From f63cd80f7104027611a4f56ba5dc4547c279d699 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 24 Sep 2024 18:19:43 +0000 Subject: [PATCH] Add changes --- data.js | 1718 ++++++++++++++++++++++++++-------------------------- skips.json | 408 ++++++------- 2 files changed, 1055 insertions(+), 1071 deletions(-) diff --git a/data.js b/data.js index 9884b52..ed3381c 100644 --- a/data.js +++ b/data.js @@ -1,5 +1,595 @@ var data = [ + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724431394.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "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/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 + }, + { + "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", + "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", + "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": 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 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "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 + }, + { + "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", + "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, + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724360758.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Wrapper for BLASSO-for-Rhodopsins", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpeyvzeavc/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/BLASSO-Rhodopsin", + "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/tmpeyvzeavc/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n assert \u0027set\u0027 in config, \"You need to specify the alignment type: --config set=original or --config set=original-profiles\"\n ^^^^^^^^^^^^^^^\n\nAssertionError: You need to specify the alignment type: --config set=original or --config set=original-profiles\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 4, + "topics": [], + "updated_at": 1724355682.0 + }, + { + "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", + "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": 1724322240.0 + }, + { + "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", + "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": 1724322240.0 + }, + { + "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, + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724320101.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724319910.0 + }, + { + "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", + "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, + "report": false, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724293620.0 + }, + { + "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", + "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, + "report": false, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724291750.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 2, + "topics": [], + "updated_at": 1725379785.0 + }, + { + "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": "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, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724259444.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 4, + "topics": [], + "updated_at": 1724242954.0 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724230991.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 4, + "topics": [], + "updated_at": 1724175546.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "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[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": 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": 1724118252.0 + }, + { + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724071470.0 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724018701.0 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 0, + "topics": [], + "updated_at": 1724018619.0 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723982118.0 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723981093.0 + }, + { + "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", + "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", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723885717.0 + }, { "config_readme": null, "data_format": 2, @@ -2881,139 +3471,6 @@ var data = "topics": [], "updated_at": 1726998055.0 }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724431394.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "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/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 - }, - { - "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", - "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", - "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": 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 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724406283.0 - }, { "config_readme": null, "data_format": 2, @@ -4315,279 +4772,6 @@ var data = "topics": [], "updated_at": 1723028673.0 }, - { - "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", - "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, - "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724293620.0 - }, - { - "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", - "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, - "report": false, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724291750.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1725379785.0 - }, - { - "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": "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, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724259444.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 4, - "topics": [], - "updated_at": 1724242954.0 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724230991.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 4, - "topics": [], - "updated_at": 1724175546.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "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[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": 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": 1724118252.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724071470.0 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724018701.0 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1724018619.0 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723982118.0 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723981093.0 - }, - { - "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", - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723885717.0 - }, { "config_readme": null, "data_format": 2, @@ -4745,166 +4929,6 @@ var data = "topics": [], "updated_at": 1723727758.0 }, - { - "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 - }, - { - "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", - "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, - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724360758.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Wrapper for BLASSO-for-Rhodopsins", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpeyvzeavc/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/BLASSO-Rhodopsin", - "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/tmpeyvzeavc/workflow/Snakefile\", line 1, in \u003cmodule\u003e\n assert \u0027set\u0027 in config, \"You need to specify the alignment type: --config set=original or --config set=original-profiles\"\n ^^^^^^^^^^^^^^^\n\nAssertionError: You need to specify the alignment type: --config set=original or --config set=original-profiles\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 4, - "topics": [], - "updated_at": 1724355682.0 - }, - { - "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", - "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": 1724322240.0 - }, - { - "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, - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724320101.0 - }, - { - "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", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724319910.0 - }, { "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, @@ -36896,6 +36920,68 @@ var data = "topics": [], "updated_at": 1614368088.0 }, + { + "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, + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.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/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/rules/ClusterTaxa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/rules/config.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": "BAMeScience/Peptonizer2000", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmpeqkfu1k6/workflow/Snakefile:\n * Absolute path \"/rules/config.smk\" 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 \"/rules/ParsePouttoUnipept.smk\" 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 * Absolute path \"/rules/ClusterTaxa.smk\" 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 \"/rules/GridSearchAnalysis.smk\" 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 * 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 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 * 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 12:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\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 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 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 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 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 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 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 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/tmpeqkfu1k6/workflow/rules/config.smk:\n * Absolute path \"/\u0027+config[\" 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 \"/\u0027 +config[\" 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 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\nLints for snakefile /tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.