n", "data_format": 2, @@ -55408,23 +55408,6 @@ var data = "topics": [], "updated_at": 1703835607.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "\ud83c\udf44 Qiime2 ITS classifiers for the UNITE database", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9o9cg3sb/colinbrislawn-unite-train-2b249fc/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "colinbrislawn/unite-train", - "latest_release": "v10.0-v04.04.2024-qiime2-2024.5", - "linting": null, - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 33, - "subscribers_count": 3, - "topics": [], - "updated_at": 1725927586.0 - }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eDependencies installation\u003c/h1\u003e\u003ca id=\"user-content-dependencies-installation\" class=\"anchor\" aria-label=\"Permalink: Dependencies installation\" href=\"#dependencies-installation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eInstall dependencies with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003emamba env create -f install/environment.yml\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eActivate environment\u003c/h1\u003e\u003ca id=\"user-content-activate-environment\" class=\"anchor\" aria-label=\"Permalink: Activate environment\" href=\"#activate-environment\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eActivate the Conda environment with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda activate zarp\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eRun the workflow on your own samples\u003c/h1\u003e\u003ca id=\"user-content-run-the-workflow-on-your-own-samples\" class=\"anchor\" aria-label=\"Permalink: Run the workflow on your own samples\" href=\"#run-the-workflow-on-your-own-samples\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003eAssuming that your current directory is the repository\u0027s root directory,\ncreate [...] and enter it, with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003emkdir config/my_run\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e config/my_run\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eCreate an empty sample table and a workflow configuration file:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003etouch samples.tsv\ntouch config.yaml\u003c/pre\u003e\u003c/div\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eUse your editor of choice to populate these files with appropriate\nvalues. Have a look at the examples in the \u003ccode\u003etests/\u003c/code\u003e directory to see what the\nfiles should look like, specifically:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"../tests/input_files/samples.tsv\"\u003esamples.tsv\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"../tests/input_files/config.yaml\"\u003econfig.yaml\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eMore execution options\u003c/h1\u003e\u003ca id=\"user-content-more-execution-options\" class=\"anchor\" aria-label=\"Permalink: More execution options\" href=\"#more-execution-options\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFor more execution options, like sample fetching from SRA, inferring sample metadata from the data itself, cluster execution, and many more, visit ZARP \u003ca href=\"../README.md\"\u003egeneral\u003c/a\u003e and \u003ca href=\"../pipeline-documentation\"\u003ein-depth pipeline docmentation\u003c/a\u003e.\u003c/p\u003e\n", "data_format": 2, @@ -55458,6 +55441,23 @@ var data = ], "updated_at": 1725478014.