From 1c4e0c1656255b69d5814baf044121cf4667345c Mon Sep 17 00:00:00 2001 From: Praveen Date: Mon, 20 Jun 2022 11:51:33 +0200 Subject: [PATCH 001/275] Bump version to v1.1.0dev --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index ee010d49..8a37c30f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -236,7 +236,7 @@ manifest { description = 'GATK4 RNA variant calling pipeline' mainScript = 'main.nf' nextflowVersion = '>=21.10.3' - version = '1.0.0' + version = '1.1.0dev' } // Load modules.config for DSL2 module specific options From b69247fb1760927e1fc736a7dec66bf680b2c1ab Mon Sep 17 00:00:00 2001 From: Praveen Date: Mon, 20 Jun 2022 11:54:52 +0200 Subject: [PATCH 002/275] Edited changelog.md --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ba683a54..ec26605f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [1.1.0dev] nfcore/rnavar + +New version with additional features and bug fixes. ## [1.0.0] nfcore/rnavar - 2022/05/24 First production release of the pipeline with latest software versions. From 6c382039e9457deed1abdc84316172bd2129e19b Mon Sep 17 00:00:00 2001 From: Praveen Raj S <43108054+praveenraj2018@users.noreply.github.com> Date: Thu, 23 Jun 2022 11:15:04 +0200 Subject: [PATCH 003/275] Updated Zenodo DOI --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 090f92b6..0cbbbe7d 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/rnavar/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+linting%22) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/rnavar/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![Cite with Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.6669637.svg)](https://doi.org/10.5281/zenodo.6669637) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/) @@ -101,6 +101,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations +If you use nf-core/rnavar for your analysis, please cite it using the following doi: [10.5281/zenodo.6669637](https://doi.org/10.5281/zenodo.6669637) + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: From 3149533049278246b1cf4acc28c83567bb0bf845 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 30 Aug 2022 13:37:56 +0000 Subject: [PATCH 004/275] Template update for nf-core/tools version 2.5 --- .editorconfig | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/ci.yml | 23 ++------ .github/workflows/linting.yml | 38 +++++++++++-- CHANGELOG.md | 2 +- CITATION.cff | 56 +++++++++++++++++++ README.md | 21 +++---- assets/email_template.txt | 1 - bin/check_samplesheet.py | 41 +++++++------- conf/base.config | 5 ++ docs/usage.md | 12 ++-- lib/WorkflowMain.groovy | 9 ++- lib/WorkflowRnavar.groovy | 5 +- main.nf | 2 +- modules.json | 22 +++++--- .../templates/dumpsoftwareversions.py | 14 +++-- nextflow.config | 23 +++++++- 17 files changed, 186 insertions(+), 93 deletions(-) create mode 100644 CITATION.cff diff --git a/.editorconfig b/.editorconfig index b6b31907..b78de6e6 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js}] +[*.{md,yml,yaml,html,css,scss,js,cff}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index ab5c01d7..5c26fb9c 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnav - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md) - - [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6cdf128e..67225b7a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -10,7 +10,6 @@ on: env: NXF_ANSI_LOG: false - CAPSULE_LOG: none jobs: test: @@ -20,27 +19,17 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - # Nextflow versions - include: - # Test pipeline minimum Nextflow version - - NXF_VER: "21.10.3" - NXF_EDGE: "" - # Test latest edge release of Nextflow - - NXF_VER: "" - NXF_EDGE: "1" + NXF_VER: + - "21.10.3" + - "latest-everything" steps: - name: Check out pipeline code uses: actions/checkout@v2 - name: Install Nextflow - env: - NXF_VER: ${{ matrix.NXF_VER }} - # Uncomment only if the edge release is more recent than the latest stable release - # See https://github.com/nextflow-io/nextflow/issues/2467 - # NXF_EDGE: ${{ matrix.NXF_EDGE }} - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 77358dee..8a5ce69b 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,6 +35,36 @@ jobs: - name: Run Prettier --check run: prettier --check ${GITHUB_WORKSPACE} + PythonBlack: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + + - name: Check code lints with Black + uses: psf/black@stable + + # If the above check failed, post a comment on the PR explaining the failure + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v1 + with: + message: | + ## Python linting (`black`) is failing + + To keep the code consistent with lots of contributors, we run automated code consistency checks. + To fix this CI test, please run: + + * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` + * Fix formatting errors in your pipeline: `black .` + + Once you push these changes the test should pass, and you can hide this comment :+1: + + We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + nf-core: runs-on: ubuntu-latest steps: @@ -42,15 +72,11 @@ jobs: uses: actions/checkout@v2 - name: Install Nextflow - env: - CAPSULE_LOG: none - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@v3 with: - python-version: "3.6" + python-version: "3.7" architecture: "x64" - name: Install dependencies diff --git a/CHANGELOG.md b/CHANGELOG.md index cb967546..9eb1e73a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## v1.1.0dev - [date] Initial release of nf-core/rnavar, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..4533e2f2 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,56 @@ +cff-version: 1.2.0 +message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" +authors: + - family-names: Ewels + given-names: Philip + - family-names: Peltzer + given-names: Alexander + - family-names: Fillinger + given-names: Sven + - family-names: Patel + given-names: Harshil + - family-names: Alneberg + given-names: Johannes + - family-names: Wilm + given-names: Andreas + - family-names: Ulysse Garcia + given-names: Maxime + - family-names: Di Tommaso + given-names: Paolo + - family-names: Nahnsen + given-names: Sven +title: "The nf-core framework for community-curated bioinformatics pipelines." +version: 2.4.1 +doi: 10.1038/s41587-020-0439-x +date-released: 2022-05-16 +url: https://github.com/nf-core/tools +prefered-citation: + type: article + authors: + - family-names: Ewels + given-names: Philip + - family-names: Peltzer + given-names: Alexander + - family-names: Fillinger + given-names: Sven + - family-names: Patel + given-names: Harshil + - family-names: Alneberg + given-names: Johannes + - family-names: Wilm + given-names: Andreas + - family-names: Ulysse Garcia + given-names: Maxime + - family-names: Di Tommaso + given-names: Paolo + - family-names: Nahnsen + given-names: Sven + doi: 10.1038/s41587-020-0439-x + journal: nature biotechnology + start: 276 + end: 278 + title: "The nf-core framework for community-curated bioinformatics pipelines." + issue: 3 + volume: 38 + year: 2020 + url: https://dx.doi.org/10.1038/s41587-020-0439-x diff --git a/README.md b/README.md index 7ba93db3..d80e7ac0 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,14 @@ # ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_light.png#gh-light-mode-only) ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_dark.png#gh-dark-mode-only) -[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?logo=Amazon%20AWS)](https://nf-co.re/rnavar/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) -[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?logo=anaconda)](https://docs.conda.io/en/latest/) -[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/) -[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/) +[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) +[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) +[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnavar) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?logo=slack)](https://nfcore.slack.com/channels/rnavar) -[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?logo=twitter)](https://twitter.com/nf_core) -[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction @@ -25,7 +20,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnavar/results). +On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnavar/results). ## Pipeline summary @@ -42,7 +37,7 @@ On release, automated continuous integration tests run the pipeline on a full-si 3. Download the pipeline and test it on a minimal dataset with a single command: - ```console + ```bash nextflow run nf-core/rnavar -profile test,YOURPROFILE --outdir ``` @@ -57,7 +52,7 @@ On release, automated continuous integration tests run the pipeline on a full-si - ```console + ```bash nextflow run nf-core/rnavar --input samplesheet.csv --outdir --genome GRCh37 -profile ``` diff --git a/assets/email_template.txt b/assets/email_template.txt index 2c43ec61..cbc1a918 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -6,7 +6,6 @@ `._,._,' nf-core/rnavar v${version} ---------------------------------------------------- - Run Name: $runName <% if (success){ diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 3652c63c..9a8b8962 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -11,7 +11,6 @@ from collections import Counter from pathlib import Path - logger = logging.getLogger() @@ -79,13 +78,15 @@ def validate_and_transform(self, row): def _validate_sample(self, row): """Assert that the sample name exists and convert spaces to underscores.""" - assert len(row[self._sample_col]) > 0, "Sample input is required." + if len(row[self._sample_col]) <= 0: + raise AssertionError("Sample input is required.") # Sanitize samples slightly. row[self._sample_col] = row[self._sample_col].replace(" ", "_") def _validate_first(self, row): """Assert that the first FASTQ entry is non-empty and has the right format.""" - assert len(row[self._first_col]) > 0, "At least the first FASTQ file is required." + if len(row[self._first_col]) <= 0: + raise AssertionError("At least the first FASTQ file is required.") self._validate_fastq_format(row[self._first_col]) def _validate_second(self, row): @@ -97,36 +98,34 @@ def _validate_pair(self, row): """Assert that read pairs have the same file extension. Report pair status.""" if row[self._first_col] and row[self._second_col]: row[self._single_col] = False - assert ( - Path(row[self._first_col]).suffixes[-2:] == Path(row[self._second_col]).suffixes[-2:] - ), "FASTQ pairs must have the same file extensions." + if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]: + raise AssertionError("FASTQ pairs must have the same file extensions.") else: row[self._single_col] = True def _validate_fastq_format(self, filename): """Assert that a given filename has one of the expected FASTQ extensions.""" - assert any(filename.endswith(extension) for extension in self.VALID_FORMATS), ( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) + if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): + raise AssertionError( + f"The FASTQ file has an unrecognized extension: {filename}\n" + f"It should be one of: {', '.join(self.VALID_FORMATS)}" + ) def validate_unique_samples(self): """ Assert that the combination of sample name and FASTQ filename is unique. - In addition to the validation, also rename the sample if more than one sample, - FASTQ file combination exists. + In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the + number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. """ - assert len(self._seen) == len(self.modified), "The pair of sample name and FASTQ must be unique." - if len({pair[0] for pair in self._seen}) < len(self._seen): - counts = Counter(pair[0] for pair in self._seen) - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - if counts[sample] > 1: - row[self._sample_col] = f"{sample}_T{seen[sample]}" + if len(self._seen) != len(self.modified): + raise AssertionError("The pair of sample name and FASTQ must be unique.") + seen = Counter() + for row in self.modified: + sample = row[self._sample_col] + seen[sample] += 1 + row[self._sample_col] = f"{sample}_T{seen[sample]}" def read_head(handle, num_lines=10): diff --git a/conf/base.config b/conf/base.config index 71e76362..fcccdad9 100644 --- a/conf/base.config +++ b/conf/base.config @@ -26,6 +26,11 @@ process { // adding in your local modules too. // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors + withLabel:process_single { + cpus = { check_max( 1 , 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 4.h * task.attempt, 'time' ) } + } withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 12.GB * task.attempt, 'memory' ) } diff --git a/docs/usage.md b/docs/usage.md index 3d9775d0..3878607a 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -12,7 +12,7 @@ You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. -```console +```bash --input '[path to samplesheet file]' ``` @@ -56,7 +56,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: -```console +```bash nextflow run nf-core/rnavar --input samplesheet.csv --outdir --genome GRCh37 -profile docker ``` @@ -64,9 +64,9 @@ This will launch the pipeline with the `docker` configuration profile. See below Note that the pipeline will create the following files in