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 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 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\nLints for snakefile /tmp/tmpeqkfu1k6/workflow/rules/ClusterTaxa.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 Also see:\n\n\nLints for snakefile /tmp/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.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 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 * 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 rule UnipeptQuery (line 1, /tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.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 ParseToUnipeptCSV (line 44, /tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.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 ClusterTaxa (line 1, /tmp/tmpeqkfu1k6/workflow/rules/ClusterTaxa.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 FindBestParameters (line 1, /tmp/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.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 Results is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/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 CreateFactorGraph (line 37, /tmp/tmpeqkfu1k6/workflow/Snakefile):\n * Param ResultsDir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/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": 1, + "topics": [], + "updated_at": 1724253874.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/consensus_transcriptome.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/transcriptome_using_genome.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/filter_repeats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/gene_annot.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/transcriptome_de_novo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/repeats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/gene_pred.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/final_models.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": "eparey/AnnotateSnakeMake", + "latest_release": "v.1.0.0", + "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/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/Snakefile\", line 2, 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/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/common.smk\", line 4, in \u003cmodule\u003e\n GENOME_PATH = config[\"genome\"]\n ~~~~~~^^^^^^^^^^^\n\nKeyError: \u0027genome\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724058389.0 + }, { "config_readme": null, "data_format": 2, @@ -38008,40 +38094,6 @@ var data = "topics": [], "updated_at": 1722958124.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.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/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/rules/ClusterTaxa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpeqkfu1k6/workflow/rules/config.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": "BAMeScience/Peptonizer2000", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpeqkfu1k6/workflow/Snakefile:\n * Absolute path \"/rules/config.smk\" 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 \"/rules/ParsePouttoUnipept.smk\" 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 * Absolute path \"/rules/ClusterTaxa.smk\" 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 \"/rules/GridSearchAnalysis.smk\" 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 * 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 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 * 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 12:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\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 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 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 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 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 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 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 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/tmpeqkfu1k6/workflow/rules/config.smk:\n * Absolute path \"/\u0027+config[\" 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 \"/\u0027 +config[\" 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 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\nLints for snakefile /tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.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 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 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\nLints for snakefile /tmp/tmpeqkfu1k6/workflow/rules/ClusterTaxa.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 Also see:\n\n\nLints for snakefile /tmp/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.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 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 * 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 rule UnipeptQuery (line 1, /tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.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 ParseToUnipeptCSV (line 44, /tmp/tmpeqkfu1k6/workflow/rules/ParsePouttoUnipept.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 ClusterTaxa (line 1, /tmp/tmpeqkfu1k6/workflow/rules/ClusterTaxa.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 FindBestParameters (line 1, /tmp/tmpeqkfu1k6/workflow/rules/GridSearchAnalysis.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 Results is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/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 CreateFactorGraph (line 37, /tmp/tmpeqkfu1k6/workflow/Snakefile):\n * Param ResultsDir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/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": 1, - "topics": [], - "updated_at": 1724253874.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/consensus_transcriptome.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/transcriptome_using_genome.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/filter_repeats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/gene_annot.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/transcriptome_de_novo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/repeats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/gene_pred.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/final_models.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": "eparey/AnnotateSnakeMake", - "latest_release": "v.1.0.0", - "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/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/Snakefile\", line 2, 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/tmpsck3w34n/eparey-AnnotateSnakeMake-706fd46/workflow/rules/common.smk\", line 4, in \u003cmodule\u003e\n GENOME_PATH = config[\"genome\"]\n ~~~~~~^^^^^^^^^^^\n\nKeyError: \u0027genome\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724058389.0 - }, { "config_readme": null, "data_format": 2, @@ -38093,34 +38145,6 @@ var data = "topics": [], "updated_at": 1723819098.0 }, - { - "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, @@ -43694,6 +43718,47 @@ var data = "topics": [], "updated_at": 1551028733.0 }, + { + "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": "\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": "Reproducible Expression Analysis for Polyploids.", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpma9x9wrm/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[ERROR] In file \"/tmp/tmpma9x9wrm/workflow/rules/homeo_ratio.smk\": NoParametersError: L11: In output definition.\n[DEBUG] In file \"/tmp/tmpma9x9wrm/workflow/rules/homeo_ratio.smk\": \n[DEBUG] \n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 1 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": "kenji-yt/REAP", + "latest_release": null, + "linting": "Lints for rule homeo_ratio (line 1, /tmp/tmpma9x9wrm/workflow/rules/homeo_ratio.smk):\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": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 2, + "subscribers_count": 2, + "topics": [], + "updated_at": 1724052866.0 + }, { "config_readme": null, "data_format": 2, @@ -44203,23 +44268,6 @@ var data = "topics": [], "updated_at": 1727079768.0 }, - { - "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, @@ -44545,30 +44593,6 @@ var data = "topics": [], "updated_at": 1723381193.0 }, - { - "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": "Reproducible Expression Analysis for Polyploids.", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpma9x9wrm/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[ERROR] In file \"/tmp/tmpma9x9wrm/workflow/rules/homeo_ratio.smk\": NoParametersError: L11: In output definition.