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "\ud83c\udf44 Qiime2 ITS classifiers for the UNITE database", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9o9cg3sb/colinbrislawn-unite-train-2b249fc/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "colinbrislawn/unite-train", + "latest_release": "v10.0-v04.04.2024-qiime2-2024.5", + "linting": null, + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 33, + "subscribers_count": 3, + "topics": [], + "updated_at": 1725927586.0 + }, { "config_readme": null, "data_format": 2, diff --git a/skips.json b/skips.json index 37d95c7..408c3f0 100644 --- a/skips.json +++ b/skips.json @@ -1,4 +1,160 @@ [ + { + "full_name": "zqfang/haplomap", + "updated_at": 1724865972.0 + }, + { + "full_name": "thebgacademy/colora", + "updated_at": 1724879405.0 + }, + { + "full_name": "wtbarnes/mocksipipeline", + "updated_at": 1724859003.0 + }, + { + "full_name": "bihealth/StemCNV-check", + "updated_at": 1724857356.0 + }, + { + "full_name": "gi-bielefeld/plast", + "updated_at": 1724839842.0 + }, + { + "full_name": "tycho-kirchner/shournal", + "updated_at": 1726048494.0 + }, + { + "full_name": "TyberiusPrime/pypipegraph2", + "updated_at": 1724827489.0 + }, + { + "full_name": "Deylab999MSKCC/cv2f", + "updated_at": 1724819145.0 + }, + { + "full_name": "cvaske/cho-skin-cd45", + "updated_at": 1724798352.0 + }, + { + "full_name": "Snitkin-Lab-Umich/nanoQC", + "updated_at": 1724791394.0 + }, + { + "full_name": "dadrasarmin/rnaseq_quantification_kallisto_pipeline", + "updated_at": 1724784689.0 + }, + { + "full_name": "sylvainschmitt/climfor", + "updated_at": 1724772527.0 + }, + { + "full_name": "Rounge-lab/mock_mycobiome", + "updated_at": 1724761553.0 + }, + { + "full_name": "maxplanck-ie/nanoporeReads_dataTransfer", + "updated_at": 1724757303.0 + }, + { + "full_name": "gputtley/INNFER", + "updated_at": 1724743561.0 + }, + { + "full_name": "vsbuffalo/grid_df", + "updated_at": 1724733824.0 + }, + { + "full_name": "Diako-Lab/SRAscraper", + "updated_at": 1724726805.0 + }, + { + "full_name": "swajid/review_and_read_ahead", + "updated_at": 1724701536.0 + }, + { + "full_name": "gurayerus/AIBIL_Workflows", + "updated_at": 1724694079.0 + }, + { + "full_name": "CCRGeneticsBranch/Oncogenomics_NF_WF", + "updated_at": 1724694618.0 + }, + { + "full_name": "akanksha-sachan/ERCC1_iPSC_analysis", + "updated_at": 1724690584.0 + }, + { + "full_name": "metagenlab/zAMP", + "updated_at": 1724676627.0 + }, + { + "full_name": "kdm9/Acanthophis", + "updated_at": 1726011337.0 + }, + { + "full_name": "snakemake/snakemake-interface-storage-plugins", + "updated_at": 1724655486.0 + }, + { + "full_name": "sagc-bioinformatics/nextflow-example-workflow-2024", + "updated_at": 1724825872.0 + }, + { + "full_name": "MetaSUB-CAMP/CAMP_Module_Template", + "updated_at": 1725187709.0 + }, + { + "full_name": "hackerzone85/Microbiome_Analysis_DIAMOND_MEGAN_Pipeline", + "updated_at": 1724497763.0 + }, + { + "full_name": "Moha-cm/AutoRNASeq", + "updated_at": 1724857295.0 + }, + { + "full_name": "ICESAT-2HackWeek/GroundingLine-Greenland", + "updated_at": 1726177759.0 + }, + { + "full_name": "adonath/chandra-im-lup-check", + "updated_at": 1724441404.0 + }, + { + "full_name": "GhedinSGS/DiVRGE", + "updated_at": 1724440766.0 + }, + { + "full_name": "zg404/Doradocker", + "updated_at": 1724439453.0 + }, + { + "full_name": "jeszyman/cfdna", + "updated_at": 1724434802.0 + }, + { + "full_name": "sylvainschmitt/treemutation", + "updated_at": 1724423917.0 + }, + { + "full_name": "paulinarosales/labeled-nascent-rnaseq-snakemake-pipeline", + "updated_at": 1724423041.0 + }, + { + "full_name": "ouslalu/cnv", + "updated_at": 1724411405.0 + }, + { + "full_name": "Wytamma/snk-cli", + "updated_at": 1724399618.0 + }, + { + "full_name": "bioc/scaeData", + "updated_at": 1724381316.0 + }, + { + "full_name": "CBICA/NiChart_Workflows", + "updated_at": 