your working directory: -```console +```bash work # Directory containing the nextflow working files - # Finished results in specified location (defined with --outdir) + # Finished results in specified location (defined with --outdir) .nextflow_log # Log file from Nextflow # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` @@ -75,7 +75,7 @@ work # Directory containing the nextflow working files When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: -```console +```bash nextflow pull nf-core/rnavar ``` @@ -251,6 +251,6 @@ Some HPC setups also allow you to run nextflow within a cluster job submitted yo In some cases, the Nextflow Java virtual machines can start to request a large amount of memory. We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`): -```console +```bash NXF_OPTS='-Xms1g -Xmx4g' ``` diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 43e5694a..35bf164f 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -59,6 +59,7 @@ class WorkflowMain { } // Print parameter summary log to screen + log.info paramsSummaryLog(workflow, params, log) // Check that a -profile or Nextflow config has been provided to run the pipeline @@ -78,17 +79,15 @@ class WorkflowMain { System.exit(1) } } - // // Get attribute from genome config file e.g. fasta // - public static String getGenomeAttribute(params, attribute) { - def val = '' + public static Object getGenomeAttribute(params, attribute) { if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { if (params.genomes[ params.genome ].containsKey(attribute)) { - val = params.genomes[ params.genome ][ attribute ] + return params.genomes[ params.genome ][ attribute ] } } - return val + return null } } diff --git a/lib/WorkflowRnavar.groovy b/lib/WorkflowRnavar.groovy index cf3ff3b6..162b1db3 100755 --- a/lib/WorkflowRnavar.groovy +++ b/lib/WorkflowRnavar.groovy @@ -10,6 +10,7 @@ class WorkflowRnavar { public static void initialise(params, log) { genomeExistsError(params, log) + if (!params.fasta) { log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." System.exit(1) @@ -41,9 +42,7 @@ class WorkflowRnavar { yaml_file_text += "data: |\n" yaml_file_text += "${summary_section}" return yaml_file_text - } - - // + }// // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { diff --git a/main.nf b/main.nf index 6fc4d58a..22dbf6ca 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,7 @@ nf-core/rnavar ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/rnavar - Website: https://nf-co.re/rnavar +Website: https://nf-co.re/rnavar Slack : https://nfcore.slack.com/channels/rnavar ---------------------------------------------------------------------------------------- */ diff --git a/modules.json b/modules.json index f3f58353..1fa2f0b1 100644 --- a/modules.json +++ b/modules.json @@ -3,14 +3,20 @@ "homePage": "https://github.com/nf-core/rnavar", "repos": { "nf-core/modules": { - "custom/dumpsoftwareversions": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" - }, - "fastqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" - }, - "multiqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" + "git_url": "https://github.com/nf-core/modules.git", + "modules": { + "custom/dumpsoftwareversions": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", + "branch": "master" + }, + "fastqc": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", + "branch": "master" + }, + "multiqc": { + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", + "branch": "master" + } } } } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index d1390392..787bdb7b 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,9 +1,10 @@ #!/usr/bin/env python -import yaml import platform from textwrap import dedent +import yaml + def _make_versions_html(versions): html = [ @@ -58,11 +59,12 @@ def _make_versions_html(versions): for process, process_versions in versions_by_process.items(): module = process.split(":")[-1] try: - assert versions_by_module[module] == process_versions, ( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) except KeyError: versions_by_module[module] = process_versions diff --git a/nextflow.config b/nextflow.config index 7199e3d5..7655f1b4 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,11 +13,11 @@ params { // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -37,6 +37,7 @@ params { schema_ignore_params = 'genomes' enable_conda = false + // Config options custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" @@ -45,6 +46,7 @@ params { config_profile_url = null config_profile_name = null + // Max resource options // Defaults only, expecting to be overwritten max_memory = '128.GB' @@ -72,6 +74,7 @@ try { // } + profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -82,6 +85,15 @@ profiles { shifter.enabled = false charliecloud.enabled = false } + mamba { + params.enable_conda = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } docker { docker.enabled = true docker.userEmulation = true @@ -119,10 +131,16 @@ profiles { podman.enabled = false shifter.enabled = false } + gitpod { + executor.name = 'local' + executor.cpus = 16 + executor.memory = 60.GB + } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } } + // Load igenomes.config if required if (!params.igenomes_ignore) { includeConfig 'conf/igenomes.config' @@ -130,6 +148,7 @@ if (!params.igenomes_ignore) { params.genomes = [:] } + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -169,7 +188,7 @@ manifest { description = 'GATK4 RNA variant calling pipeline' mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' - version = '1.0dev' + version = '1.1.0dev' } // Load modules.config for DSL2 module specific options From c0049b9ce49e2fe8862789df8e5d498608106c11 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 1 Sep 2022 13:31:48 +0000 Subject: [PATCH 005/275] Template update for nf-core/tools version 2.5.1 --- bin/check_samplesheet.py | 9 ++++++--- pyproject.toml | 10 ++++++++++ 2 files changed, 16 insertions(+), 3 deletions(-) create mode 100644 pyproject.toml diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 9a8b8962..11b15572 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -98,7 +98,9 @@ def _validate_pair(self, row): """Assert that read pairs have the same file extension. Report pair status.""" if row[self._first_col] and row[self._second_col]: row[self._single_col] = False - if Path(row[self._first_col]).suffixes[-2:] != Path(row[self._second_col]).suffixes[-2:]: + first_col_suffix = Path(row[self._first_col]).suffixes[-2:] + second_col_suffix = Path(row[self._second_col]).suffixes[-2:] + if first_col_suffix != second_col_suffix: raise AssertionError("FASTQ pairs must have the same file extensions.") else: row[self._single_col] = True @@ -157,7 +159,7 @@ def sniff_format(handle): handle.seek(0) sniffer = csv.Sniffer() if not sniffer.has_header(peek): - logger.critical(f"The given sample sheet does not appear to contain a header.") + logger.critical("The given sample sheet does not appear to contain a header.") sys.exit(1) dialect = sniffer.sniff(peek) return dialect @@ -195,7 +197,8 @@ def check_samplesheet(file_in, file_out): reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) # Validate the existence of the expected header columns. if not required_columns.issubset(reader.fieldnames): - logger.critical(f"The sample sheet **must** contain the column headers: {', '.join(required_columns)}.") + req_cols = ", ".join(required_columns) + logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") sys.exit(1) # Validate each row. checker = RowChecker() diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..0d62beb6 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,10 @@ +# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. +# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. +[tool.black] +line-length = 120 +target_version = ["py37", "py38", "py39", "py310"] + +[tool.isort] +profile = "black" +known_first_party = ["nf_core"] +multi_line_output = 3 From dca413e39c4a01b4aa862c512c6110ed48e4db60 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 4 Oct 2022 22:04:09 +0000 Subject: [PATCH 006/275] Template update for nf-core/tools version 2.6 --- .github/workflows/awsfulltest.yml | 4 ++ .github/workflows/awstest.yml | 4 ++ .prettierignore | 1 + CITATION.cff | 8 +-- assets/adaptivecard.json | 67 +++++++++++++++++++ assets/methods_description_template.yml | 25 +++++++ assets/multiqc_config.yml | 6 +- docs/usage.md | 8 +++ lib/NfcoreTemplate.groovy | 55 +++++++++++++++ lib/Utils.groovy | 21 ++++-- lib/WorkflowRnavar.groovy | 19 ++++++ main.nf | 3 +- modules.json | 27 ++++---- .../custom/dumpsoftwareversions/main.nf | 8 +-- .../custom/dumpsoftwareversions/meta.yml | 0 .../templates/dumpsoftwareversions.py | 0 modules/nf-core/{modules => }/fastqc/main.nf | 12 ++++ modules/nf-core/{modules => }/fastqc/meta.yml | 0 modules/nf-core/modules/multiqc/main.nf | 31 --------- modules/nf-core/multiqc/main.nf | 53 +++++++++++++++ .../nf-core/{modules => }/multiqc/meta.yml | 15 +++++ nextflow.config | 5 +- nextflow_schema.json | 18 +++++ workflows/rnavar.nf | 26 ++++--- 24 files changed, 345 insertions(+), 71 deletions(-) create mode 100644 assets/adaptivecard.json create mode 100644 assets/methods_description_template.yml mode change 100755 => 100644 lib/Utils.groovy rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/main.nf (79%) rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/meta.yml (100%) rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py (100%) rename modules/nf-core/{modules => }/fastqc/main.nf (85%) rename modules/nf-core/{modules => }/fastqc/meta.yml (100%) delete mode 100644 modules/nf-core/modules/multiqc/main.nf create mode 100644 modules/nf-core/multiqc/main.nf rename modules/nf-core/{modules => }/multiqc/meta.yml (73%) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7b3d239a..50a7398e 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -28,3 +28,7 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-${{ github.sha }}" } profiles: test_full,aws_tower + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index a05594d9..84a22495 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -23,3 +23,7 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-test-${{ github.sha }}" } profiles: test,aws_tower + - uses: actions/upload-artifact@v3 + with: + name: Tower debug log file + path: tower_action_*.log diff --git a/.prettierignore b/.prettierignore index d0e7ae58..eb74a574 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,4 +1,5 @@ email_template.html +adaptivecard.json .nextflow* work/ data/ diff --git a/CITATION.cff b/CITATION.cff index 4533e2f2..017666c0 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -13,8 +13,8 @@ authors: given-names: Johannes - family-names: Wilm given-names: Andreas - - family-names: Ulysse Garcia - given-names: Maxime + - family-names: Garcia + given-names: Maxime Ulysse - family-names: Di Tommaso given-names: Paolo - family-names: Nahnsen @@ -39,8 +39,8 @@ prefered-citation: given-names: Johannes - family-names: Wilm given-names: Andreas - - family-names: Ulysse Garcia - given-names: Maxime + - family-names: Garcia + given-names: Maxime Ulysse - family-names: Di Tommaso given-names: Paolo - family-names: Nahnsen diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json new file mode 100644 index 00000000..2b1d36cb --- /dev/null +++ b/assets/adaptivecard.json @@ -0,0 +1,67 @@ +{ + "type": "message", + "attachments": [ + { + "contentType": "application/vnd.microsoft.card.adaptive", + "contentUrl": null, + "content": { + "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", + "msteams": { + "width": "Full" + }, + "type": "AdaptiveCard", + "version": "1.2", + "body": [ + { + "type": "TextBlock", + "size": "Large", + "weight": "Bolder", + "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", + "text": "nf-core/rnavar v${version} - ${runName}", + "wrap": true + }, + { + "type": "TextBlock", + "spacing": "None", + "text": "Completed at ${dateComplete} (duration: ${duration})", + "isSubtle": true, + "wrap": true + }, + { + "type": "TextBlock", + "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", + "wrap": true + }, + { + "type": "TextBlock", + "text": "The command used to launch the workflow was as follows:", + "wrap": true + }, + { + "type": "TextBlock", + "text": "${commandLine}", + "isSubtle": true, + "wrap": true + } + ], + "actions": [ + { + "type": "Action.ShowCard", + "title": "Pipeline Configuration", + "card": { + "type": "AdaptiveCard", + "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", + "body": [ + { + "type": "FactSet", + "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> + ] + } + ] + } + } + ] + } + } + ] +} diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml new file mode 100644 index 00000000..f2bc183b --- /dev/null +++ b/assets/methods_description_template.yml @@ -0,0 +1,25 @@ +id: "nf-core-rnavar-methods-description" +description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." +section_name: "nf-core/rnavar Methods Description" +section_href: "https://github.com/nf-core/rnavar" +plot_type: "html" +## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## You inject any metadata in the Nextflow '${workflow}' object +data: | +