\n[DEBUG] In file \"/tmp/tmpma9x9wrm/workflow/rules/homeo_ratio.smk\": \n[DEBUG] \n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 1 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": "kenji-yt/REAP", - "latest_release": null, - "linting": "Lints for rule homeo_ratio (line 1, /tmp/tmpma9x9wrm/workflow/rules/homeo_ratio.smk):\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": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 2, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724052866.0 - }, { "config_readme": null, "data_format": 2, @@ -47245,6 +47269,93 @@ var data = ], "updated_at": 1617804426.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake pipeline for running Virushunter and Virusgatherer", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpw4rid20a/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": "lauberlab/VirusHunterGatherer", + "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/tmpw4rid20a/Snakefile\", line 23, 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/data/virushunter\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 3, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724249241.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "genomic-medicine-sweden/poppy", + "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 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_a2kolfa/genomic-medicine-sweden-poppy-6144c05/workflow/Snakefile\", line 15, in \u003cmodule\u003e\n include: \"rules/annotation_vep_pindel.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/tmp_a2kolfa/genomic-medicine-sweden-poppy-6144c05/workflow/rules/common.smk\", line 18, 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": 3, + "subscribers_count": 10, + "topics": [], + "updated_at": 1724154060.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "General purpose Snakemake pipeline for PanTools v4.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_explore.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_phylogeny.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_phased.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_map.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_variation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_msa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_characterize.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_construct.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/validate_paths.smk\": Formatted content is different from original\n[INFO] 11 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "PanUtils/pantools-pipeline-v4", + "latest_release": null, + "linting": "RuleException in rule get_group_ids in file /tmp/tmpm0875cgn/workflow/rules/pantools_construct.smk, line 490:\nInput and output files have to be specified as strings or lists of strings.\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 3, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724148272.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Progress tracker of HiGHS performance in PyPSA problems", + "formatting": null, + "full_name": "fneum/highs-pypsa-progress", + "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/tmpof2_a9t9/Snakefile\", line 5, 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": 3, + "subscribers_count": 1, + "topics": [], + "updated_at": 1724138933.0 + }, + { + "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\"\u003eSample sheet\u003c/h1\u003e\u003ca id=\"user-content-sample-sheet\" class=\"anchor\" aria-label=\"Permalink: Sample sheet\" href=\"#sample-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/samples.tsv\u003c/code\u003e. For each sample, the columns \u003ccode\u003esample_name\u003c/code\u003e, \u003ccode\u003eplatform\u003c/code\u003e, and \u003ccode\u003egroup\u003c/code\u003e have to be defined.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eSamples within the same \u003ccode\u003egroup\u003c/code\u003e will be called jointly.\u003c/li\u003e\n\u003cli\u003eThe \u003ccode\u003eplatform\u003c/code\u003e column needs to contain the used sequencing plaform (\u0027illumina\u0027,\u0027nanopore\u0027). Note that Illumina data is supplementary, i.e. circles will only be called for sample groups that have at at least \u0027nanopore\u0027 as their platform.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\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\u003eFor each sample, add one or more sequencing units (runs, lanes or replicates) to the unit sheet \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003eunit\u003c/code\u003e name, which can be e.g. a running number, or an actual run, lane or replicate id.\u003c/li\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003esample\u003c/code\u003e name, which associates it with the biological sample it comes from.\u003c/li\u003e\n\u003cli\u003eFor each unit, define either one (column \u003ccode\u003efq1\u003c/code\u003e) or two (columns \u003ccode\u003efq1\u003c/code\u003e, \u003ccode\u003efq2\u003c/code\u003e) FASTQ files (these can point to anywhere in your system).\u003c/li\u003e\n\u003cli\u003eAlternatively, you can define an SRA (sequence read archive) accession (starting with e.g. ERR or SRR) by using a column \u003ccode\u003esra\u003c/code\u003e. In the latter case, the pipeline will automatically download the corresponding paired end reads from SRA. If both local files and SRA accession are available, the local files will be preferred.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\u003c/p\u003e\n", + "data_format": 2, + "description": "A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd31l3ja7/snakemake-workflows-cyrcular-calling-61b6005/workflow/rules/map.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] 8 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "snakemake-workflows/cyrcular-calling", + "latest_release": "v2.1.1", + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 3, + "subscribers_count": 2, + "topics": [], + "updated_at": 1724078847.0 + }, { "config_readme": null, "data_format": 2, @@ -47658,93 +47769,6 @@ var data = ], "updated_at": 1723737700.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake pipeline for running Virushunter and Virusgatherer", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpw4rid20a/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": "lauberlab/VirusHunterGatherer", - "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/tmpw4rid20a/Snakefile\", line 23, 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/data/virushunter\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 3, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724249241.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "genomic-medicine-sweden/poppy", - "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 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_a2kolfa/genomic-medicine-sweden-poppy-6144c05/workflow/Snakefile\", line 15, in \u003cmodule\u003e\n include: \"rules/annotation_vep_pindel.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/tmp_a2kolfa/genomic-medicine-sweden-poppy-6144c05/workflow/rules/common.smk\", line 18, 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": 3, - "subscribers_count": 10, - "topics": [], - "updated_at": 1724154060.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "General purpose Snakemake pipeline for PanTools v4.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_explore.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_phylogeny.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_phased.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_map.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_variation.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_msa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_characterize.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/pantools_construct.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpm0875cgn/workflow/rules/validate_paths.smk\": Formatted content is different from original\n[INFO] 11 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "PanUtils/pantools-pipeline-v4", - "latest_release": null, - "linting": "RuleException in rule get_group_ids in file /tmp/tmpm0875cgn/workflow/rules/pantools_construct.smk, line 490:\nInput and output files have to be specified as strings or lists of strings.\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 3, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724148272.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Progress tracker of HiGHS performance in PyPSA problems", - "formatting": null, - "full_name": "fneum/highs-pypsa-progress", - "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/tmpof2_a9t9/Snakefile\", line 5, 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": 3, - "subscribers_count": 1, - "topics": [], - "updated_at": 1724138933.0 - }, - { - "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\"\u003eSample sheet\u003c/h1\u003e\u003ca id=\"user-content-sample-sheet\" class=\"anchor\" aria-label=\"Permalink: Sample sheet\" href=\"#sample-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/samples.tsv\u003c/code\u003e. For each sample, the columns \u003ccode\u003esample_name\u003c/code\u003e, \u003ccode\u003eplatform\u003c/code\u003e, and \u003ccode\u003egroup\u003c/code\u003e have to be defined.