1725038727.0 + }, { "full_name": "reanahub/reana", "updated_at": 1725436751.0 @@ -1815,146 +1971,6 @@ "full_name": "tsnorri/panvc3", "updated_at": 1724056129.0 }, - { - "full_name": "gi-bielefeld/plast", - "updated_at": 1724839842.0 - }, - { - "full_name": "tycho-kirchner/shournal", - "updated_at": 1726048494.0 - }, - { - "full_name": "TyberiusPrime/pypipegraph2", - "updated_at": 1724827489.0 - }, - { - "full_name": "Deylab999MSKCC/cv2f", - "updated_at": 1724819145.0 - }, - { - "full_name": "cvaske/cho-skin-cd45", - "updated_at": 1724798352.0 - }, - { - "full_name": "Snitkin-Lab-Umich/nanoQC", - "updated_at": 1724791394.0 - }, - { - "full_name": "dadrasarmin/rnaseq_quantification_kallisto_pipeline", - "updated_at": 1724784689.0 - }, - { - "full_name": "sylvainschmitt/climfor", - "updated_at": 1724772527.0 - }, - { - "full_name": "Rounge-lab/mock_mycobiome", - "updated_at": 1724761553.0 - }, - { - "full_name": "maxplanck-ie/nanoporeReads_dataTransfer", - "updated_at": 1724757303.0 - }, - { - "full_name": "gputtley/INNFER", - "updated_at": 1724743561.0 - }, - { - "full_name": "vsbuffalo/grid_df", - "updated_at": 1724733824.0 - }, - { - "full_name": "Diako-Lab/SRAscraper", - "updated_at": 1724726805.0 - }, - { - "full_name": "swajid/review_and_read_ahead", - "updated_at": 1724701536.0 - }, - { - "full_name": "gurayerus/AIBIL_Workflows", - "updated_at": 1724694079.0 - }, - { - "full_name": "CCRGeneticsBranch/Oncogenomics_NF_WF", - "updated_at": 1724694618.0 - }, - { - "full_name": "akanksha-sachan/ERCC1_iPSC_analysis", - "updated_at": 1724690584.0 - }, - { - "full_name": "metagenlab/zAMP", - "updated_at": 1724676627.0 - }, - { - "full_name": "kdm9/Acanthophis", - "updated_at": 1726011337.0 - }, - { - "full_name": "snakemake/snakemake-interface-storage-plugins", - "updated_at": 1724655486.0 - }, - { - "full_name": "sagc-bioinformatics/nextflow-example-workflow-2024", - "updated_at": 1724825872.0 - }, - { - "full_name": "MetaSUB-CAMP/CAMP_Module_Template", - "updated_at": 1725187709.0 - }, - { - "full_name": "hackerzone85/Microbiome_Analysis_DIAMOND_MEGAN_Pipeline", - "updated_at": 1724497763.0 - }, - { - "full_name": "Moha-cm/AutoRNASeq", - "updated_at": 1724857295.0 - }, - { - "full_name": "ICESAT-2HackWeek/GroundingLine-Greenland", - "updated_at": 1726177759.0 - }, - { - "full_name": "adonath/chandra-im-lup-check", - "updated_at": 1724441404.0 - }, - { - "full_name": "GhedinSGS/DiVRGE", - "updated_at": 1724440766.0 - }, - { - "full_name": "zg404/Doradocker", - "updated_at": 1724439453.0 - }, - { - "full_name": "jeszyman/cfdna", - "updated_at": 1724434802.0 - }, - { - "full_name": "sylvainschmitt/treemutation", - "updated_at": 1724423917.0 - }, - { - "full_name": "paulinarosales/labeled-nascent-rnaseq-snakemake-pipeline", - "updated_at": 1724423041.0 - }, - { - "full_name": "ouslalu/cnv", - "updated_at": 1724411405.0 - }, - { - "full_name": "Wytamma/snk-cli", - "updated_at": 1724399618.0 - }, - { - "full_name": "bioc/scaeData", - "updated_at": 1724381316.0 - }, - { - "full_name": "CBICA/NiChart_Workflows", - "updated_at": 1725038727.0 - }, { "full_name": "NIGMS/RNA-Seq-Differential-Expression-Analysis", "updated_at": 1724351986.0 @@ -1967,22 +1983,6 @@ "full_name": "xindong95/DEAP", "updated_at": 1724332304.0 }, - { - "full_name": "zqfang/haplomap", - "updated_at": 1724865972.0 - }, - { - "full_name": "thebgacademy/colora", - "updated_at": 1724879405.0 - }, - { - "full_name": "wtbarnes/mocksipipeline", - "updated_at": 1724859003.0 - }, - { - "full_name": "bihealth/StemCNV-check", - "updated_at": 1724857356.0 - }, { "full_name": "ravinpoudel/ravinpoudel", "updated_at": 1720569701.0