Methods

+

Data was processed using nf-core/rnavar v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

+ 
${workflow.commandLine}
+

References

+
    +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
    • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
    • +
+
+
Notes:
+
    + ${nodoi_text} +
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • +
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • +
+
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f3b0ac1d..2689c2b9 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,11 @@ report_comment: > analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: - software_versions: + "nf-core-rnavar-methods-description": order: -1000 - "nf-core-rnavar-summary": + software_versions: order: -1001 + "nf-core-rnavar-summary": + order: -1002 export_plots: true diff --git a/docs/usage.md b/docs/usage.md index 3878607a..db4e6f4d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -237,6 +237,14 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). +## Azure Resource Requests + +To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. +We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. + +Note that the choice of VM size depends on your quota and the overall workload during the analysis. +For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). + ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 2fc0a9b9..27feb009 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -145,6 +145,61 @@ class NfcoreTemplate { output_tf.withWriter { w -> w << email_txt } } + // + // Construct and send adaptive card + // https://adaptivecards.io + // + public static void adaptivecard(workflow, params, summary_params, projectDir, log) { + def hook_url = params.hook_url + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = workflow.manifest.version + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + def hf = new File("$projectDir/assets/adaptivecard.json") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } + } + // // Print pipeline summary on completion // diff --git a/lib/Utils.groovy b/lib/Utils.groovy old mode 100755 new mode 100644 index 28567bd7..8d030f4e --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -21,19 +21,26 @@ class Utils { } // Check that all channels are present - def required_channels = ['conda-forge', 'bioconda', 'defaults'] - def conda_check_failed = !required_channels.every { ch -> ch in channels } + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda')) - conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults')) + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } - if (conda_check_failed) { + if (channels_missing | channel_priority_violation) { log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" + - " NB: The order of the channels matters!\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } } diff --git a/lib/WorkflowRnavar.groovy b/lib/WorkflowRnavar.groovy index 162b1db3..6f2ab32d 100755 --- a/lib/WorkflowRnavar.groovy +++ b/lib/WorkflowRnavar.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the workflow/rnavar.nf in the nf-core/rnavar pipeline // +import groovy.text.SimpleTemplateEngine + class WorkflowRnavar { // @@ -42,6 +44,23 @@ class WorkflowRnavar { yaml_file_text += "data: |\n" yaml_file_text += "${summary_section}" return yaml_file_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = run_workflow.toMap() + meta["manifest_map"] = run_workflow.manifest.toMap() + + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + def methods_text = mqc_methods_yaml.text + + def engine = new SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html }// // Exit pipeline if incorrect --genome key provided // diff --git a/main.nf b/main.nf index 22dbf6ca..bd3b64d2 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,8 @@ nf-core/rnavar ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/rnavar -Website: https://nf-co.re/rnavar + + Website: https://nf-co.re/rnavar Slack : https://nfcore.slack.com/channels/rnavar ---------------------------------------------------------------------------------------- */ diff --git a/modules.json b/modules.json index 1fa2f0b1..b4e3abcc 100644 --- a/modules.json +++ b/modules.json @@ -2,20 +2,21 @@ "name": "nf-core/rnavar", "homePage": "https://github.com/nf-core/rnavar", "repos": { - "nf-core/modules": { - "git_url": "https://github.com/nf-core/modules.git", + "https://github.com/nf-core/modules.git": { "modules": { - "custom/dumpsoftwareversions": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" - }, - "fastqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" - }, - "multiqc": { - "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d", - "branch": "master" + "nf-core": { + "custom/dumpsoftwareversions": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "fastqc": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + }, + "multiqc": { + "branch": "master", + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + } } } } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf similarity index 79% rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf rename to modules/nf-core/custom/dumpsoftwareversions/main.nf index 327d5100..cebb6e05 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -1,11 +1,11 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_low' + label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? "bioconda::multiqc=1.11" : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml similarity index 100% rename from modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml rename to modules/nf-core/custom/dumpsoftwareversions/meta.yml diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py similarity index 100% rename from modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py rename to modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/fastqc/main.nf similarity index 85% rename from modules/nf-core/modules/fastqc/main.nf rename to modules/nf-core/fastqc/main.nf index ed6b8c50..05730368 100644 --- a/modules/nf-core/modules/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -44,4 +44,16 @@ process FASTQC { END_VERSIONS """ } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.html + touch ${prefix}.zip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ } diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml similarity index 100% rename from modules/nf-core/modules/fastqc/meta.yml rename to modules/nf-core/fastqc/meta.yml diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/modules/multiqc/main.nf deleted file mode 100644 index 1264aac1..00000000 --- a/modules/nf-core/modules/multiqc/main.nf +++ /dev/null @@ -1,31 +0,0 @@ -process MULTIQC { - label 'process_medium' - - conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" - - input: - path multiqc_files - - output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - """ - multiqc -f $args . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf new file mode 100644 index 00000000..a8159a57 --- /dev/null +++ b/modules/nf-core/multiqc/main.nf @@ -0,0 +1,53 @@ +process MULTIQC { + label 'process_single' + + conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + + input: + path multiqc_files, stageAs: "?/*" + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) + + output: + path "*multiqc_report.html", emit: report + path "*_data" , emit: data + path "*_plots" , optional:true, emit: plots + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' + def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + """ + multiqc \\ + --force \\ + $args \\ + $config \\ + $extra_config \\ + . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ + + stub: + """ + touch multiqc_data + touch multiqc_plots + touch multiqc_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml similarity index 73% rename from modules/nf-core/modules/multiqc/meta.yml rename to modules/nf-core/multiqc/meta.yml index 6fa891ef..ebc29b27 100644 --- a/modules/nf-core/modules/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -12,11 +12,25 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + input: - multiqc_files: type: file description: | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + output: - report: type: file @@ -38,3 +52,4 @@ authors: - "@abhi18av" - "@bunop" - "@drpatelh" + - "@jfy133" diff --git a/nextflow.config b/nextflow.config index 7655f1b4..c80668dd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -21,7 +21,9 @@ params { // MultiQC options multiqc_config = null multiqc_title = null + multiqc_logo = null max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Boilerplate options outdir = null @@ -31,6 +33,7 @@ params { email_on_fail = null plaintext_email = false monochrome_logs = false + hook_url = null help = false validate_params = true show_hidden_params = false @@ -74,7 +77,6 @@ try { // } - profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { @@ -189,6 +191,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' version = '1.1.0dev' + doi = '' } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index 62e73f72..51870fa6 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -213,12 +213,30 @@ "fa_icon": "fas fa-palette", "hidden": true }, + "hook_url": { + "type": "string", + "description": "Incoming hook URL for messaging service", + "fa_icon": "fas fa-people-group", + "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.", + "hidden": true + }, "multiqc_config": { "type": "string", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true }, + "multiqc_logo": { + "type": "string", + "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", + "fa_icon": "fas fa-image", + "hidden": true + }, + "multiqc_methods_description": { + "type": "string", + "description": "Custom MultiQC yaml file containing HTML including a methods description.", + "fa_icon": "fas fa-cog" + }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 4132f35a..1042cc76 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -23,8 +23,10 @@ if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input sample ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() +ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() +ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() +ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46,9 +48,9 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' // // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/modules/fastqc/main' -include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -89,15 +91,20 @@ workflow RNAVAR { workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) + methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + ch_methods_description = Channel.value(methods_description) + ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) MULTIQC ( - ch_multiqc_files.collect() + ch_multiqc_files.collect(), + ch_multiqc_config.collect().ifEmpty([]), + ch_multiqc_custom_config.collect().ifEmpty([]), + ch_multiqc_logo.collect().ifEmpty([]) ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) @@ -114,6 +121,9 @@ workflow.onComplete { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) } NfcoreTemplate.summary(workflow, params, log) + if (params.hook_url) { + NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log) + } } /* From 4f31fe05586fcf5604fec08347763e6dbff8efb0 Mon Sep 17 00:00:00 2001 From: mcharles Date: Thu, 24 Nov 2022 14:50:12 +0100 Subject: [PATCH 007/275] First commit --- conf/modules.config | 26 ++++ modules.json | 6 + modules/local/gtf2bed.nf | 14 +- .../nf-core/modules/bedtools/merge/main.nf | 36 +++++ .../nf-core/modules/bedtools/merge/meta.yml | 39 +++++ modules/nf-core/modules/bedtools/sort/main.nf | 37 +++++ .../nf-core/modules/bedtools/sort/meta.yml | 46 ++++++ .../modules/gatk4/combinegvcfs/main.nf | 48 ++++++ .../modules/gatk4/combinegvcfs/meta.yml | 61 ++++++++ subworkflows/local/prepare_genome.nf | 24 ++- workflows/rnavar.nf | 138 +++++++++++++++--- 11 files changed, 448 insertions(+), 27 deletions(-) mode change 100644 => 100755 conf/modules.config mode change 100644 => 100755 modules.json mode change 100644 => 100755 modules/local/gtf2bed.nf create mode 100644 modules/nf-core/modules/bedtools/merge/main.nf create mode 100644 modules/nf-core/modules/bedtools/merge/meta.yml create mode 100644 modules/nf-core/modules/bedtools/sort/main.nf create mode 100644 modules/nf-core/modules/bedtools/sort/meta.yml create mode 100755 modules/nf-core/modules/gatk4/combinegvcfs/main.nf create mode 100755 modules/nf-core/modules/gatk4/combinegvcfs/meta.yml mode change 100644 => 100755 subworkflows/local/prepare_genome.nf mode change 100644 => 100755 workflows/rnavar.nf diff --git a/conf/modules.config b/conf/modules.config old mode 100644 new mode 100755 index 61cf9ba1..a9ff5d12 --- a/conf/modules.config +++ b/conf/modules.config @@ -93,6 +93,7 @@ process { ] } + withName: SAMTOOLS_FAIDX { publishDir = [ path: { "${params.outdir}/genome" }, @@ -316,6 +317,22 @@ process { ].join(' ').trim() publishDir = [ enabled: false ] } + + withName: GATK4_HAPLOTYPECALLERGVCF { + ext.args = [ + '--dont-use-soft-clipped-bases', + params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '', + params.bam_csi_index ? "--create-output-variant-index false" : "", "-ERC GVCF" + ].join(' ').trim() + ext.prefix = {"${meta.id}.haplotypecaller"} + publishDir = [ enabled: false ] + } + + withName: GATK4_INDEXFEATUREFILE { + publishDir = [ + enabled: false + ] + } withName: GATK4_MERGEVCFS { ext.prefix = {"${meta.id}.haplotypecaller"} @@ -326,6 +343,15 @@ process { pattern: "*.{vcf.gz}" ] } + + withName: GATK4_COMBINEGVCFS { + ext.prefix = {"${meta.id}.haplotypecaller"} + publishDir = [ + path: { "${params.outdir}/variant_calling/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*.{vcf.gz}" + ] + } withName: TABIX_TABIX { ext.args = params.bam_csi_index ? '--csi' : '' diff --git a/modules.json b/modules.json old mode 100644 new mode 100755 index c35f0779..6962f631 --- a/modules.json +++ b/modules.json @@ -57,6 +57,12 @@ "multiqc": { "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe" }, + "bedtools/merge": { + "git_sha": "4bb1d4e362a38642e877afe41aaf58ded9e56c86" + }, + "bedtools/sort": { + "git_sha": "4bb1d4e362a38642e877afe41aaf58ded9e56c86" + }, "samtools/faidx": { "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773" }, diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf old mode 100644 new mode 100755 index 0c434dcb..73d8a271 --- a/modules/local/gtf2bed.nf +++ b/modules/local/gtf2bed.nf @@ -5,11 +5,12 @@ process GTF2BED { conda (params.enable_conda ? "conda-forge::r-base=3.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-base:3.5.0' : - 'quay.io/biocontainers/r-base:3.5.0' }" + 'quay.io/biocontainers/r-base:3.5.0'}" input: path gtf - + val feature_type + output: path '*.bed' , emit: bed path "versions.yml", emit: versions @@ -18,15 +19,20 @@ process GTF2BED { task.ext.when == null || task.ext.when script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/ + def allowed_type = ["exon", "transcript", "gene"]; + if (feature_type){ + feature_type = allowed_type.contains(feature_type) ? feature_type : "exon" + } + """ Rscript --no-save -<<'RCODE' gtf = read.table("${gtf}", sep="\t") - gtf = subset(gtf, V3 == "exon") + gtf = subset(gtf, V3 == "${feature_type}") write.table(data.frame(chrom=gtf[,'V1'], start=gtf[,'V4'], end=gtf[,'V5']), "tmp.exome.bed", quote = F, sep="\t", col.names = F, row.names = F) RCODE awk '{print \$1 "\t" (\$2 - 1) "\t" \$3}' tmp.exome.bed > exome.bed - rm tmp.exome.bed + rm -rf tmp.exome.bed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/modules/bedtools/merge/main.nf b/modules/nf-core/modules/bedtools/merge/main.nf new file mode 100644 index 00000000..06dad822 --- /dev/null +++ b/modules/nf-core/modules/bedtools/merge/main.nf @@ -0,0 +1,36 @@ +process BEDTOOLS_MERGE { + tag "$meta.id" + label 'process_single' + + conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + + input: + tuple val(meta), path(bed) + + output: + tuple val(meta), path('*.bed'), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bed" == "${prefix}.bed") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + bedtools \\ + merge \\ + -i $bed \\ + $args \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/modules/bedtools/merge/meta.yml b/modules/nf-core/modules/bedtools/merge/meta.yml new file mode 100644 index 00000000..76743679 --- /dev/null +++ b/modules/nf-core/modules/bedtools/merge/meta.yml @@ -0,0 +1,39 @@ +name: bedtools_merge +description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +keywords: + - bed + - merge +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/nf-core/modules/bedtools/sort/main.nf b/modules/nf-core/modules/bedtools/sort/main.nf new file mode 100644 index 00000000..331c129a --- /dev/null +++ b/modules/nf-core/modules/bedtools/sort/main.nf @@ -0,0 +1,37 @@ +process BEDTOOLS_SORT { + tag "$meta.id" + label 'process_single' + + conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : + 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + + input: + tuple val(meta), path(intervals) + val extension + + output: + tuple val(meta), path("*.${extension}"), emit: sorted + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$intervals" == "${prefix}.${extension}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + bedtools \\ + sort \\ + -i $intervals \\ + $args \\ + > ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/modules/bedtools/sort/meta.yml b/modules/nf-core/modules/bedtools/sort/meta.yml new file mode 100644 index 00000000..369e51ff --- /dev/null +++ b/modules/nf-core/modules/bedtools/sort/meta.yml @@ -0,0 +1,46 @@ +name: bedtools_sort +description: Sorts a feature file by chromosome and other criteria. +keywords: + - bed + - sort +tools: + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" + + - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + + - sorted: + type: file + description: Sorted output file + pattern: "*.