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eSamples within the same \u003ccode\u003egroup\u003c/code\u003e will be called jointly.\u003c/li\u003e\n\u003cli\u003eThe \u003ccode\u003eplatform\u003c/code\u003e column needs to contain the used sequencing plaform (\u0027illumina\u0027,\u0027nanopore\u0027). Note that Illumina data is supplementary, i.e. circles will only be called for sample groups that have at at least \u0027nanopore\u0027 as their platform.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\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\u003eFor each sample, add one or more sequencing units (runs, lanes or replicates) to the unit sheet \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003eunit\u003c/code\u003e name, which can be e.g. a running number, or an actual run, lane or replicate id.\u003c/li\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003esample\u003c/code\u003e name, which associates it with the biological sample it comes from.\u003c/li\u003e\n\u003cli\u003eFor each unit, define either one (column \u003ccode\u003efq1\u003c/code\u003e) or two (columns \u003ccode\u003efq1\u003c/code\u003e, \u003ccode\u003efq2\u003c/code\u003e) FASTQ files (these can point to anywhere in your system).\u003c/li\u003e\n\u003cli\u003eAlternatively, you can define an SRA (sequence read archive) accession (starting with e.g. ERR or SRR) by using a column \u003ccode\u003esra\u003c/code\u003e. In the latter case, the pipeline will automatically download the corresponding paired end reads from SRA. If both local files and SRA accession are available, the local files will be preferred.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\u003c/p\u003e\n", - "data_format": 2, - "description": "A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd31l3ja7/snakemake-workflows-cyrcular-calling-61b6005/workflow/rules/map.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] 8 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "snakemake-workflows/cyrcular-calling", - "latest_release": "v2.1.1", - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 3, - "subscribers_count": 2, - "topics": [], - "updated_at": 1724078847.0 - }, { "config_readme": null, "data_format": 2, @@ -49343,6 +49367,40 @@ var data = "topics": [], "updated_at": 1616871931.0 }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains", + "latest_release": "v1.0", + "linting": "Lints for rule create_file (line 6, /tmp/tmpc1lvu2e1/Arcadia-Science-2024-Ecoli-amr-genotype-phenotype_7000strains-21aa07e/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.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": 4, + "subscribers_count": 2, + "topics": [], + "updated_at": 1726614952.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/strandseq_breakpoints.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/sample_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/evaluate.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/collect_output.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/align_to_reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "marschall-lab/strand-seq-graph-phasing", + "latest_release": "v0.5.01", + "linting": "KeyError in file /tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile, line 11:\n\u0027segmentLengthThreshold\u0027\n File \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 2, + "topics": [], + "updated_at": 1726760797.0 + }, { "config_readme": null, "data_format": 2, @@ -49405,29 +49463,6 @@ var data = ], "updated_at": 1724849292.0 }, - { - "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, @@ -49656,40 +49691,6 @@ var data = ], "updated_at": 1723580418.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains", - "latest_release": "v1.0", - "linting": "Lints for rule create_file (line 6, /tmp/tmpc1lvu2e1/Arcadia-Science-2024-Ecoli-amr-genotype-phenotype_7000strains-21aa07e/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.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": 4, - "subscribers_count": 2, - "topics": [], - "updated_at": 1726614952.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/strandseq_breakpoints.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/sample_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/evaluate.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/collect_output.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/align_to_reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "marschall-lab/strand-seq-graph-phasing", - "latest_release": "v0.5.01", - "linting": "KeyError in file /tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile, line 11:\n\u0027segmentLengthThreshold\u0027\n File \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 2, - "topics": [], - "updated_at": 1726760797.0 - }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eWorkflow configuration\u003c/h1\u003e\u003ca id=\"user-content-workflow-configuration\" class=\"anchor\" aria-label=\"Permalink: Workflow configuration\" href=\"#workflow-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\"\u003eConfiguration\u003c/h2\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\u003eTo configure the workflow, modifiy \u003ccode\u003econfig/config.yaml\u003c/code\u003e according\nto your needs.\u003c/p\u003e\n\u003cp\u003eFor specific details about the parameters\ncheck the documentation.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eOptimized configuration for 16S birds and mammals metabarcoding\u003c/h3\u003e\u003ca id=\"user-content-optimized-configuration-for-16s-birds-and-mammals-metabarcoding\" class=\"anchor\" aria-label=\"Permalink: Optimized configuration for 16S birds and mammals metabarcoding\" href=\"#optimized-configuration-for-16s-birds-and-mammals-metabarcoding\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA configuration file with optimized parameters (with no warranty!) for\nthe analysis of 16S metabarcoding experiments of birds and mammals is\nincluded in this folder.\n\u003cstrong\u003eYou will still need to modify the indicated paths to match your own folder structure.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSee for reference:\u003c/p\u003e\n\u003cp\u003eDenay, G.; Preckel, L.; Petersen, H.; Pietsch, K.; W\u00f6hlke, A.; Br\u00fcnen-Nieweler, C.\nBenchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding.\nFoods 2023, 12, 968. \u003ca href=\"https://doi.org/10.3390/foods12050968\" rel=\"nofollow\"\u003ehttps://doi.org/10.3390/foods12050968\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample sheet\u003c/h2\u003e\u003ca id=\"user-content-sample-sheet\" class=\"anchor\" aria-label=\"Permalink: Sample sheet\" href=\"#sample-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd your samples to \u003ccode\u003econfig/samples.tsv\u003c/code\u003e or use the\nthe helper script from Bundes Insitut f\u00fcr Risikobewertung in\n\u003ccode\u003eressources/creat_sampleSheet.sh\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eReference table\u003c/h2\u003e\u003ca id=\"user-content-reference-table\" class=\"anchor\" aria-label=\"Permalink: Reference table\" href=\"#reference-table\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIf using the benchmark mode, sdd information for your reference samples in the \u003ccode\u003ereference.tsv\u003c/code\u003e template.\nNote that proportions are given as fractions in the [0, 1] interval.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eParameter space exploration configuration\u003c/h2\u003e\u003ca id=\"user-content-parameter-space-exploration-configuration\" class=\"anchor\" aria-label=\"Permalink: Parameter space exploration configuration\" href=\"#parameter-space-exploration-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure a parameter space exploration analysis, modify the file\n\u003ccode\u003econfig_paramspace.yaml\u003c/code\u003e according to your needs.\u003c/p\u003e\n\u003cp\u003eFor specific details about the parameters\ncheck the documentation.\u003c/p\u003e\n", "data_format": 2, @@ -51565,6 +51566,32 @@ var data = ], "updated_at": 1602644548.0 }, + { + "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\u003eCreate and activate the virtual environment with the required dependencies\nwith Conda:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda env create -f environment.yml\nconda activate mirflowz\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIf you plan to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e via Conda, we recommend using the following\ncommand for a faster environment creation, specially if you will run it on an\nHPC cluster.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda config --set channel_priority strict\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eFor a faster creation of the environment (and Conda environments in general),\nyou can also install \u003ca href=\"https://github.com/mamba-org/mamba\"\u003eMamba\u003c/a\u003e on top of Conda. In that case, replace\n\u003ccode\u003econda\u003c/code\u003e with \u003ccode\u003emamba\u003c/code\u003e in the commands above (particularly in\n\u003ccode\u003econda env create\u003c/code\u003e).