${extension}" + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" + - "@chris-cheshire" diff --git a/modules/nf-core/modules/gatk4/combinegvcfs/main.nf b/modules/nf-core/modules/gatk4/combinegvcfs/main.nf new file mode 100755 index 00000000..488666b3 --- /dev/null +++ b/modules/nf-core/modules/gatk4/combinegvcfs/main.nf @@ -0,0 +1,48 @@ +process GATK4_COMBINEGVCFS { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0': + 'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }" + + input: + tuple val(meta), path(vcf) + tuple val(meta), path(vcf_idx) + path fasta + path fai + path dict + + output: + tuple val(meta), path("*.combined.g.vcf.gz"), emit: combined_gvcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def input_list = vcf.collect{"--variant $it"}.join(' ') + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK COMBINEGVCFS] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" CombineGVCFs \\ + $input_list \\ + --output ${prefix}.combined.g.vcf.gz \\ + --reference ${fasta} \\ + --tmp-dir . \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/modules/gatk4/combinegvcfs/meta.yml b/modules/nf-core/modules/gatk4/combinegvcfs/meta.yml new file mode 100755 index 00000000..9330e084 --- /dev/null +++ b/modules/nf-core/modules/gatk4/combinegvcfs/meta.yml @@ -0,0 +1,61 @@ +name: gatk4_combinegvcfs +description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file +keywords: + - gvcf + - gatk4 + - vcf + - combinegvcfs + - Short_Variant_Discovery +tools: + - gatk4: + description: + Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs + tool_dev_url: https://github.com/broadinstitute/gatk + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: Compressed VCF files + pattern: "*.vcf.gz" + - vcf_idx: + type: file + description: VCF Index file + pattern: "*.vcf.gz.idx" + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - fai: + type: file + description: FASTA index file + pattern: "*.fasta.fai" + - dict: + type: file + description: FASTA dictionary file + pattern: "*.dict" +output: + - gvcf: + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@sateeshperi" + - "@mjcipriano" + - "@hseabolt" + - "@maxulysse" diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf old mode 100644 new mode 100755 index e4760b57..8768a515 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -4,7 +4,9 @@ include { GATK4_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main' //addParams(options: params.genome_options) include { GFFREAD } from '../../modules/nf-core/modules/gffread/main' //addParams(options: params.gffread_options) -include { GTF2BED } from '../../modules/local/gtf2bed' //addParams(options: params.genome_options) +include { GTF2BED } from '../../modules/local/gtf2bed' +include { BEDTOOLS_SORT } from '../../modules/nf-core/modules/bedtools/sort/main' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/modules/bedtools/merge/main' include { GUNZIP as GUNZIP_FASTA } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) include { GUNZIP as GUNZIP_GENE_BED } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) include { GUNZIP as GUNZIP_GFF } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) @@ -17,6 +19,7 @@ include { UNTAR as UNTAR_STAR_INDEX } from '../../modules/nf-core/module workflow PREPARE_GENOME { take: prepare_tool_indices + feature_type main: @@ -83,9 +86,24 @@ workflow PREPARE_GENOME { ch_gene_bed = Channel.fromPath(params.exon_bed).collect() } } else { - ch_exon_bed = GTF2BED ( ch_gtf ).bed.collect() + ch_exon_bed = GTF2BED ( ch_gtf , feature_type).bed.collect() ch_versions = ch_versions.mix(GTF2BED.out.versions) } + + ch_exon_bed.map{ it -> [[id:'exome'], it] } + + // Bedtools sort + ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed, 'sorted').sorted.collect() + ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions) + + + // Bedtools merge + //ch_test_meta=BEDTOOLS_SORT.out[0] + //ch_test_path=BEDTOOLS_SORT.out[1] + //ch_bedtools_merge = BEDTOOLS_MERGE(BEDTOOLS_SORT.out.sorted.collect()) + ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort) + ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) + // Index the genome fasta ch_fasta_fai = Channel.empty() @@ -141,6 +159,8 @@ workflow PREPARE_GENOME { dict = ch_fasta_dict // path: genome.fasta.dict gtf = ch_gtf // path: genome.gtf exon_bed = ch_exon_bed // path: exon.bed + bedtools_sort = ch_bedtools_sort // path: sort.bed + bedtools_merge = ch_bedtools_merge // path: merge.bed star_index = ch_star_index // path: star/index/ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf old mode 100644 new mode 100755 index 34688263..c434eefe --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -57,19 +57,30 @@ include { ANNOTATE } from '../subworkflows/local/annotate' ======================================================================================== */ -include { FASTQC } from '../modules/nf-core/modules/fastqc/main' -include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' -include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main' -include { GATK4_BASERECALIBRATOR } from '../modules/nf-core/modules/gatk4/baserecalibrator/main' -include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/modules/gatk4/bedtointervallist/main' -include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/modules/gatk4/intervallisttools/main' -include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' -include { GATK4_MERGEVCFS } from '../modules/nf-core/modules/gatk4/mergevcfs/main' -include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/modules/gatk4/indexfeaturefile/main' -include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/modules/gatk4/variantfiltration/main' -include { SAMTOOLS_INDEX } from '../modules/nf-core/modules/samtools/index/main' -include { TABIX_TABIX as TABIX } from '../modules/nf-core/modules/tabix/tabix/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/modules/fastqc/main' +include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' +include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main' +include { GATK4_BASERECALIBRATOR } from '../modules/nf-core/modules/gatk4/baserecalibrator/main' +include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/modules/gatk4/bedtointervallist/main' +include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/modules/gatk4/intervallisttools/main' +include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' +include { GATK4_HAPLOTYPECALLER as GATK4_HAPLOTYPECALLERGVCF } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' +include { GATK4_MERGEVCFS } from '../modules/nf-core/modules/gatk4/mergevcfs/main' +include { GATK4_COMBINEGVCFS } from '../modules/nf-core/modules/gatk4/combinegvcfs/main' +include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/modules/gatk4/indexfeaturefile/main' +include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/modules/gatk4/variantfiltration/main' +include { SAMTOOLS_INDEX } from '../modules/nf-core/modules/samtools/index/main' +include { TABIX_TABIX as TABIX } from '../modules/nf-core/modules/tabix/tabix/main' +include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/modules/tabix/tabix/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' + +/* +======================================================================================== + IMPORT LOCAL MODULES +======================================================================================== +*/ + +include { GTF2BED } from '../modules/local/gtf2bed' /* ======================================================================================== @@ -99,7 +110,7 @@ ch_dbsnp_tbi = params.dbsnp_tbi ? Channel.fromPath(params.dbs ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.empty() ch_known_indels_tbi = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : Channel.empty() -// Initialize varaint annotation associated channels +// Initialize variant annotation associated channels ch_snpeff_db = params.snpeff_db ?: Channel.empty() ch_vep_cache_version = params.vep_cache_version ?: Channel.empty() ch_vep_genome = params.vep_genome ?: Channel.empty() @@ -110,6 +121,13 @@ ch_vep_cache = params.vep_cache ? Channel.fromPath(params. // MultiQC reporting def multiqc_report = [] +// GTF2bed parameters +def feature_type = params.feature_type ? params.feature_type : "exon" + + +// generate_gvcf parameters +def generate_gvcf = params.generate_gvcf ? params.generate_gvcf : false + /* ======================================================================================== RUN MAIN WORKFLOW RNAVAR @@ -127,7 +145,8 @@ workflow RNAVAR { // SUBWORKFLOW: Uncompress and prepare reference genome files // PREPARE_GENOME ( - prepareToolIndices + prepareToolIndices, + feature_type ) ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) @@ -338,6 +357,7 @@ workflow RNAVAR { // MODULE: HaplotypeCaller from GATK4 // Calls germline SNPs and indels via local re-assembly of haplotypes. // + GATK4_HAPLOTYPECALLER( ch_haplotypecaller_interval_bam, PREPARE_GENOME.out.fasta, @@ -346,15 +366,16 @@ workflow RNAVAR { ch_dbsnp, ch_dbsnp_tbi ) - + + ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf - .map{ meta, vcf -> - meta.id = meta.sample - [meta, vcf]} - .groupTuple() + .map{ meta, vcf -> + meta.id = meta.sample + [meta, vcf]} + .groupTuple() ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) - + // // MODULE: MergeVCFS from GATK4 // Merge multiple VCF files into one VCF @@ -366,6 +387,81 @@ workflow RNAVAR { ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) + if (generate_gvcf){ + GATK4_HAPLOTYPECALLERGVCF( + ch_haplotypecaller_interval_bam, + PREPARE_GENOME.out.fasta, + PREPARE_GENOME.out.fai, + PREPARE_GENOME.out.dict, + ch_dbsnp, + ch_dbsnp_tbi + ) + + ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf + .map{ meta, vcf -> + meta.id = meta.sample + [meta, vcf]} + .groupTuple() + + ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) + // + // MODULE: IndexFeatureFile from GATK4 + // Index the gVCF files + // + GATK4_INDEXFEATUREFILE( + GATK4_HAPLOTYPECALLERGVCF.out.vcf + ) + + ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index + .map{ meta, idx -> + meta.id = meta.sample + [meta, idx]} + .groupTuple() + + ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) + + // + // MODULE: CombineGVCFS from GATK4 + // Merge multiple GVCF files into one GVCF + // + + //ch_haplotypecallergvcf_raw_tbi = ch_haplotypecallergvcf_raw + // .join(ch_haplotypecallergvcf_raw_index, by: [0], remainder: true) + // .map{meta, vcf, tbi -> + // [meta, vcf, tbi] + // } + + + + GATK4_COMBINEGVCFS( + ch_haplotypecallergvcf_raw, + ch_haplotypecallergvcf_raw_index, + PREPARE_GENOME.out.fasta, + PREPARE_GENOME.out.fai, + PREPARE_GENOME.out.dict + ) + ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf + ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) + + // + // MODULE: Index the VCF using TABIX + // + TABIXGVCF( + ch_haplotypecaller_gvcf + ) + + ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf + .join(TABIXGVCF.out.tbi, by: [0], remainder: true) + .join(TABIXGVCF.out.csi, by: [0], remainder: true) + .map{meta, vcf, tbi, csi -> + if (tbi) [meta, vcf, tbi] + else [meta, vcf, csi] + } + + ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) + + } + // // MODULE: Index the VCF using TABIX // From c686eef9a1a6129c4315f2bf4a4a1bc64c1eaf77 Mon Sep 17 00:00:00 2001 From: mcharles Date: Wed, 30 Nov 2022 10:52:02 +0100 Subject: [PATCH 008/275] Add params to config and json files --- nextflow.config | 6 ++++-- nextflow_schema.json | 12 +++++++++++- subworkflows/local/prepare_genome.nf | 12 +++++------- workflows/rnavar.nf | 14 +++++--------- 4 files changed, 25 insertions(+), 19 deletions(-) diff --git a/nextflow.config b/nextflow.config index ee010d49..70b9ad23 100644 --- a/nextflow.config +++ b/nextflow.config @@ -20,6 +20,7 @@ params { igenomes_ignore = false save_reference = false save_merged_fastq = false + feature_type = 'exon' // Sequence read information read_length = 150 // Required for STAR to build index and align reads @@ -42,7 +43,7 @@ params { // Variant calling no_intervals = false - + // Variant annotation annotate_tools = null // List of annotation tools to run - snpeff or vep or merge annotation_cache = false // Annotation cache disabled @@ -67,8 +68,9 @@ params { // GATK intervallist parameters gatk_interval_scatter_count = 25 - //GATK haplotypecaller parameters + // GATK haplotypecaller parameters gatk_hc_call_conf = 20 + generate_gvcf = false //GATK variant filter parameters gatk_vf_window_size = 35 diff --git a/nextflow_schema.json b/nextflow_schema.json index b8bfe2a1..f71d87f3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -156,6 +156,11 @@ "type": "string", "fa_icon": "fas fa-tag", "description": "VEP cache version" + }, + "feature_type": { + "type": "string", + "description": "Type of feature to parse from annotation file", + "help_text": "This parameter value can be exon, transcript or gene. Default exon" } } }, @@ -260,7 +265,12 @@ "description": "The minimum phred-scaled confidence threshold at which variants should be called.", "help_text": "Specify the minimum phred-scaled confidence threshold at which variants should be called.", "hidden": false - } + }, + "generate_gvcf": { + "type": "boolean", + "description": "Enable generation of GVCFs by sample additionnaly to the VCFs.", + "help_text": "This parameter enables GATK HAPLOTYPECALLER to generate GVCFs. Default false." + }, } }, "variant_annotation": { diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 8768a515..74acecc8 100755 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -90,18 +90,16 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(GTF2BED.out.versions) } - ch_exon_bed.map{ it -> [[id:'exome'], it] } - + //ch_exon_bed.view() + //ch_exon_bed.map{ it -> [[id:'exome'], it] } + //ch_exon_bed.view() // Bedtools sort - ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed, 'sorted').sorted.collect() + ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed.map{ it -> [[id:'exome'], it] }, 'sorted').sorted.collect() ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions) // Bedtools merge - //ch_test_meta=BEDTOOLS_SORT.out[0] - //ch_test_path=BEDTOOLS_SORT.out[1] - //ch_bedtools_merge = BEDTOOLS_MERGE(BEDTOOLS_SORT.out.sorted.collect()) - ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort) + ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort).bed ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index c434eefe..94d202dd 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -23,7 +23,8 @@ def checkPathParamList = [ params.known_indels_tbi, params.snpeff_cache, params.vep_cache, - params.star_index] + params.star_index, +] for (param in checkPathParamList) {if (param) file(param, checkIfExists: true)} @@ -121,12 +122,6 @@ ch_vep_cache = params.vep_cache ? Channel.fromPath(params. // MultiQC reporting def multiqc_report = [] -// GTF2bed parameters -def feature_type = params.feature_type ? params.feature_type : "exon" - - -// generate_gvcf parameters -def generate_gvcf = params.generate_gvcf ? params.generate_gvcf : false /* ======================================================================================== @@ -144,9 +139,10 @@ workflow RNAVAR { // // SUBWORKFLOW: Uncompress and prepare reference genome files // + PREPARE_GENOME ( prepareToolIndices, - feature_type + params.feature_type ) ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) @@ -387,7 +383,7 @@ workflow RNAVAR { ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) - if (generate_gvcf){ + if (params.generate_gvcf){ GATK4_HAPLOTYPECALLERGVCF( ch_haplotypecaller_interval_bam, PREPARE_GENOME.out.fasta, From 88ade604c45334586f343426559bab6b4f3c7757 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 5 Dec 2022 09:27:15 +0000 Subject: [PATCH 009/275] [automated] Fix linting with Prettier --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index f71d87f3..e0ec0fc1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -270,7 +270,7 @@ "type": "boolean", "description": "Enable generation of GVCFs by sample additionnaly to the VCFs.", "help_text": "This parameter enables GATK HAPLOTYPECALLER to generate GVCFs. Default false." - }, + } } }, "variant_annotation": { From 86460530bff9b5ca9f078f4cf3666e0ed17f8da0 Mon Sep 17 00:00:00 2001 From: "Maxime U. Garcia" Date: Mon, 5 Dec 2022 10:33:56 +0100 Subject: [PATCH 010/275] Apply suggestions from code review remove trailing spaces --- conf/modules.config | 3 --- modules/local/gtf2bed.nf | 4 +--- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a9ff5d12..f05b3322 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -317,7 +317,6 @@ process { ].join(' ').trim() publishDir = [ enabled: false ] } - withName: GATK4_HAPLOTYPECALLERGVCF { ext.args = [ '--dont-use-soft-clipped-bases', @@ -327,7 +326,6 @@ process { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ enabled: false ] } - withName: GATK4_INDEXFEATUREFILE { publishDir = [ enabled: false @@ -343,7 +341,6 @@ process { pattern: "*.{vcf.gz}" ] } - withName: GATK4_COMBINEGVCFS { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf index 73d8a271..a8baa452 100755 --- a/modules/local/gtf2bed.nf +++ b/modules/local/gtf2bed.nf @@ -10,7 +10,6 @@ process GTF2BED { input: path gtf val feature_type - output: path '*.bed' , emit: bed path "versions.yml", emit: versions @@ -23,11 +22,10 @@ process GTF2BED { if (feature_type){ feature_type = allowed_type.contains(feature_type) ? feature_type : "exon" } - """ Rscript --no-save -<<'RCODE' gtf = read.table("${gtf}", sep="\t") - gtf = subset(gtf, V3 == "${feature_type}") + gtf = subset(gtf, V3 == "${feature_type}") write.table(data.frame(chrom=gtf[,'V1'], start=gtf[,'V4'], end=gtf[,'V5']), "tmp.exome.bed", quote = F, sep="\t", col.names = F, row.names = F) RCODE From 681ca7e527fcc9cbc1f48d16b7887a6b63a5eea6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 8 Dec 2022 13:14:26 +0000 Subject: [PATCH 011/275] Template update for nf-core/tools version 2.7.1 --- .devcontainer/devcontainer.json | 27 +++++++++++++ .gitattributes | 1 + .github/CONTRIBUTING.md | 16 ++++++++ .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/ci.yml | 8 +++- .github/workflows/fix-linting.yml | 6 +-- .github/workflows/linting.yml | 18 +++++---- .github/workflows/linting_comment.yml | 2 +- .prettierignore | 2 + CITATION.cff | 56 --------------------------- README.md | 4 +- assets/slackreport.json | 34 ++++++++++++++++ docs/usage.md | 24 +++++++----- lib/NfcoreSchema.groovy | 1 - lib/NfcoreTemplate.groovy | 41 +++++++++++++++----- lib/WorkflowMain.groovy | 18 ++++++--- modules.json | 9 +++-- modules/local/samplesheet_check.nf | 4 ++ nextflow.config | 12 ++++-- nextflow_schema.json | 8 +++- workflows/rnavar.nf | 11 +++--- 21 files changed, 193 insertions(+), 111 deletions(-) create mode 100644 .devcontainer/devcontainer.json delete mode 100644 CITATION.cff create mode 100644 assets/slackreport.json diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..ea27a584 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,27 @@ +{ + "name": "nfcore", + "image": "nfcore/gitpod:latest", + "remoteUser": "gitpod", + + // Configure tool-specific properties. + "customizations": { + // Configure properties specific to VS Code. + "vscode": { + // Set *default* container specific settings.json values on container create. + "settings": { + "python.defaultInterpreterPath": "/opt/conda/bin/python", + "python.linting.enabled": true, + "python.linting.pylintEnabled": true, + "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", + "python.formatting.yapfPath": "/opt/conda/bin/yapf", + "python.linting.flake8Path": "/opt/conda/bin/flake8", + "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", + "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", + "python.linting.pylintPath": "/opt/conda/bin/pylint" + }, + + // Add the IDs of extensions you want installed when the container is created. + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + } + } +} diff --git a/.gitattributes b/.gitattributes index 050bb120..7a2dabc2 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,3 +1,4 @@ *.config linguist-language=nextflow +*.nf.test linguist-language=nextflow modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 7a76df36..dae092ad 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ ### Images and figures For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). + +## GitHub Codespaces + +This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. + +To get started: + +- Open the repo in [Codespaces](https://github.com/nf-core/rnavar/codespaces) +- Tools installed + - nf-core + - Nextflow + +Devcontainer specs: + +- [DevContainer config](.devcontainer/devcontainer.json) +- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index fb5c200e..212481be 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 21.10.3)_ + * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 67225b7a..9a080ef2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,6 +11,10 @@ on: env: NXF_ANSI_LOG: false +concurrency: + group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" + cancel-in-progress: true + jobs: test: name: Run pipeline with test data @@ -20,11 +24,11 @@ jobs: strategy: matrix: NXF_VER: - - "21.10.3" + - "22.10.1" - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index e67cdc60..34ea8bd5 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -24,7 +24,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v2 + - uses: actions/setup-node@v3 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "::set-output name=result::pass" + echo "name=result::pass" >> $GITHUB_OUTPUT else - echo "::set-output name=result::fail" + echo "name=result::fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 8a5ce69b..858d622e 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -4,6 +4,8 @@ name: nf-core linting # that the code meets the nf-core guidelines. on: push: + branches: + - dev pull_request: release: types: [published] @@ -12,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: actions/setup-node@v2 + - uses: actions/setup-node@v3 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -25,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: actions/setup-node@v2 + - uses: actions/setup-node@v3 - name: Install Prettier run: npm install -g prettier @@ -38,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Check code lints with Black uses: psf/black@stable @@ -69,12 +71,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@v3 + - uses: actions/setup-python@v4 with: python-version: "3.7" architecture: "x64" @@ -97,7 +99,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v3 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 04758f61..39635186 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)" + run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/.prettierignore b/.prettierignore index eb74a574..437d763d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,5 +1,6 @@ email_template.html adaptivecard.json +slackreport.json .nextflow* work/ data/ @@ -8,3 +9,4 @@ results/ testing/ testing* *.pyc +bin/ diff --git a/CITATION.cff b/CITATION.cff deleted file mode 100644 index 017666c0..00000000 --- a/CITATION.cff +++ /dev/null @@ -1,56 +0,0 @@ -cff-version: 1.2.0 -message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" -authors: - - family-names: Ewels - given-names: Philip - - family-names: Peltzer - given-names: Alexander - - family-names: Fillinger - given-names: Sven - - family-names: Patel - given-names: Harshil - - family-names: Alneberg - given-names: Johannes - - family-names: Wilm - given-names: Andreas - - family-names: Garcia - given-names: Maxime Ulysse - - family-names: Di Tommaso - given-names: Paolo - - family-names: Nahnsen - given-names: Sven -title: "The nf-core framework for community-curated bioinformatics pipelines." -version: 2.4.1 -doi: 10.1038/s41587-020-0439-x -date-released: 2022-05-16 -url: https://github.com/nf-core/tools -prefered-citation: - type: article - authors: - - family-names: Ewels - given-names: Philip - - family-names: Peltzer - given-names: Alexander - - family-names: Fillinger - given-names: Sven - - family-names: Patel - given-names: Harshil - - family-names: Alneberg - given-names: Johannes - - family-names: Wilm - given-names: Andreas - - family-names: Garcia - given-names: Maxime Ulysse - - family-names: Di Tommaso - given-names: Paolo - - family-names: Nahnsen - given-names: Sven - doi: 10.1038/s41587-020-0439-x - journal: nature biotechnology - start: 276 - end: 278 - title: "The nf-core framework for community-curated bioinformatics pipelines." - issue: 3 - volume: 38 - year: 2020 - url: https://dx.doi.org/10.1038/s41587-020-0439-x diff --git a/README.md b/README.md index d80e7ac0..d4fab95f 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -31,7 +31,7 @@ On release, automated continuous integration tests run the pipeline on a full-si ## Quick Start -1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) +1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. diff --git a/assets/slackreport.json b/assets/slackreport.json new file mode 100644 index 00000000..043d02f2 --- /dev/null +++ b/assets/slackreport.json @@ -0,0 +1,34 @@ +{ + "attachments": [ + { + "fallback": "Plain-text summary of the attachment.", + "color": "<% if (success) { %>good<% } else { %>danger<%} %>", + "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", + "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", + "fields": [ + { + "title": "Command used to launch the workflow", + "value": "```${commandLine}```", + "short": false + } + <% + if (!success) { %> + , + { + "title": "Full error message", + "value": "```${errorReport}```", + "short": false + }, + { + "title": "Pipeline configuration", + "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", + "short": false + } + <% } + %> + ], + "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" + } + ] +} diff --git a/docs/usage.md b/docs/usage.md index db4e6f4d..8f140452 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -83,9 +83,9 @@ nextflow pull nf-core/rnavar It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. -First, go to the [nf-core/rnavar releases page](https://github.com/nf-core/rnavar/releases) and find the latest version number - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. +First, go to the [nf-core/rnavar releases page](https://github.com/nf-core/rnavar/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. -This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. +This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. ## Core Nextflow arguments @@ -95,7 +95,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. When using Biocontainers, most of these software packaging methods pull Docker containers from quay.io e.g [FastQC](https://quay.io/repository/biocontainers/fastqc) except for Singularity which directly downloads Singularity images via https hosted by the [Galaxy project](https://depot.galaxyproject.org/singularity/) and Conda which downloads and installs software locally from [Bioconda](https://bioconda.github.io/). +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -104,8 +104,11 @@ The pipeline also dynamically loads configurations from [https://github.com/nf-c Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +- `test` + - A profile with a complete configuration for automated testing + - Includes links to test data so needs no other parameters - `docker` - A generic configuration profile to be used with [Docker](https://docker.com/) - `singularity` @@ -118,9 +121,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. -- `test` - - A profile with a complete configuration for automated testing - - Includes links to test data so needs no other parameters ### `-resume` @@ -169,8 +169,14 @@ Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` ``` +#### For beginners + +A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. + +#### Advanced option on process level + To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/software/star/align/main.nf`. +We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. @@ -189,7 +195,7 @@ process { > > If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. -### Updating containers +### Updating containers (advanced users) The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index b3d092f8..33cd4f6e 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -46,7 +46,6 @@ class NfcoreSchema { 'quiet', 'syslog', 'v', - 'version', // Options for `nextflow run` command 'ansi', diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 27feb009..25a0a74a 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -32,6 +32,25 @@ class NfcoreTemplate { } } + // + // Generate version string + // + public static String version(workflow) { + String version_string = "" + + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string + } + // // Construct and send completion email // @@ -61,7 +80,7 @@ class NfcoreTemplate { misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] - email_fields['version'] = workflow.manifest.version + email_fields['version'] = NfcoreTemplate.version(workflow) email_fields['runName'] = workflow.runName email_fields['success'] = workflow.success email_fields['dateComplete'] = workflow.complete @@ -146,10 +165,10 @@ class NfcoreTemplate { } // - // Construct and send adaptive card - // https://adaptivecards.io + // Construct and send a notification to a web server as JSON + // e.g. Microsoft Teams and Slack // - public static void adaptivecard(workflow, params, summary_params, projectDir, log) { + public static void IM_notification(workflow, params, summary_params, projectDir, log) { def hook_url = params.hook_url def summary = [:] @@ -170,7 +189,7 @@ class NfcoreTemplate { misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] - msg_fields['version'] = workflow.manifest.version + msg_fields['version'] = NfcoreTemplate.version(workflow) msg_fields['runName'] = workflow.runName msg_fields['success'] = workflow.success msg_fields['dateComplete'] = workflow.complete @@ -178,13 +197,16 @@ class NfcoreTemplate { msg_fields['exitStatus'] = workflow.exitStatus msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") msg_fields['projectDir'] = workflow.projectDir msg_fields['summary'] = summary << misc_fields // Render the JSON template def engine = new groovy.text.GStringTemplateEngine() - def hf = new File("$projectDir/assets/adaptivecard.json") + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("$projectDir/assets/${json_path}") def json_template = engine.createTemplate(hf).make(msg_fields) def json_message = json_template.toString() @@ -209,7 +231,7 @@ class NfcoreTemplate { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" } } else { log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" @@ -297,6 +319,7 @@ class NfcoreTemplate { // public static String logo(workflow, monochrome_logs) { Map colors = logColours(monochrome_logs) + String workflow_version = NfcoreTemplate.version(workflow) String.format( """\n ${dashedLine(monochrome_logs)} @@ -305,7 +328,7 @@ class NfcoreTemplate { ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} ${dashedLine(monochrome_logs)} """.stripIndent() ) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 35bf164f..8309481f 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -19,7 +19,7 @@ class WorkflowMain { } // - // Print help to screen if required + // Generate help string // public static String help(workflow, params, log) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" @@ -32,7 +32,7 @@ class WorkflowMain { } // - // Print parameter summary log to screen + // Generate parameter summary log string // public static String paramsSummaryLog(workflow, params, log) { def summary_log = '' @@ -53,15 +53,21 @@ class WorkflowMain { System.exit(0) } - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) + // Print workflow version and exit on --version + if (params.version) { + String workflow_version = NfcoreTemplate.version(workflow) + log.info "${workflow.manifest.name} ${workflow_version}" + System.exit(0) } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + // Validate workflow parameters via the JSON schema + if (params.validate_params) { + NfcoreSchema.validateParameters(workflow, params, log) + } + // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/modules.json b/modules.json index b4e3abcc..48ebc0a1 100644 --- a/modules.json +++ b/modules.json @@ -7,15 +7,18 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "installed_by": ["modules"] } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 553da8c9..08f6035c 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -1,5 +1,6 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" + label 'process_single' conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -13,6 +14,9 @@ process SAMPLESHEET_CHECK { path '*.csv' , emit: csv path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/rnavar/bin/ """ check_samplesheet.py \\ diff --git a/nextflow.config b/nextflow.config index c80668dd..bbdc1216 100644 --- a/nextflow.config +++ b/nextflow.config @@ -35,6 +35,7 @@ params { monochrome_logs = false hook_url = null help = false + version = false validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' @@ -81,6 +82,7 @@ profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { params.enable_conda = true + conda.enabled = true docker.enabled = false singularity.enabled = false podman.enabled = false @@ -89,6 +91,7 @@ profiles { } mamba { params.enable_conda = true + conda.enabled = true conda.useMamba = true docker.enabled = false singularity.enabled = false @@ -104,6 +107,9 @@ profiles { shifter.enabled = false charliecloud.enabled = false } + arm { + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } singularity { singularity.enabled = true singularity.autoMounts = true @@ -185,11 +191,11 @@ dag { manifest { name = 'nf-core/rnavar' - author = '@praveenraj2018' + author = """@praveenraj2018""" homePage = 'https://github.com/nf-core/rnavar' - description = 'GATK4 RNA variant calling pipeline' + description = """GATK4 RNA variant calling pipeline""" mainScript = 'main.nf' - nextflowVersion = '!>=21.10.3' + nextflowVersion = '!>=22.10.1' version = '1.1.0dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 51870fa6..0e344fd0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -176,6 +176,12 @@ "fa_icon": "fas fa-question-circle", "hidden": true }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, "publish_dir_mode": { "type": "string", "default": "copy", @@ -217,7 +223,7 @@ "type": "string", "description": "Incoming hook URL for messaging service", "fa_icon": "fas fa-people-group", - "help_text": "Incoming hook URL for messaging service. Currently, only MS Teams is supported.", + "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, "multiqc_config": { diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 1042cc76..146f99b0 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -82,7 +82,7 @@ workflow RNAVAR { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') + ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') ) // @@ -102,12 +102,11 @@ workflow RNAVAR { MULTIQC ( ch_multiqc_files.collect(), - ch_multiqc_config.collect().ifEmpty([]), - ch_multiqc_custom_config.collect().ifEmpty([]), - ch_multiqc_logo.collect().ifEmpty([]) + ch_multiqc_config.toList(), + ch_multiqc_custom_config.toList(), + ch_multiqc_logo.toList() ) multiqc_report = MULTIQC.out.report.toList() - ch_versions = ch_versions.mix(MULTIQC.out.versions) } /* @@ -122,7 +121,7 @@ workflow.onComplete { } NfcoreTemplate.summary(workflow, params, log) if (params.hook_url) { - NfcoreTemplate.adaptivecard(workflow, params, summary_params, projectDir, log) + NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) } } From e5294c1454e8d470b5eff3fe39c489cf60c06053 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 19 Dec 2022 12:08:15 +0000 Subject: [PATCH 012/275] Template update for nf-core/tools version 2.7.2 --- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting_comment.yml | 2 +- lib/WorkflowMain.groovy | 2 +- modules.json | 6 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 2 +- .../templates/dumpsoftwareversions.py | 99 ++++++++++--------- modules/nf-core/fastqc/main.nf | 40 +++----- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 3 - nextflow_schema.json | 6 -- workflows/rnavar.nf | 2 +- 12 files changed, 82 insertions(+), 88 deletions(-) mode change 100644 => 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 34ea8bd5..aedaa933 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -34,9 +34,9 @@ jobs: id: prettier_status run: | if prettier --check ${GITHUB_WORKSPACE}; then - echo "name=result::pass" >> $GITHUB_OUTPUT + echo "result=pass" >> $GITHUB_OUTPUT else - echo "name=result::fail" >> $GITHUB_OUTPUT + echo "result=fail" >> $GITHUB_OUTPUT fi - name: Run 'prettier --write' diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 39635186..0bbcd30f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -18,7 +18,7 @@ jobs: - name: Get PR number id: pr_number - run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment uses: marocchino/sticky-pull-request-comment@v2 diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 8309481f..977ba948 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -72,7 +72,7 @@ class WorkflowMain { NfcoreTemplate.checkConfigProvided(workflow, log) // Check that conda channels are set-up correctly - if (params.enable_conda) { + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { Utils.checkCondaChannels(log) } diff --git a/modules.json b/modules.json index 48ebc0a1..02df1b22 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 08f6035c..95d6727a 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -2,7 +2,7 @@ process SAMPLESHEET_CHECK { tag "$samplesheet" label 'process_single' - conda (params.enable_conda ? "conda-forge::python=3.8.3" : null) + conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : 'quay.io/biocontainers/python:3.8.3' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index cebb6e05..3df21765 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py old mode 100644 new mode 100755 index 787bdb7b..e55b8d43 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -1,5 +1,9 @@ #!