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eRunning \u003cem\u003eMIRFLOWZ\u003c/em\u003e with Singularity\u003c/h2\u003e\u003ca id=\"user-content-running-mirflowz-with-singularity\" class=\"anchor\" aria-label=\"Permalink: Running MIRFLOWZ with Singularity\" href=\"#running-mirflowz-with-singularity\"\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 run \u003cem\u003eMIRFLOWZ\u003c/em\u003e via Singularity and do not already\nhave it installed globally on your system, you must further update the Conda\nenvironment with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda env update -f environment.root.yml\u003c/pre\u003e\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eMind that you must have the environment activated and root permissions on\nyour system to install Singularity. If you want to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e on an HPC\ncluster (recommended in almost all cases), ask your system administrator\nabout Singularity.\u003c/p\u003e\n\u003c/blockquote\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\u003cp\u003eIn order to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e on your own samples, we recommend having all the\ninput files inside a dedicated directory. This way, it is easier to keep the\ndata together and reproduce an analysis. Assuming that your current directory\nis the repository\u0027s root directory, create a directory to store all your data\nand traverse to it with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003emkdir path/to/your_run\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e path/to/your_run\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e1. Prepare the sample table\u003c/h2\u003e\u003ca id=\"user-content-1-prepare-the-sample-table\" class=\"anchor\" aria-label=\"Permalink: 1. Prepare the sample table\" href=\"#1-prepare-the-sample-table\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCreate an empty sample table. Refer to the\n\u003ca href=\"../test/test_files/samples_table.tsv\"\u003esample.tsv\u003c/a\u003e test file to see what the\ntable must look like or use it as a template.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003etouch samples.tsv\u003c/pre\u003e\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eFill the sample table according to the following requirements:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample\u003c/code\u003e. Arbitrary name for the miRNA sequencing library.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003esample_file\u003c/code\u003e. Path to the miRNA sequencing library file. The path must be\nrelative to the directory where the workflow will be run.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eadapter\u003c/code\u003e. Sequence of the 3\u0027-end adapter used during library preparation.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eformat\u003c/code\u003e. One of \u003ccode\u003efa\u003c/code\u003e/\u003ccode\u003efasta\u003c/code\u003e or \u003ccode\u003efq\u003c/code\u003e/\u003ccode\u003efastq\u003c/code\u003e, if the library file is in\nFASTA or FASTQ format, respectively.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e2. Prepare the genome resources\u003c/h2\u003e\u003ca id=\"user-content-2-prepare-the-genome-resources\" class=\"anchor\" aria-label=\"Permalink: 2. Prepare the genome resources\" href=\"#2-prepare-the-genome-resources\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThere are 4 files you must provide:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003eA \u003cstrong\u003e\u003ccode\u003egzip\u003c/code\u003eped FASTA\u003c/strong\u003e file containing \u003cstrong\u003ereference sequences\u003c/strong\u003e, typically the\ngenome of the source/organism from which the library was extracted.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eA \u003cstrong\u003e\u003ccode\u003egzip\u003c/code\u003eped GTF\u003c/strong\u003e file with matching \u003cstrong\u003egene annotations\u003c/strong\u003e for the\nreference sequences above.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003e\u003cem\u003eMIRFLOWZ\u003c/em\u003e expects both the reference sequence and gene annotation files to\nfollow \u003ca href=\"https://ensembl.org/\" rel=\"nofollow\"\u003eEnsembl\u003c/a\u003e style/formatting. If you obtained these files from\na source other than Ensembl, you must ensure that they adhere to the\nexpected format by converting them, if necessary.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003col start=\"3\"\u003e\n\u003cli\u003eAn \u003cstrong\u003euncompressed GFF3\u003c/strong\u003e file with \u003cstrong\u003emicroRNA annotations\u003c/strong\u003e for the reference\nsequences above.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003e\u003cem\u003eMIRFLOWZ\u003c/em\u003e expects the miRNA annotations to follow \u003ca href=\"https://mirbase.org/\" rel=\"nofollow\"\u003emiRBase\u003c/a\u003e\nstyle/formatting. If you obtained this file from a source other than miRBase,\nyou must ensure that it adheres to the expected format by converting it, if\nnecessary.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003col start=\"4\"\u003e\n\u003cli\u003e\n\u003cp\u003eAn \u003cstrong\u003euncompressed tab-separated file\u003c/strong\u003e with a \u003cstrong\u003emapping between the\nreference names\u003c/strong\u003e used in the miRNA annotation file (column 1; \"UCSC style\")\nand in the gene annotations and reference sequence files (column 2; \"Ensembl\nstyle\"). Values in column 1 are expected to be unique, no header is\nexpected, and any additional columns will be ignored. \u003ca href=\"https://github.com/dpryan79/ChromosomeMappings\"\u003eThis\nresource\u003c/a\u003e provides such files for various organisms, and in the\nexpected format.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003cstrong\u003eOPTIONAL\u003c/strong\u003e: A \u003cstrong\u003eBED6\u003c/strong\u003e file with regions for which to produce\n\u003ca href=\"https://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup\" rel=\"nofollow\"\u003eASCII-style alignment pileups\u003c/a\u003e. If not provided, no pileups\nwill be generated. See \u003ca href=\"https://gist.github.com/deliaBlue/19ad3740c95937378bd9281bd9d1bc72\"\u003ehere\u003c/a\u003e for the expected format.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003eGeneral note: If you want to process the genome resources before use (e.g.,\nfiltering), you can do that, but make sure the formats of any modified\nresource files meet the formatting expectations outlined above!\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e3. Prepare the configuration file\u003c/h2\u003e\u003ca id=\"user-content-3-prepare-the-configuration-file\" class=\"anchor\" aria-label=\"Permalink: 3. Prepare the configuration file\" href=\"#3-prepare-the-configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eWe recommend creating a copy of the\n\u003ca href=\"config_template.yaml\"\u003econfiguration file template\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003ecp ../config/config_template.yaml config.yaml\n\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eOpen the new copy in your editor of choice and adjust the configuration\nparameters to your liking. The template explains what each of the parameters\nmean and how you can meaningfully adjust them.\u003c/p\u003e\n", + "data_format": 2, + "description": "Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.", + "formatting": null, + "full_name": "zavolanlab/mirflowz", + "latest_release": null, + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": true + }, + "standardized": true, + "stargazers_count": 6, + "subscribers_count": 4, + "topics": [ + "bioinformatics", + "isomirs", + "mirna", + "snakemake", + "workflow" + ], + "updated_at": 1724063254.0 + }, { "config_readme": null, "data_format": 2, @@ -51672,32 +51699,6 @@ var data = "topics": [], "updated_at": 1723560372.0 }, - { - "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\u003eCreate and activate the virtual environment with the required dependencies\nwith Conda:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda env create -f environment.yml\nconda activate mirflowz\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIf you plan to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e via Conda, we recommend using the following\ncommand for a faster environment creation, specially if you will run it on an\nHPC cluster.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda config --set channel_priority strict\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eFor a faster creation of the environment (and Conda environments in general),\nyou can also install \u003ca href=\"https://github.com/mamba-org/mamba\"\u003eMamba\u003c/a\u003e on top of Conda. In that case, replace\n\u003ccode\u003econda\u003c/code\u003e with \u003ccode\u003emamba\u003c/code\u003e in the commands above (particularly in\n\u003ccode\u003econda env create\u003c/code\u003e).