/usr/bin/env python + +"""Provide functions to merge multiple versions.yml files.""" + + import platform from textwrap import dedent @@ -7,6 +11,7 @@ def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" html = [ dedent( """\\ @@ -45,47 +50,53 @@ def _make_versions_html(versions): return "\\n".join(html) -versions_this_module = {} -versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, -} - -with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - -# aggregate versions by the module name (derived from fully-qualified process name) -versions_by_module = {} -for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - -versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", -} - -versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), -} - -with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) -with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - -with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 05730368..9ae58381 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : 'quay.io/biocontainers/fastqc:0.11.9--0' }" @@ -20,30 +20,22 @@ process FASTQC { script: def args = task.ext.args ?: '' - // Add soft-links to original FastQs for consistent naming in pipeline def prefix = task.ext.prefix ?: "${meta.id}" - if (meta.single_end) { - """ - [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz - fastqc $args --threads $task.cpus ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } else { - """ - [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz - [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz - fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } + // Make list of old name and new name pairs to use for renaming in the bash while loop + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + """ + printf "%s %s\\n" $rename_to | while read old_name new_name; do + [ -f "\${new_name}" ] || ln -s \$old_name \$new_name + done + fastqc $args --threads $task.cpus $renamed_files + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ stub: def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index a8159a57..68f66bea 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null) + conda "bioconda::multiqc=1.13" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" diff --git a/nextflow.config b/nextflow.config index bbdc1216..f4a47634 100644 --- a/nextflow.config +++ b/nextflow.config @@ -39,7 +39,6 @@ params { validate_params = true show_hidden_params = false schema_ignore_params = 'genomes' - enable_conda = false // Config options @@ -81,7 +80,6 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true conda.enabled = true docker.enabled = false singularity.enabled = false @@ -90,7 +88,6 @@ profiles { charliecloud.enabled = false } mamba { - params.enable_conda = true conda.enabled = true conda.useMamba = true docker.enabled = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 0e344fd0..4395e63f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -263,12 +263,6 @@ "description": "Show all params when using `--help`", "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "enable_conda": { - "type": "boolean", - "description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.", - "hidden": true, - "fa_icon": "fas fa-bacon" } } } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 146f99b0..6d42ac31 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -82,7 +82,7 @@ workflow RNAVAR { ch_versions = ch_versions.mix(FASTQC.out.versions.first()) CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml') + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) // From feac5802049ff07b59b9390b66bd6488b1811240 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Apr 2023 14:26:15 +0000 Subject: [PATCH 013/275] Template update for nf-core/tools version 2.8 --- .editorconfig | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 24 ++++ .github/workflows/linting.yml | 2 +- .pre-commit-config.yaml | 5 + README.md | 74 ++++++---- bin/check_samplesheet.py | 3 - conf/base.config | 2 +- conf/igenomes.config | 8 ++ conf/test_full.config | 2 + docs/usage.md | 130 +++++------------- lib/NfcoreSchema.groovy | 4 +- lib/WorkflowMain.groovy | 13 +- lib/WorkflowRnavar.groovy | 12 +- main.nf | 1 - modules.json | 4 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 2 + modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 3 +- nextflow.config | 29 +++- tower.yml | 5 + 27 files changed, 193 insertions(+), 157 deletions(-) create mode 100644 .github/workflows/clean-up.yml create mode 100644 .pre-commit-config.yaml create mode 100644 tower.yml diff --git a/.editorconfig b/.editorconfig index b78de6e6..b6b31907 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js,cff}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 212481be..c06c21f5 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -45,6 +45,6 @@ body: * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ * Version of nf-core/rnavar _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 5c26fb9c..80d8e275 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnav - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 50a7398e..ed4f93c0 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 84a22495..97d65891 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 377dde74..40e9c617 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/rnavar' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnavar ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnavar ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 00000000..694e90ec --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622e..888cb4bc 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..0c31cdb9 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,5 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.7.1" + hooks: + - id: prettier diff --git a/README.md b/README.md index d4fab95f..381dd4b4 100644 --- a/README.md +++ b/README.md @@ -8,57 +8,71 @@ [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnavar) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction - +**nf-core/rnavar** is a bioinformatics pipeline that ... -**nf-core/rnavar** is a bioinformatics best-practice analysis pipeline for GATK4 RNA variant calling pipeline. - -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - - - -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnavar/results). - -## Pipeline summary + + 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -## Quick Start +## Usage + +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. + + - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. +Now, you can run the pipeline using: - > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + -4. Start running your own analysis! +```bash +nextflow run nf-core/rnavar \ + -profile \ + --input samplesheet.csv \ + --outdir +``` - +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). - ```bash - nextflow run nf-core/rnavar --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` +For more details, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters). -## Documentation +## Pipeline output -The nf-core/rnavar pipeline comes with documentation about the pipeline [usage](https://nf-co.re/rnavar/usage), [parameters](https://nf-co.re/rnavar/parameters) and [output](https://nf-co.re/rnavar/output). +To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page. +For more details about the output files and reports, please refer to the +[output documentation](https://nf-co.re/rnavar/output). ## Credits diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 11b15572..4a758fe0 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -158,9 +158,6 @@ def sniff_format(handle): peek = read_head(handle) handle.seek(0) sniffer = csv.Sniffer() - if not sniffer.has_header(peek): - logger.critical("The given sample sheet does not appear to contain a header.") - sys.exit(1) dialect = sniffer.sniff(peek) return dialect diff --git a/conf/base.config b/conf/base.config index fcccdad9..89b498e5 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/igenomes.config b/conf/igenomes.config index 7a1b3ac6..3f114377 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -36,6 +36,14 @@ params { macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" } + 'CHM13' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" + gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" + mito_name = "chrM" + } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" diff --git a/conf/test_full.config b/conf/test_full.config index 979f49f7..718622c4 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,8 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 8f140452..08da8b39 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -71,6 +71,29 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/rnavar -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +input: 'data' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -87,6 +110,10 @@ First, go to the [nf-core/rnavar releases page](https://github.com/nf-core/rnava This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. + ## Core Nextflow arguments > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). @@ -95,7 +122,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -119,8 +146,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. ### `-resume` @@ -138,102 +167,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: - -```console -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' - -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) - -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - - -Command exit status: - 137 - -Command output: - (empty) - -Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. -Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb - -Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` - -#### For beginners - -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. - -#### Advanced option on process level - -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. -The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. - -```nextflow -process { - withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { - memory = 100.GB - } -} -``` - -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. - -### Updating containers (advanced users) - -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. - -1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) -2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) -3. Create the custom config accordingly: - - - For Docker: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +### Custom Containers - - For Singularity: +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. - - For Conda: +### Custom Tool Arguments - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 33cd4f6e..9b34804d 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -2,6 +2,7 @@ // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. // +import nextflow.Nextflow import org.everit.json.schema.Schema import org.everit.json.schema.loader.SchemaLoader import org.everit.json.schema.ValidationException @@ -83,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', @@ -177,7 +179,7 @@ class NfcoreSchema { } if (has_error) { - System.exit(1) + Nextflow.error('Exiting!') } } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 977ba948..f5bdc826 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the main.nf workflow in the nf-core/rnavar pipeline // +import nextflow.Nextflow + class WorkflowMain { // @@ -21,7 +23,7 @@ class WorkflowMain { // // Generate help string // - public static String help(workflow, params, log) { + public static String help(workflow, params) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) @@ -34,7 +36,7 @@ class WorkflowMain { // // Generate parameter summary log string // - public static String paramsSummaryLog(workflow, params, log) { + public static String paramsSummaryLog(workflow, params) { def summary_log = '' summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) @@ -49,7 +51,7 @@ class WorkflowMain { public static void initialise(workflow, params, log) { // Print help to screen if required if (params.help) { - log.info help(workflow, params, log) + log.info help(workflow, params) System.exit(0) } @@ -61,7 +63,7 @@ class WorkflowMain { } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + log.info paramsSummaryLog(workflow, params) // Validate workflow parameters via the JSON schema if (params.validate_params) { @@ -81,8 +83,7 @@ class WorkflowMain { // Check input has been provided if (!params.input) { - log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" - System.exit(1) + Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") } } // diff --git a/lib/WorkflowRnavar.groovy b/lib/WorkflowRnavar.groovy index 6f2ab32d..52176347 100755 --- a/lib/WorkflowRnavar.groovy +++ b/lib/WorkflowRnavar.groovy @@ -2,6 +2,7 @@ // This file holds several functions specific to the workflow/rnavar.nf in the nf-core/rnavar pipeline // +import nextflow.Nextflow import groovy.text.SimpleTemplateEngine class WorkflowRnavar { @@ -14,8 +15,7 @@ class WorkflowRnavar { if (!params.fasta) { - log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - System.exit(1) + Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } @@ -61,17 +61,19 @@ class WorkflowRnavar { def description_html = engine.createTemplate(methods_text).make(meta) return description_html - }// + } + + // // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - System.exit(1) + Nextflow.error(error_string) } } } diff --git a/main.nf b/main.nf index bd3b64d2..6fc4d58a 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,6 @@ nf-core/rnavar ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/rnavar - Website: https://nf-co.re/rnavar Slack : https://nfcore.slack.com/channels/rnavar ---------------------------------------------------------------------------------------- diff --git a/modules.json b/modules.json index 02df1b22..26009d50 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", "installed_by": ["modules"] }, "fastqc": { @@ -17,7 +17,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 95d6727a..852dcbf9 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'quay.io/biocontainers/python:3.8.3' }" + 'biocontainers/python:3.8.3' }" input: path samplesheet diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 3df21765..800a6099 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a0..c32657de 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66bea..4b604749 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ebc29b27..f93b5ee5 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: @@ -37,7 +38,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: diff --git a/nextflow.config b/nextflow.config index f4a47634..50f76a90 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,7 +78,11 @@ try { profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false + } conda { conda.enabled = true docker.enabled = false @@ -86,6 +90,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } mamba { conda.enabled = true @@ -95,14 +100,18 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } docker { docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = true + conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -110,31 +119,49 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } podman { podman.enabled = true + podman.registry = 'quay.io' + conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } shifter { shifter.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false charliecloud.enabled = false + apptainer.enabled = false } charliecloud { charliecloud.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } gitpod { executor.name = 'local' diff --git a/tower.yml b/tower.yml new file mode 100644 index 00000000..787aedfe --- /dev/null +++ b/tower.yml @@ -0,0 +1,5 @@ +reports: + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths" From 259c1c47a8f290823f747457ea7eaf36b0ba7d92 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:15:42 +0000 Subject: [PATCH 014/275] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-rnavar_logo_light.png | Bin 9910 -> 65097 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowMain.groovy | 37 -- lib/WorkflowRnavar.groovy | 45 +- main.nf | 16 + nextflow.config | 52 ++- nextflow_schema.json | 36 +- workflows/rnavar.nf | 25 +- 22 files changed, 175 insertions(+), 637 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index dae092ad..90bd1ebb 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index c06c21f5..b70618d8 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index ed4f93c0..3e2b977a 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnavar/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 97d65891..ea0bd288 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnavar/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnavar/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9a080ef2..f9eb2e39 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CITATIONS.md b/CITATIONS.md index 0eae2ebf..27fb294e 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index 381dd4b4..5c7f0b4f 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -66,11 +66,11 @@ nextflow run nf-core/rnavar \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/rnavar/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index f2bc183b..46025e30 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/rnavar Methods Description" section_href: "https://github.com/nf-core/rnavar" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