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eRunning \u003cem\u003eMIRFLOWZ\u003c/em\u003e with Singularity\u003c/h2\u003e\u003ca id=\"user-content-running-mirflowz-with-singularity\" class=\"anchor\" aria-label=\"Permalink: Running MIRFLOWZ with Singularity\" href=\"#running-mirflowz-with-singularity\"\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 run \u003cem\u003eMIRFLOWZ\u003c/em\u003e via Singularity and do not already\nhave it installed globally on your system, you must further update the Conda\nenvironment with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda env update -f environment.root.yml\u003c/pre\u003e\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eMind that you must have the environment activated and root permissions on\nyour system to install Singularity. If you want to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e on an HPC\ncluster (recommended in almost all cases), ask your system administrator\nabout Singularity.\u003c/p\u003e\n\u003c/blockquote\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\u003cp\u003eIn order to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e on your own samples, we recommend having all the\ninput files inside a dedicated directory. This way, it is easier to keep the\ndata together and reproduce an analysis. Assuming that your current directory\nis the repository\u0027s root directory, create a directory to store all your data\nand traverse to it with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003emkdir path/to/your_run\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e path/to/your_run\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e1. Prepare the sample table\u003c/h2\u003e\u003ca id=\"user-content-1-prepare-the-sample-table\" class=\"anchor\" aria-label=\"Permalink: 1. Prepare the sample table\" href=\"#1-prepare-the-sample-table\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCreate an empty sample table. Refer to the\n\u003ca href=\"../test/test_files/samples_table.tsv\"\u003esample.tsv\u003c/a\u003e test file to see what the\ntable must look like or use it as a template.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003etouch samples.tsv\u003c/pre\u003e\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eFill the sample table according to the following requirements:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample\u003c/code\u003e. Arbitrary name for the miRNA sequencing library.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003esample_file\u003c/code\u003e. Path to the miRNA sequencing library file. The path must be\nrelative to the directory where the workflow will be run.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eadapter\u003c/code\u003e. Sequence of the 3\u0027-end adapter used during library preparation.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eformat\u003c/code\u003e. One of \u003ccode\u003efa\u003c/code\u003e/\u003ccode\u003efasta\u003c/code\u003e or \u003ccode\u003efq\u003c/code\u003e/\u003ccode\u003efastq\u003c/code\u003e, if the library file is in\nFASTA or FASTQ format, respectively.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e2. Prepare the genome resources\u003c/h2\u003e\u003ca id=\"user-content-2-prepare-the-genome-resources\" class=\"anchor\" aria-label=\"Permalink: 2. Prepare the genome resources\" href=\"#2-prepare-the-genome-resources\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThere are 4 files you must provide:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003eA \u003cstrong\u003e\u003ccode\u003egzip\u003c/code\u003eped FASTA\u003c/strong\u003e file containing \u003cstrong\u003ereference sequences\u003c/strong\u003e, typically the\ngenome of the source/organism from which the library was extracted.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eA \u003cstrong\u003e\u003ccode\u003egzip\u003c/code\u003eped GTF\u003c/strong\u003e file with matching \u003cstrong\u003egene annotations\u003c/strong\u003e for the\nreference sequences above.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003e\u003cem\u003eMIRFLOWZ\u003c/em\u003e expects both the reference sequence and gene annotation files to\nfollow \u003ca href=\"https://ensembl.org/\" rel=\"nofollow\"\u003eEnsembl\u003c/a\u003e style/formatting. If you obtained these files from\na source other than Ensembl, you must ensure that they adhere to the\nexpected format by converting them, if necessary.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003col start=\"3\"\u003e\n\u003cli\u003eAn \u003cstrong\u003euncompressed GFF3\u003c/strong\u003e file with \u003cstrong\u003emicroRNA annotations\u003c/strong\u003e for the reference\nsequences above.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003e\u003cem\u003eMIRFLOWZ\u003c/em\u003e expects the miRNA annotations to follow \u003ca href=\"https://mirbase.org/\" rel=\"nofollow\"\u003emiRBase\u003c/a\u003e\nstyle/formatting. If you obtained this file from a source other than miRBase,\nyou must ensure that it adheres to the expected format by converting it, if\nnecessary.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003col start=\"4\"\u003e\n\u003cli\u003e\n\u003cp\u003eAn \u003cstrong\u003euncompressed tab-separated file\u003c/strong\u003e with a \u003cstrong\u003emapping between the\nreference names\u003c/strong\u003e used in the miRNA annotation file (column 1; \"UCSC style\")\nand in the gene annotations and reference sequence files (column 2; \"Ensembl\nstyle\"). Values in column 1 are expected to be unique, no header is\nexpected, and any additional columns will be ignored. \u003ca href=\"https://github.com/dpryan79/ChromosomeMappings\"\u003eThis\nresource\u003c/a\u003e provides such files for various organisms, and in the\nexpected format.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003cstrong\u003eOPTIONAL\u003c/strong\u003e: A \u003cstrong\u003eBED6\u003c/strong\u003e file with regions for which to produce\n\u003ca href=\"https://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup\" rel=\"nofollow\"\u003eASCII-style alignment pileups\u003c/a\u003e. If not provided, no pileups\nwill be generated. See \u003ca href=\"https://gist.github.com/deliaBlue/19ad3740c95937378bd9281bd9d1bc72\"\u003ehere\u003c/a\u003e for the expected format.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003eGeneral note: If you want to process the genome resources before use (e.g.,\nfiltering), you can do that, but make sure the formats of any modified\nresource files meet the formatting expectations outlined above!\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e3. Prepare the configuration file\u003c/h2\u003e\u003ca id=\"user-content-3-prepare-the-configuration-file\" class=\"anchor\" aria-label=\"Permalink: 3. Prepare the configuration file\" href=\"#3-prepare-the-configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eWe recommend creating a copy of the\n\u003ca href=\"config_template.yaml\"\u003econfiguration file template\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003ecp ../config/config_template.yaml config.yaml\n\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eOpen the new copy in your editor of choice and adjust the configuration\nparameters to your liking. The template explains what each of the parameters\nmean and how you can meaningfully adjust them.\u003c/p\u003e\n", - "data_format": 2, - "description": "Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.", - "formatting": null, - "full_name": "zavolanlab/mirflowz", - "latest_release": null, - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": true - }, - "standardized": true, - "stargazers_count": 6, - "subscribers_count": 4, - "topics": [ - "bioinformatics", - "isomirs", - "mirna", - "snakemake", - "workflow" - ], - "updated_at": 1724063254.0 - }, { "config_readme": null, "data_format": 2, @@ -53379,19 +53380,19 @@ var data = { "config_readme": null, "data_format": 2, - "description": "Open-source bioinformatics pipeline for the preprocessing of raw amplicon sequencing / metabarcoding data.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/read_correction.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/merging.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/clustering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/read_assembly.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/quality_control.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/pr2_unite_silva.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/dereplication.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/demultiplexing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/blast.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/chim_rm.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/vsearch_clust.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/pychop.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/read_correction (copy).smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/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[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/Snakefile\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/mumu.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 43)\n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/mumu.smk\": \n[DEBUG] In file \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/rules/classify.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 15 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "dbeisser/Natrix2", - "latest_release": "v1.0.0", - "linting": "KeyError in file /tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/Snakefile, line 7:\n\u0027general\u0027\n File \"/tmp/tmpw609e_jx/dbeisser-Natrix2-42f4855/Snakefile\", line 7, in \u003cmodule\u003e\n", + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/meth_qc_quant.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/reads_qc.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:2: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[WARNING] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/aggregating.smk\": Keyword \"shell\" at line 213 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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/aggregating.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/extra_env.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/fragment_profile.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": "pughlab/MEDIPIPE", + "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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/mapping.smk\" ## bwa, samtools, infer intert size\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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/common.smk\", line 1, in \u003cmodule\u003e\n workdir: config[\u0027work_dir\u0027] ## Configure Working Directory\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, "stargazers_count": 10, - "subscribers_count": 1, + "subscribers_count": 4, "topics": [], - "updated_at": 1726975151.0 + "updated_at": 1724246455.0 }, { "config_readme": null, @@ -53590,23 +53591,6 @@ var data = "topics": [], "updated_at": 1723234279.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/meth_qc_quant.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/reads_qc.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:2: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[WARNING] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/aggregating.smk\": Keyword \"shell\" at line 213 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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/aggregating.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/extra_env.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/fragment_profile.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": "pughlab/MEDIPIPE", - "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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/mapping.smk\" ## bwa, samtools, infer intert size\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/tmpqmnaw4nz/pughlab-MEDIPIPE-fa70560/workflow/rules/common.smk\", line 1, in \u003cmodule\u003e\n workdir: config[\u0027work_dir\u0027] ## Configure Working Directory\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 10, - "subscribers_count": 4, - "topics": [], - "updated_at": 1724246455.0 - }, { "config_readme": null, "data_format": 2, @@ -56275,18 +56259,18 @@ var data = "config_readme": null, "data_format": 2, "description": "CADD scripts release for offline scoring. For more information about CADD, please visit our website", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9fulvec4/kircherlab-CADD-scripts-203ee3b/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp1gr0lsy0/kircherlab-CADD-scripts-203ee3b/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": "kircherlab/CADD-scripts", "latest_release": "v1.7", - "linting": "WorkflowError in file /tmp/tmp9fulvec4/kircherlab-CADD-scripts-203ee3b/Snakefile, line 14:\nError validating config file.\nValidationError: \u0027REFERENCEpath\u0027 is a required property\n\nFailed validating \u0027required\u0027 in schema[\u0027allOf\u0027][0][\u0027then\u0027]:\n {\u0027required\u0027: [\u0027REFERENCEpath\u0027, \u0027MMSPLICEpath\u0027]}\n\nOn instance:\n {\u0027Header\u0027: \u0027##CADD GRCh37-v1.7 (c) University of Washington, \u0027\n \u0027Hudson-Alpha Institute for Biotechnology and Berlin \u0027\n \u0027Institute of Health at Charite - Universitaetsmedizin \u0027\n \u0027Berlin 2013-2023. All rights reserved.\u0027,\n \u0027Annotation\u0027: False,\n \u0027EnsemblDB\u0027: 110,\n \u0027ESMmodels\u0027: [\u0027esm1v_t33_650M_UR90S_1\u0027,\n \u0027esm1v_t33_650M_UR90S_2\u0027,\n \u0027esm1v_t33_650M_UR90S_3\u0027,\n \u0027esm1v_t33_650M_UR90S_4\u0027,\n \u0027esm1v_t33_650M_UR90S_5\u0027],\n \u0027ESMbatchsize\u0027: 1}\n", + "linting": "WorkflowError in file /tmp/tmp1gr0lsy0/kircherlab-CADD-scripts-203ee3b/Snakefile, line 14:\nError validating config file.\nValidationError: \u0027REFERENCEpath\u0027 is a required property\n\nFailed validating \u0027required\u0027 in schema[\u0027allOf\u0027][0][\u0027then\u0027]:\n {\u0027required\u0027: [\u0027REFERENCEpath\u0027, \u0027MMSPLICEpath\u0027]}\n\nOn instance:\n {\u0027Header\u0027: \u0027##CADD GRCh37-v1.7 (c) University of Washington, \u0027\n \u0027Hudson-Alpha Institute for Biotechnology and Berlin \u0027\n \u0027Institute of Health at Charite - Universitaetsmedizin \u0027\n \u0027Berlin 2013-2023. All rights reserved.\u0027,\n \u0027Annotation\u0027: False,\n \u0027EnsemblDB\u0027: 110,\n \u0027ESMmodels\u0027: [\u0027esm1v_t33_650M_UR90S_1\u0027,\n \u0027esm1v_t33_650M_UR90S_2\u0027,\n \u0027esm1v_t33_650M_UR90S_3\u0027,\n \u0027esm1v_t33_650M_UR90S_4\u0027,\n \u0027esm1v_t33_650M_UR90S_5\u0027],\n \u0027ESMbatchsize\u0027: 1}\n", "mandatory_flags": [], "report": false, "software_stack_deployment": null, "standardized": false, - "stargazers_count": 66, + "stargazers_count": 67, "subscribers_count": 5, "topics": [], - "updated_at": 1726758591.0 + "updated_at": 1727149869.0 }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003esv-callers\u003c/h1\u003e\u003ca id=\"user-content-sv-callers\" class=\"anchor\" aria-label=\"Permalink: sv-callers\" href=\"#sv-callers\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003e\u003ca href=\"https://doi.org/10.5281/zenodo.1217111\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/9b5ee3b043c6cfa8a16408d79adf6ad4a44a7810a46c45993538588825a1e742/68747470733a2f2f7a656e6f646f2e6f72672f62616467652f444f492f31302e353238312f7a656e6f646f2e313231373131312e737667\" alt=\"DOI\" data-canonical-src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.1217111.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://doi.org/10.7717/peerj.8214\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/a10cc462826830761587cffb2f634edd4e400ad085b778be8eca43e3e152bd17/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f7075626c6973686564253230696e2d506565724a2d626c75652e737667\" alt=\"Published in PeerJ\" data-canonical-src=\"https://img.shields.io/badge/published%20in-PeerJ-blue.svg\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://github.com/GooglingTheCancerGenome/sv-callers/actions/workflows/ci.yaml\"\u003e\u003cimg src=\"https://github.com/GooglingTheCancerGenome/sv-callers/actions/workflows/ci.yaml/badge.svg?branch=master\" alt=\"CI\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://www.codacy.com/gh/GooglingTheCancerGenome/sv-callers/dashboard?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=GooglingTheCancerGenome/sv-callers\u0026amp;utm_campaign=Badge_Grade\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/e8324516fbfbc460a5290c2cc7407eff0c3c08f273caa60fd5f68e67b87eb857/68747470733a2f2f6170702e636f646163792e636f6d2f70726f6a6563742f62616467652f47726164652f6561613333643764303930303438383938633131326134613837383135343739\" alt=\"Codacy Badge\" data-canonical-src=\"https://app.codacy.com/project/badge/Grade/eaa33d7d090048898c112a4a87815479\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\n\u003ca href=\"https://www.codacy.com/gh/GooglingTheCancerGenome/sv-callers/dashboard?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=GooglingTheCancerGenome/sv-callers\u0026amp;utm_campaign=Badge_Coverage\" rel=\"nofollow\"\u003e\u003cimg src=\"https://camo.githubusercontent.com/c1067f812f9b25af3aa98ecec78f73f2376f5b2362965f7197f5cbf9463ab826/68747470733a2f2f6170702e636f646163792e636f6d2f70726f6a6563742f62616467652f436f7665726167652f6561613333643764303930303438383938633131326134613837383135343739\" alt=\"Codacy Badge\" data-canonical-src=\"https://app.codacy.com/project/badge/Coverage/eaa33d7d090048898c112a4a87815479\" style=\"max-width: 100%;\"\u003e\u003c/a\u003e\u003c/p\u003e\n\u003cp\u003eStructural variants (SVs) are an important class of genetic variation implicated in a wide array of genetic diseases. \u003cem\u003esv-callers\u003c/em\u003e is a \u003cem\u003eSnakemake\u003c/em\u003e-based workflow that combines several state-of-the-art tools for detecting SVs in whole genome sequencing (WGS) data. The workflow is easy to use and deploy on any Linux-based machine. In particular, the workflow supports automated software deployment, easy configuration and addition of new analysis tools as well as enables to scale from a single computer to different HPC clusters with minimal effort.