    Methods

    -

    Data was processed using nf-core/rnavar v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

    +

    Data was processed using nf-core/rnavar v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

    The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

    ${workflow.commandLine}
    +

    ${tool_citations}

    References

      -
    • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
      • -
    • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
      • +
    • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
      • +
    • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
      • +
    • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
      • +
    • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
      • + ${tool_bibliography}
    Notes:
    diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 2689c2b9..76550af1 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnavar + This report has been generated by the nf-core/rnavar analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnavar-methods-description": order: -1000 diff --git a/assets/nf-core-rnavar_logo_light.png b/assets/nf-core-rnavar_logo_light.png index 9cca37e801c2dad85523ea3419b9aa15f0468640..509f923f092c056161198ce9745d0fe4fc83e867 100644 GIT binary patch literal 65097 zcmeEt`9IX_`~RRQS?ZKSWhn*~p=96c5GGq9OZHNfecuPCQz(&w!1jG0qM))u18{N;szxKLnntC7*Z0~7*=;B1!jv^4p5Gb_^hQ29NgTYTSd@O|5 zS3HI44fR<@BwC_WweNAg^K`t?ay|Ua^`zuS;o*5X;p5j0nLR_3TdTw-*C$<<{Vk$; z9`%au>-b1%=CCl=x~!Jp!Br{RFpzjKp!3X+Tb;*QRKss@Kb){h^c+@seV?p-3zMBT zv9)Zlu({<`v3Pc z_~QTk@G~L)&kz6ShyTBGp!b^mFYH1%8g&}PE+NMRdy{Rgwkaa9QvrRQY2HJz)6`6H z9;J$!8p?T$p0J;N*Ye!J#ykH8M)iUCxVX5E!@pK|Rzc1t45Gxe-2E^GvsRWhY(8G+ zqQw!LH!;zIl^)J$8$X^IcCItbD!;xEnF(K*M&+X@JSfW~(%%?AjAD}I{FvT)!b;+< zT`3RVvHyDV#tr{F?pFSzX|tN{P8k1QHN6RI-9sVD@-lUEm%l0Eg`Uqb{CpIznVgoC zqUmmd=@Irb{U+;BnnF@S4JpEd=f8=bxA|}L4A?vsm9JMY?xEj%PSrz{(B9T6zCrD{ 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zE%-g^)t8LRvz$|8^WhE2OM}wyN#^5VLWLQ>{{NijDsj7r>Y?Z00~good<% } else { %>danger<%} %>", - "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_name": "nf-core/rnavar v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index 718622c4..979f49f7 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 08da8b39..3a706bbf 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/rnavar --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/rnavar --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/rnavar -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index f5bdc826..3124b731 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } // Print workflow version and exit on --version if (params.version) { @@ -62,14 +33,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/lib/WorkflowRnavar.groovy b/lib/WorkflowRnavar.groovy index 52176347..72f686fd 100755 --- a/lib/WorkflowRnavar.groovy +++ b/lib/WorkflowRnavar.groovy @@ -11,6 +11,7 @@ class WorkflowRnavar { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowRnavar { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/main.nf b/main.nf index 6fc4d58a..866aebfc 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index 50f76a90..fe9cde98 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/rnavar profiles: ${params.custom_config_base}/pipeline/rnavar.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -219,7 +227,7 @@ manifest { homePage = 'https://github.com/nf-core/rnavar' description = """GATK4 RNA variant calling pipeline""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '1.1.0dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 4395e63f..9d2c4bde 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/rnavar/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,12 +256,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 6d42ac31..fd6c2b0c 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowRnavar.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowRnavar.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow RNAVAR { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow RNAVAR { workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From dd90d55300efa261888e990a1ab103925320d4e2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 12:23:48 +0200 Subject: [PATCH 015/275] typo --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 643ec742..21484ba3 100644 --- a/README.md +++ b/README.md @@ -73,9 +73,9 @@ Each row represents a fastq file (single-end) or a pair of fastq files (paired e Now, you can run the pipeline using: - ```console - nextflow run nf-core/rnavar -profile --input samplesheet.csv --outdir --genome GRCh38 - ``` +```console +nextflow run nf-core/rnavar -profile --input samplesheet.csv --outdir --genome GRCh38 +``` > **Warning:** > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those From 6331c1424da3116c9d3495c2fdec30c44ed04d75 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 12:34:11 +0200 Subject: [PATCH 016/275] update all modules --- modules.json | 206 ++++++++++++------ .../local/custom/dumpsoftwareversions/main.nf | 6 +- modules/local/gtf2bed.nf | 2 +- modules/nf-core/bedtools/merge/main.nf | 17 +- modules/nf-core/bedtools/merge/meta.yml | 2 + modules/nf-core/bedtools/sort/main.nf | 18 +- modules/nf-core/bedtools/sort/meta.yml | 2 + modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/cat/fastq/meta.yml | 3 +- .../custom/dumpsoftwareversions/main.nf | 6 +- modules/nf-core/ensemblvep/vep/main.nf | 21 +- modules/nf-core/ensemblvep/vep/meta.yml | 22 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/fastqc/tests/main.nf.test | 32 +++ modules/nf-core/gatk4/applybqsr/main.nf | 12 +- modules/nf-core/gatk4/applybqsr/meta.yml | 17 +- .../nf-core/gatk4/baserecalibrator/main.nf | 12 +- .../nf-core/gatk4/baserecalibrator/meta.yml | 16 +- .../nf-core/gatk4/bedtointervallist/main.nf | 14 +- .../nf-core/gatk4/bedtointervallist/meta.yml | 7 + modules/nf-core/gatk4/combinegvcfs/main.nf | 12 +- .../gatk4/createsequencedictionary/main.nf | 18 +- .../gatk4/createsequencedictionary/meta.yml | 41 ++-- modules/nf-core/gatk4/haplotypecaller/main.nf | 12 +- .../nf-core/gatk4/haplotypecaller/meta.yml | 16 +- .../nf-core/gatk4/indexfeaturefile/main.nf | 12 +- .../nf-core/gatk4/intervallisttools/main.nf | 12 +- modules/nf-core/gatk4/markduplicates/main.nf | 32 ++- modules/nf-core/gatk4/mergevcfs/main.nf | 12 +- .../nf-core/gatk4/splitncigarreads/main.nf | 12 +- .../nf-core/gatk4/variantfiltration/main.nf | 18 +- .../nf-core/gatk4/variantfiltration/meta.yml | 17 ++ modules/nf-core/gffread/main.nf | 2 +- modules/nf-core/gunzip/main.nf | 12 +- modules/nf-core/gunzip/meta.yml | 35 +-- modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/samtools/faidx/main.nf | 22 +- modules/nf-core/samtools/faidx/meta.yml | 14 +- modules/nf-core/samtools/flagstat/main.nf | 17 +- modules/nf-core/samtools/flagstat/meta.yml | 2 +- modules/nf-core/samtools/idxstats/main.nf | 18 +- modules/nf-core/samtools/idxstats/meta.yml | 2 +- modules/nf-core/samtools/index/main.nf | 6 +- modules/nf-core/samtools/index/meta.yml | 2 +- modules/nf-core/samtools/merge/main.nf | 10 +- modules/nf-core/samtools/merge/meta.yml | 21 +- modules/nf-core/samtools/sort/main.nf | 14 +- modules/nf-core/samtools/sort/meta.yml | 2 +- modules/nf-core/samtools/stats/main.nf | 8 +- modules/nf-core/samtools/stats/meta.yml | 24 +- modules/nf-core/snpeff/snpeff/main.nf | 10 +- modules/nf-core/snpeff/snpeff/meta.yml | 6 +- modules/nf-core/star/align/main.nf | 28 ++- modules/nf-core/star/align/meta.yml | 32 +++ modules/nf-core/star/genomegenerate/main.nf | 10 +- modules/nf-core/star/genomegenerate/meta.yml | 15 ++ modules/nf-core/tabix/bgziptabix/main.nf | 10 +- modules/nf-core/tabix/bgziptabix/meta.yml | 5 + modules/nf-core/tabix/tabix/main.nf | 2 +- modules/nf-core/untar/main.nf | 4 +- modules/nf-core/untar/meta.yml | 1 + 61 files changed, 652 insertions(+), 327 deletions(-) create mode 100644 modules/nf-core/fastqc/tests/main.nf.test diff --git a/modules.json b/modules.json index 0abe555e..3e8235c2 100755 --- a/modules.json +++ b/modules.json @@ -7,173 +7,241 @@ "nf-core": { "bedtools/merge": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", - "git_sha": "f1f473b21811b958d1317c4a97c56e16d3ee40f9", - "installed_by": ["modules"] + "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", - "installed_by": ["modules"] + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "bea3ca998816a7f812b1bbbcb27c3a9ffbac0706", - "installed_by": ["modules"] + "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", + "installed_by": [ + "modules" + ] }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", - "installed_by": ["modules"] + "git_sha": "240937a2a9c30298110753292be041188891f2cb", + "installed_by": [ + "modules" + ] }, "gatk4/baserecalibrator": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", + "installed_by": [ + "modules" + ] }, "gatk4/combinegvcfs": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", + "installed_by": [ + "modules" + ] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/indexfeaturefile": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "0a261469640941da2488e1a5aa023b64db837c70", + "installed_by": [ + "modules" + ] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/splitncigarreads": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", + "installed_by": [ + "modules" + ] }, "gffread": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57", + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", - "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba", - "installed_by": ["modules"] + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", + "installed_by": [ + "modules" + ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639", + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "installed_by": [ + "modules" + ] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "03eae88f7c30fbad0152b941bbeba48ae8bc3d07", - "installed_by": ["modules"] + "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537", + "installed_by": [ + "modules" + ] }, "star/align": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", + "installed_by": [ + "modules" + ] }, "star/genomegenerate": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e", + "installed_by": [ + "modules" + ] }, "tabix/tabix": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", - "installed_by": ["modules"] + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", - "git_sha": "cc1f997fab6d8fde5dc0e6e2a310814df5b53ce7", - "installed_by": ["modules"] + "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", + "installed_by": [ + "modules" + ] } } }, @@ -182,4 +250,4 @@ } } } -} +} \ No newline at end of file diff --git a/modules/local/custom/dumpsoftwareversions/main.nf b/modules/local/custom/dumpsoftwareversions/main.nf index 3df21765..c9d014b1 100644 --- a/modules/local/custom/dumpsoftwareversions/main.nf +++ b/modules/local/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf index 42589bbd..b0c7e42a 100755 --- a/modules/local/gtf2bed.nf +++ b/modules/local/gtf2bed.nf @@ -5,7 +5,7 @@ process GTF2BED { conda "conda-forge::r-base=3.5.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-base:3.5.0' : - 'quay.io/biocontainers/r-base:3.5.0'}" + 'biocontainers/r-base:3.5.0'}" input: path gtf diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 21b2e645..6868d39f 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -2,10 +2,10 @@ process BEDTOOLS_MERGE { tag "$meta.id" label 'process_single' - conda "bioconda::bedtools=2.30.0" + conda "bioconda::bedtools=2.31.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' : + 'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }" input: tuple val(meta), path(bed) @@ -33,4 +33,15 @@ process BEDTOOLS_MERGE { bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ } diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index 76743679..82248afe 100644 --- a/modules/nf-core/bedtools/merge/meta.yml +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -3,6 +3,8 @@ description: combines overlapping or “book-ended” features in an interval fi keywords: - bed - merge + - bedtools + - overlapped bed tools: - bedtools: description: | diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index a0ddddd1..df372bc5 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -2,10 +2,10 @@ process BEDTOOLS_SORT { tag "$meta.id" label 'process_single' - conda "bioconda::bedtools=2.30.0" + conda "bioconda::bedtools=2.31.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' : - 'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }" + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' : + 'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }" input: tuple val(meta), path(intervals) @@ -39,4 +39,16 @@ process BEDTOOLS_SORT { bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + extension = task.ext.suffix ?: intervals.extension + """ + touch ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ } diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 1b6ebbcb..3a3b4e4d 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -3,6 +3,8 @@ description: Sorts a feature file by chromosome and other criteria. keywords: - bed - sort + - bedtools + - chromosome tools: - bedtools: description: | diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 8a0b5600..5021e6fc 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -5,7 +5,7 @@ process CAT_FASTQ { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index c836598e..8a39e309 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -1,6 +1,7 @@ name: cat_fastq description: Concatenates fastq files keywords: + - cat - fastq - concatenate tools: @@ -16,7 +17,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: - type: list + type: file description: | List of input FastQ files to be concatenated. output: diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 800a6099..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index e9d25f3d..da0e3646 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -2,26 +2,26 @@ process ENSEMBLVEP_VEP { tag "$meta.id" label 'process_medium' - conda "bioconda::ensembl-vep=108.2" + conda "bioconda::ensembl-vep=110.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:108.2--pl5321h4a94de4_0' : - 'quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" input: - tuple val(meta), path(vcf) + tuple val(meta), path(vcf), path(custom_extra_files) val genome val species val cache_version path cache - path fasta + tuple val(meta2), path(fasta) path extra_files output: tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf tuple val(meta), path("*.tab.gz") , optional:true, emit: tab tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , emit: report - path "versions.yml" , emit: versions + path "*.summary.html" , emit: report + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -33,7 +33,6 @@ process ENSEMBLVEP_VEP { def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" def reference = fasta ? "--fasta $fasta" : "" - """ vep \\ -i $vcf \\ @@ -59,9 +58,9 @@ process ENSEMBLVEP_VEP { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.ann.vcf.gz - touch ${prefix}.ann.tab.gz - touch ${prefix}.ann.json.gz + touch ${prefix}.vcf.gz + touch ${prefix}.tab.gz + touch ${prefix}.json.gz touch ${prefix}.summary.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 3a4f8d1d..7783847d 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -2,6 +2,9 @@ name: ENSEMBLVEP_VEP description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation + - vcf + - json + - tab tools: - ensemblvep: description: | @@ -20,29 +23,39 @@ input: type: file description: | vcf to annotate + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) - genome: - type: value + type: string description: | which genome to annotate with - species: - type: value + type: string description: | which species to annotate with - cache_version: - type: value + type: integer description: | which version of the cache to annotate with - cache: type: file description: | path to VEP cache (optional) + - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] - fasta: type: file description: | reference FASTA file (optional) pattern: "*.{fasta,fa}" - extra_files: - type: tuple + type: file description: | path to file(s) needed for plugins (optional) output: @@ -72,3 +85,4 @@ output: authors: - "@maxulysse" - "@matthdsm" + - "@nvnieuwk" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9ae58381..249f9064 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -5,7 +5,7 @@ process FASTQC { conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" + 'biocontainers/fastqc:0.11.9--0' }" input: tuple val(meta), path(reads) @@ -29,7 +29,11 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - fastqc $args --threads $task.cpus $renamed_files + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..3961de60 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test Process FASTQC" + script "modules/nf-core/fastqc/main.nf" + process "FASTQC" + tag "fastqc" + + test("Single-Read") { + + when { + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assert process.success + assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" + assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") + assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + } + + } + +} diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 9dc6ac68..b515f1c5 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -2,10 +2,10 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) @@ -26,14 +26,14 @@ process GATK4_APPLYBQSR { def prefix = task.ext.prefix ?: "${meta.id}" def interval_command = intervals ? "--intervals $intervals" : "" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" ApplyBQSR \\ + gatk --java-options "-Xmx${avail_mem}M" ApplyBQSR \\ --input $input \\ --output ${prefix}.${input.getExtension()} \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml index 3fc93f10..3002ab60 100644 --- a/modules/nf-core/gatk4/applybqsr/meta.yml +++ b/modules/nf-core/gatk4/applybqsr/meta.yml @@ -3,16 +3,17 @@ description: Apply base quality score recalibration (BQSR) to a bam file keywords: - bqsr - bam + - base quality score recalibration tools: - gatk4: - description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s - doi: 10.1158/1538-7445.AM2017-3590 - licence: ["Apache-2.0"] + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index b668a1fc..318703a4 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) @@ -28,14 +28,14 @@ process GATK4_BASERECALIBRATOR { def interval_command = intervals ? "--intervals $intervals" : "" def sites_command = known_sites.collect{"--known-sites $it"}.join(' ') - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator \\ + gatk --java-options "-Xmx${avail_mem}M" BaseRecalibrator \\ --input $input \\ --output ${prefix}.table \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml index 08c1ebbf..a6b06c73 100644 --- a/modules/nf-core/gatk4/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4/baserecalibrator/meta.yml @@ -4,14 +4,14 @@ keywords: - sort tools: - gatk4: - description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s - doi: 10.1158/1538-7445.AM2017-3590 - licence: ["Apache-2.0"] + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 41fab003..a23abd06 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -2,14 +2,14 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(bed) - path dict + tuple val(meta2), path(dict) output: tuple val(meta), path('*.interval_list'), emit: interval_list @@ -22,14 +22,14 @@ process GATK4_BEDTOINTERVALLIST { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" BedToIntervalList \\ + gatk --java-options "-Xmx${avail_mem}M" BedToIntervalList \\ --INPUT $bed \\ --OUTPUT ${prefix}.interval_list \\ --SEQUENCE_DICTIONARY $dict \\ diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 986f1592..40daf752 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -3,6 +3,7 @@ description: Creates an interval list from a bed file and a reference dict keywords: - bed - interval list + - bedtointervallist tools: - gatk4: description: | @@ -23,6 +24,11 @@ input: type: file description: Input bed file pattern: "*.bed" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - dict: type: file description: Sequence dictionary @@ -38,3 +44,4 @@ output: pattern: "versions.yml" authors: - "@kevinmenden" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index 035c171b..152fef42 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_idx) @@ -25,14 +25,14 @@ process GATK4_COMBINEGVCFS { def prefix = task.ext.prefix ?: "${meta.id}" def input_list = vcf.collect{"--variant $it"}.join(' ') - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK COMBINEGVCFS] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" CombineGVCFs \\ + gatk --java-options "-Xmx${avail_mem}M" CombineGVCFs \\ $input_list \\ --output ${prefix}.combined.g.vcf.gz \\ --reference ${fasta} \\ diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index bc324ada..15a86bea 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,17 +2,17 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: - path fasta + tuple val(meta), path(fasta) output: - path "*.dict" , emit: dict - path "versions.yml" , emit: versions + tuple val(meta), path('*.dict') , emit: dict + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,14 +20,14 @@ process GATK4_CREATESEQUENCEDICTIONARY { script: def args = task.ext.args ?: '' - def avail_mem = 6 + def avail_mem = 6144 if (!task.memory) { log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" CreateSequenceDictionary \\ + gatk --java-options "-Xmx${avail_mem}M" CreateSequenceDictionary \\ --REFERENCE $fasta \\ --URI $fasta \\ --TMP_DIR . \\ diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index bd247888..a421e681 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -3,30 +3,37 @@ description: Creates a sequence dictionary for a reference sequence keywords: - dictionary - fasta + - createsequencedictionary tools: - gatk: - description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s - doi: 10.1158/1538-7445.AM2017-3590 - licence: ["Apache-2.0"] + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] input: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: - type: file - description: Input fasta file - pattern: "*.