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eDependencies\u003c/h2\u003e\u003ca id=\"user-content-dependencies\" class=\"anchor\" aria-label=\"Permalink: Dependencies\" href=\"#dependencies\"\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\u003ca href=\"https://www.python.org/\" rel=\"nofollow\"\u003ePython\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\n\u003ca href=\"https://conda.io/\" rel=\"nofollow\"\u003eConda\u003c/a\u003e - package/environment management system\u003c/li\u003e\n\u003cli\u003e\n\u003ca href=\"https://snakemake.readthedocs.io/\" rel=\"nofollow\"\u003eSnakemake\u003c/a\u003e - workflow management system\u003c/li\u003e\n\u003cli\u003e\n\u003ca href=\"https://github.com/NLeSC/xenon-cli\"\u003eXenon CLI\u003c/a\u003e - command-line interface to compute and storage resources\u003c/li\u003e\n\u003cli\u003e\n\u003ca href=\"https://stedolan.github.io/jq/\" rel=\"nofollow\"\u003ejq\u003c/a\u003e - command-line JSON processor (optional)\u003c/li\u003e\n\u003cli\u003e\n\u003ca href=\"https://github.com/yatiml/yatiml\"\u003eYAtiML\u003c/a\u003e - library for YAML type inference and schema validation\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe workflow includes the following bioinformatics tools:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eSV callers\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/Illumina/manta\"\u003eManta\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/dellytools/delly\"\u003eDELLY\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/arq5x/lumpy-sv\"\u003eLUMPY\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/PapenfussLab/gridss\"\u003eGRIDSS\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003ePost-processing\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/samtools/bcftools\"\u003eBCFtools\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/dermasugita/Viola-SV\"\u003eViola-SV\u003c/a\u003e\u003c/li\u003e\n\u003cli\u003e\u003ca href=\"https://github.com/fritzsedlazeck/SURVIVOR\"\u003eSURVIVOR\u003c/a\u003e\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe software dependencies can be found in the conda environment files: \u003ca href=\"/environment.yaml\"\u003e[1]\u003c/a\u003e,\u003ca href=\"/workflow/envs/caller.yaml\"\u003e[2]\u003c/a\u003e,\u003ca href=\"/workflow/envs/postproc.yaml\"\u003e[3]\u003c/a\u003e.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e1. Clone this repo.\u003c/strong\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003egit clone https://github.com/GooglingTheCancerGenome/sv-callers.git\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e sv-callers\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003e\u003cstrong\u003e2. Install dependencies.\u003c/strong\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e download Miniconda3 installer\u003c/span\u003e\nwget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e install Conda (respond by \u0027yes\u0027)\u003c/span\u003e\nbash miniconda.sh\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e update Conda\u003c/span\u003e\nconda update -y conda\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e install Mamba\u003c/span\u003e\nconda install -n base -c conda-forge -y mamba\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e create a new environment with dependencies \u0026amp; activate it\u003c/span\u003e\nmamba env create -n wf -f environment.yaml\nconda activate wf\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003e\u003cstrong\u003e3. Configure the workflow.\u003c/strong\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003e\u003cstrong\u003econfig files\u003c/strong\u003e:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ca href=\"/config/analysis.yaml\"\u003e\u003ccode\u003eanalysis.yaml\u003c/code\u003e\u003c/a\u003e - analysis-specific settings (e.g., workflow mode, I/O files, SV callers, post-processing or resources used etc.)\u003c/li\u003e\n\u003cli\u003e\n\u003ca href=\"/config/samples.csv\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/a\u003e - list of (paired) samples\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003cstrong\u003einput files\u003c/strong\u003e:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eexample data in \u003ccode\u003eworkflow/data\u003c/code\u003e directory\u003c/li\u003e\n\u003cli\u003ereference genome in \u003ccode\u003e.fasta\u003c/code\u003e (incl. index files)\u003c/li\u003e\n\u003cli\u003eexcluded regions in \u003ccode\u003e.bed\u003c/code\u003e (optional)\u003c/li\u003e\n\u003cli\u003eWGS samples in \u003ccode\u003e.bam\u003c/code\u003e (incl. index files)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003cstrong\u003eoutput files\u003c/strong\u003e:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e(filtered) SVs per caller and merged calls in \u003ccode\u003e.vcf\u003c/code\u003e (incl. index files)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e\u003cstrong\u003e4. Execute the workflow.\u003c/strong\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e workflow\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003e\u003cem\u003eLocally\u003c/em\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e \u0027dry\u0027 run only checks I/O files\u003c/span\u003e\nsnakemake -np\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e \u0027vanilla\u0027 run if echo_run set to 1 (default) in analysis.yaml,\u003c/span\u003e\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e it merely mimics the execution of SV callers by writing (dummy) VCF files;\u003c/span\u003e\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e SV calling if echo_run set to 0\u003c/span\u003e\nsnakemake --use-conda --jobs\n\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003e\u003cem\u003eSubmit jobs to Slurm or GridEngine cluster\u003c/em\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003eSCH=slurm \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e or gridengine\u003c/span\u003e\nsnakemake --use-conda --latency-wait 30 --jobs \\\n--cluster \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003exenon scheduler \u003cspan class=\"pl-smi\"\u003e$SCH\u003c/span\u003e --location local:// submit --name smk.{rule} --inherit-env --cores-per-task {threads} --max-run-time 1 --max-memory {resources.mem_mb} --working-directory . --stderr stderr-%j.log --stdout stdout-%j.log\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-k\"\u003e\u0026amp;\u003c/span\u003e\u003cspan class=\"pl-k\"\u003e\u0026gt;\u003c/span\u003esmk.log\u003cspan class=\"pl-k\"\u003e\u0026amp;\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eNote: One sample or a tumor/normal pair generates in total 18 SV calling and post-processing jobs. See the workflow instance of \u003ca href=\"doc/sv-callers_single.svg\"\u003esingle-sample\u003c/a\u003e (germline) or \u003ca href=\"doc/sv-callers_paired.svg\"\u003epaired-sample\u003c/a\u003e (somatic) analysis.\u003c/p\u003e\n\u003cp\u003eTo perform SV calling:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cp\u003eedit (default) parameters in \u003ccode\u003eanalysis.yaml\u003c/code\u003e\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eset \u003ccode\u003eecho_run\u003c/code\u003e to \u003ccode\u003e0\u003c/code\u003e\n\u003c/li\u003e\n\u003cli\u003echoose between two workflow \u003ccode\u003emode\u003c/code\u003es: single- (\u003ccode\u003es\u003c/code\u003e) or paired-sample (\u003ccode\u003ep\u003c/code\u003e - default)\u003c/li\u003e\n\u003cli\u003eselect one or more callers using \u003ccode\u003eenable_callers\u003c/code\u003e (default all)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003euse \u003ccode\u003exenon\u003c/code\u003e CLI to set:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003e--max-run-time\u003c/code\u003e of workflow jobs (in minutes)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003e--temp-space\u003c/code\u003e (optional, in MB)\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eadjust compute requirements per SV caller according to the system used:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003ethe number of \u003ccode\u003ethreads\u003c/code\u003e,\u003c/li\u003e\n\u003cli\u003ethe amount of \u003ccode\u003ememory\u003c/code\u003e(in MB),\u003c/li\u003e\n\u003cli\u003ethe amount of temporary disk space or \u003ccode\u003etmpspace\u003c/code\u003e (path in \u003ccode\u003eTMPDIR\u003c/code\u003e env variable) can be used for intermediate files by LUMPY and GRIDSS only.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003e\u003cem\u003eQuery job accounting information\u003c/em\u003e\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003eSCH=slurm \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e or gridengine\u003c/span\u003e\nxenon --json scheduler \u003cspan class=\"pl-smi\"\u003e$SCH\u003c/span\u003e --location local:// list --identifier [jobID] \u003cspan class=\"pl-k\"\u003e|\u003c/span\u003e jq ...\u003c/pre\u003e\u003c/div\u003e\n", diff --git a/skips.json b/skips.json index efec856..403a337 100644 --- a/skips.json +++ b/skips.json @@ -1,4 +1,208 @@ [ + { + "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 + }, + { + "full_name": "xindong95/DEAP", + "updated_at": 1724332304.0 + }, + { + "full_name": "AGImkeller/scaeData", + "updated_at": 1724331800.0 + }, + { + "full_name": "albarema/haplo_faro", + "updated_at": 1724331605.0 + }, + { + "full_name": "sahuno/dorado_ont_wf", + "updated_at": 1724324737.0 + }, + { + "full_name": "sahuno/dorado_ont_wf", + "updated_at": 1724324737.0 + }, + { + "full_name": "KatharinaHoff/braker-snake", + "updated_at": 1724319691.0 + }, + { + "full_name": "jinghuazhao/Omics-analysis", + "updated_at": 1724318771.0 + }, + { + "full_name": "AEWesdorp/cfSPI", + "updated_at": 1724318641.0 + }, + { + "full_name": "furwellness/snakemake-wrappers", + "updated_at": 1724263879.0 + }, + { + "full_name": "CompEpigen/scformatter", + 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