{fasta,fa}" + type: file + description: Input fasta file + pattern: "*.{fasta,fa}" output: - dict: - type: file - description: gatk dictionary file - pattern: "*.{dict}" + type: file + description: gatk dictionary file + pattern: "*.{dict}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index c011376a..478681bd 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) @@ -32,14 +32,14 @@ process GATK4_HAPLOTYPECALLER { def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : "" def bamout_command = args.contains("--bam-writer-type") ? "--bam-output ${prefix.replaceAll('.g\\s*$', '')}.realigned.bam" : "" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" HaplotypeCaller \\ + gatk --java-options "-Xmx${avail_mem}M" HaplotypeCaller \\ --input $input \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index cef608b4..27633cca 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -6,14 +6,14 @@ keywords: - haplotype tools: - gatk4: - description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s - doi: 10.1158/1538-7445.AM2017-3590 - licence: ["Apache-2.0"] + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index 9793c90c..d3bb04a7 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE { tag "$meta.id" label 'process_low' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(feature_file) @@ -20,14 +20,14 @@ process GATK4_INDEXFEATUREFILE { script: def args = task.ext.args ?: '' - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK IndexFeatureFile] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" IndexFeatureFile \\ + gatk --java-options "-Xmx${avail_mem}M" IndexFeatureFile \\ --input $feature_file \\ --tmp-dir . \\ $args diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 84da7bf7..0054659a 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(intervals) @@ -21,17 +21,17 @@ process GATK4_INTERVALLISTTOOLS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK IntervalListTools] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ mkdir ${prefix}_split - gatk --java-options "-Xmx${avail_mem}g" IntervalListTools \\ + gatk --java-options "-Xmx${avail_mem}M" IntervalListTools \\ --INPUT $intervals \\ --OUTPUT ${prefix}_split \\ --TMP_DIR . \\ diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index af9a7cf2..f4b3f6dc 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0 bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0': + 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0' }" input: tuple val(meta), path(bam) @@ -25,33 +25,43 @@ process GATK4_MARKDUPLICATES { script: def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}.bam" + + // If the extension is CRAM, then change it to BAM + prefix_bam = prefix.tokenize('.')[-1] == 'cram' ? "${prefix.substring(0, prefix.lastIndexOf('.'))}.bam" : prefix + def input_list = bam.collect{"--INPUT $it"}.join(' ') def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } + + // Using samtools and not Markduplicates to compress to CRAM speeds up computation: + // https://medium.com/@acarroll.dna/looking-at-trade-offs-in-compression-levels-for-genomics-tools-eec2834e8b94 """ - gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\ + gatk --java-options "-Xmx${avail_mem}M" MarkDuplicates \\ $input_list \\ - --OUTPUT ${prefix} \\ + --OUTPUT ${prefix_bam} \\ --METRICS_FILE ${prefix}.metrics \\ --TMP_DIR . \\ ${reference} \\ $args - - if [[ ${prefix} == *.cram ]]; then - mv ${prefix}.bai ${prefix}.crai + # If cram files are wished as output, the run samtools for conversion + if [[ ${prefix} == *.cram ]]; then + samtools view -Ch -T ${fasta} -o ${prefix} ${prefix_bam} + rm ${prefix_bam} + samtools index ${prefix} fi cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index d418468f..dfb5b33a 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(vcf) @@ -25,14 +25,14 @@ process GATK4_MERGEVCFS { def input_list = vcf.collect{ "--INPUT $it"}.join(' ') def reference_command = dict ? "--SEQUENCE_DICTIONARY $dict" : "" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK MergeVcfs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" MergeVcfs \\ + gatk --java-options "-Xmx${avail_mem}M" MergeVcfs \\ $input_list \\ --OUTPUT ${prefix}.vcf.gz \\ $reference_command \\ diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 77092a29..0178976c 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(intervals) @@ -25,14 +25,14 @@ process GATK4_SPLITNCIGARREADS { def prefix = task.ext.prefix ?: "${meta.id}" def interval_command = intervals ? "--intervals $intervals" : "" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK SplitNCigarReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" SplitNCigarReads \\ + gatk --java-options "-Xmx${avail_mem}M" SplitNCigarReads \\ --input $bam \\ --output ${prefix}.bam \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index e2837a91..387ff8ca 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -2,16 +2,16 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) - path fasta - path fai - path dict + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) output: tuple val(meta), path("*.vcf.gz"), emit: vcf @@ -25,14 +25,14 @@ process GATK4_VARIANTFILTRATION { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK VariantFiltration] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.toGiga() + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}G" VariantFiltration \\ + gatk --java-options "-Xmx${avail_mem}M" VariantFiltration \\ --variant $vcf \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/variantfiltration/meta.yml b/modules/nf-core/gatk4/variantfiltration/meta.yml index 04b1c086..2260f37b 100644 --- a/modules/nf-core/gatk4/variantfiltration/meta.yml +++ b/modules/nf-core/gatk4/variantfiltration/meta.yml @@ -3,6 +3,7 @@ description: Filter variants keywords: - vcf - filter + - variantfiltration tools: - gatk4: description: | @@ -27,14 +28,29 @@ input: type: list description: List of VCF file indexes pattern: "*.{idx,tbi}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: type: file description: Fasta file of reference genome pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fai: type: file description: Index of fasta file pattern: "*.fasta.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - dict: type: file description: Sequence dictionary of fastea file @@ -54,3 +70,4 @@ output: pattern: "versions.yml" authors: - "@kevinmenden" + - "@ramprasadn" diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index b1a8996f..f4472b0e 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -5,7 +5,7 @@ process GFFREAD { conda "bioconda::gffread=0.12.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : - 'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }" + 'biocontainers/gffread:0.12.1--h8b12597_0' }" input: path gff diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index d906034c..73bf08cd 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -5,7 +5,7 @@ process GUNZIP { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(archive) @@ -21,10 +21,14 @@ process GUNZIP { def args = task.ext.args ?: '' gunzip = archive.toString() - '.gz' """ - gunzip \\ - -f \\ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ $args \\ - $archive + $archive \\ + > $gunzip cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 4d2ebc84..4cdcdf4c 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -3,31 +3,32 @@ description: Compresses and decompresses files. keywords: - gunzip - compression + - decompression tools: - gunzip: - description: | - gzip is a file format and a software application used for file compression and decompression. - documentation: https://www.gnu.org/software/gzip/manual/gzip.html - licence: ["GPL-3.0-or-later"] + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] input: - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 4b604749..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index ce6580d2..59ed3088 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,18 +2,20 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(fasta) + tuple val(meta2), path(fai) output: - tuple val(meta), path ("*.fai"), emit: fai - tuple val(meta), path ("*.gzi"), emit: gzi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,8 +25,8 @@ process SAMTOOLS_FAIDX { """ samtools \\ faidx \\ - $args \\ - $fasta + $fasta \\ + $args cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -33,8 +35,12 @@ process SAMTOOLS_FAIDX { """ stub: + def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() + def fastacmd = match[0] ? "touch ${match[0][1]}" : '' """ + ${fastacmd} touch ${fasta}.fai + cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index fe2fe9a1..957b25e5 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -3,6 +3,7 @@ description: Index FASTA file keywords: - index - fasta + - faidx tools: - samtools: description: | @@ -17,12 +18,21 @@ input: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: type: file description: FASTA file pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - meta: type: map diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 2120cd7d..b75707ec 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(bam), path(bai) @@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.flagstat + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 95269063..954225df 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -14,7 +14,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index a7b87d8b..83c7c34b 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_IDXSTATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(bam), path(bai) @@ -33,4 +33,16 @@ process SAMTOOLS_IDXSTATS { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.idxstats + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 3710ab88..dda87e1e 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -15,7 +15,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8b95687a..0b20aa4b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index e5cadbc2..8bd2fa6f 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -12,7 +12,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index a80ff3a2..b73b7cb2 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -2,15 +2,15 @@ process SAMTOOLS_MERGE { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") - path fasta - path fai + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) output: tuple val(meta), path("${prefix}.bam") , optional:true, emit: bam diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 5bd84bc5..3a815f74 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -12,7 +12,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: @@ -25,13 +25,23 @@ input: type: file description: BAM/CRAM file pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: - type: optional file - description: Reference file the CRAM was created with + type: file + description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fai: - type: optional file - description: Index of the reference file the CRAM was created with + type: file + description: Index of the reference file the CRAM was created with (optional) pattern: "*.fai" output: - meta: @@ -60,3 +70,4 @@ authors: - "@yuukiiwa " - "@maxulysse" - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 84c167cd..2b7753fd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(bam) @@ -23,7 +23,13 @@ process SAMTOOLS_SORT { def prefix = task.ext.prefix ?: "${meta.id}" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam + samtools sort \\ + $args \\ + -@ $task.cpus \\ + -o ${prefix}.bam \\ + -T $prefix \\ + $bam + cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 09289751..07328431 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -12,7 +12,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 0a2a3640..4a2607de 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,14 +2,14 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input), path(input_index) - path fasta + tuple val(meta2), path(fasta) output: tuple val(meta), path("*.stats"), emit: stats diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index cac50b1c..90e6345f 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -13,7 +13,7 @@ tools: short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html + documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: @@ -23,16 +23,21 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: - type: optional file - description: Reference file the CRAM was created with + type: file + description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" output: - meta: @@ -51,3 +56,4 @@ output: authors: - "@drpatelh" - "@FriederikeHanssen" + - "@ramprasadn" diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index ad5bd4f4..e92c1597 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -5,12 +5,12 @@ process SNPEFF_SNPEFF { conda "bioconda::snpeff=5.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/snpeff:5.1--hdfd78af_2' : - 'quay.io/biocontainers/snpeff:5.1--hdfd78af_2' }" + 'biocontainers/snpeff:5.1--hdfd78af_2' }" input: tuple val(meta), path(vcf) val db - path cache + tuple val(meta2), path(cache) output: tuple val(meta), path("*.ann.vcf"), emit: vcf @@ -24,17 +24,17 @@ process SNPEFF_SNPEFF { script: def args = task.ext.args ?: '' - def avail_mem = 6 + def avail_mem = 6144 if (!task.memory) { log.info '[snpEff] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } def prefix = task.ext.prefix ?: "${meta.id}" def cache_command = cache ? "-dataDir \${PWD}/${cache}" : "" """ snpEff \\ - -Xmx${avail_mem}g \\ + -Xmx${avail_mem}M \\ $db \\ $args \\ -csvStats ${prefix}.csv \\ diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 28973c78..44bada23 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -2,6 +2,10 @@ name: SNPEFF_SNPEFF description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation + - effect prediction + - snpeff + - variant + - vcf tools: - snpeff: description: | @@ -21,7 +25,7 @@ input: description: | vcf to annotate - db: - type: value + type: string description: | which db to annotate with - cache: diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 0e3bd713..d0e20384 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -5,30 +5,34 @@ process STAR_ALIGN { conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" input: - tuple val(meta), path(reads) - path index - path gtf + tuple val(meta), path(reads, stageAs: "input*/*") + tuple val(meta2), path(index) + tuple val(meta3), path(gtf) val star_ignore_sjdbgtf val seq_platform val seq_center output: - tuple val(meta), path('*d.out.bam') , emit: bam tuple val(meta), path('*Log.final.out') , emit: log_final tuple val(meta), path('*Log.out') , emit: log_out tuple val(meta), path('*Log.progress.out'), emit: log_progress path "versions.yml" , emit: versions + tuple val(meta), path('*d.out.bam') , optional:true, emit: bam tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq tuple val(meta), path('*.tab') , optional:true, emit: tab + tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab + tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab tuple val(meta), path('*.out.junction') , optional:true, emit: junction tuple val(meta), path('*.out.sam') , optional:true, emit: sam + tuple val(meta), path('*.wig') , optional:true, emit: wig + tuple val(meta), path('*.bg') , optional:true, emit: bedgraph when: task.ext.when == null || task.ext.when @@ -36,20 +40,23 @@ process STAR_ALIGN { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def reads1 = [], reads2 = [] + meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" - def seq_center = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform " + def seq_center = seq_center ? "'CN:$seq_center'" : "" + def attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ STAR \\ --genomeDir $index \\ - --readFilesIn $reads \\ + --readFilesIn ${reads1.join(",")} ${reads2.join(",")} \\ --runThreadN $task.cpus \\ --outFileNamePrefix $prefix. \\ $out_sam_type \\ $ignore_gtf \\ - $seq_center \\ + $attrRG \\ $args $mv_unsorted_bam @@ -81,11 +88,16 @@ process STAR_ALIGN { touch ${prefix}.sortedByCoord.out.bam touch ${prefix}.toTranscriptome.out.bam touch ${prefix}.Aligned.unsort.out.bam + touch ${prefix}.Aligned.sortedByCoord.out.bam touch ${prefix}.unmapped_1.fastq.gz touch ${prefix}.unmapped_2.fastq.gz touch ${prefix}.tab + touch ${prefix}.SJ.out.tab + touch ${prefix}.ReadsPerGene.out.tab touch ${prefix}.Chimeric.out.junction touch ${prefix}.out.sam + touch ${prefix}.Signal.UniqueMultiple.str1.out.wig + touch ${prefix}.Signal.UniqueMultiple.str1.out.bg cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index 7ee10f1c..3d8fed0c 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -25,10 +25,34 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - index: type: directory description: STAR genome index pattern: "star" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - seq_platform: + type: string + description: Sequencing platform + - seq_center: + type: string + description: Sequencing center + output: - bam: type: file @@ -74,6 +98,14 @@ output: type: file description: STAR chimeric junction output file (optional) pattern: "*.out.junction" + - wig: + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" + - bedgraph: + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 91462489..43424042 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -5,15 +5,15 @@ process STAR_GENOMEGENERATE { conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" input: - path fasta - path gtf + tuple val(meta), path(fasta) + tuple val(meta2), path(gtf) output: - path "star" , emit: index - path "versions.yml", emit: versions + tuple val(meta), path("star") , emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 8181157a..eba2d9cf 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -15,14 +15,29 @@ tools: doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Fasta file of the reference genome + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - gtf: type: file description: GTF file of the reference genome output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - index: type: directory description: Folder containing the star index files diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index d3a3bbff..d6c5a760 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -5,13 +5,14 @@ process TABIX_BGZIPTABIX { conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + 'biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(input) output: - tuple val(meta), path("*.gz"), path("*.tbi"), emit: gz_tbi + tuple val(meta), path("*.gz"), path("*.tbi"), optional: true, emit: gz_tbi + tuple val(meta), path("*.gz"), path("*.csi"), optional: true, emit: gz_csi path "versions.yml" , emit: versions when: @@ -34,8 +35,9 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.gz - touch ${prefix}.gz.tbi + touch ${prefix}.${input.getExtension()}.gz + touch ${prefix}.${input.getExtension()}.gz.tbi + touch ${prefix}.${input.getExtension()}.gz.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 49c03289..2761e271 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -37,9 +37,14 @@ output: type: file description: tabix index file pattern: "*.{gz.tbi}" + - csi: + type: file + description: tabix alternate index file + pattern: "*.{gz.csi}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@maxulysse" + - "@DLBPointon" diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 9a404db9..5bf332ef 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -5,7 +5,7 @@ process TABIX_TABIX { conda "bioconda::tabix=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }" + 'biocontainers/tabix:1.11--hdfd78af_0' }" input: tuple val(meta), path(tab) diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 3384847a..61461c39 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -2,10 +2,10 @@ process UNTAR { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34" + conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(archive) diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index ea7a3f38..db241a6e 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -3,6 +3,7 @@ description: Extract files. keywords: - untar - uncompress + - extract tools: - untar: description: | From 4976312eba55df37f941fe7e680dd14b2c75f472 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 12:34:27 +0200 Subject: [PATCH 017/275] prettier --- modules.json | 138 +++++++++++++-------------------------------------- 1 file changed, 35 insertions(+), 103 deletions(-) diff --git a/modules.json b/modules.json index 3e8235c2..1e399602 100755 --- a/modules.json +++ b/modules.json @@ -8,240 +8,172 @@ "bedtools/merge": { "branch": "master", "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/applybqsr": { "branch": "master", "git_sha": "240937a2a9c30298110753292be041188891f2cb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/combinegvcfs": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", "git_sha": "0a261469640941da2488e1a5aa023b64db837c70", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/splitncigarreads": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gffread": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", "git_sha": "4d584d5cf6ed5f7363a51cdb4b3eb25398e9e537", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/align": { "branch": "master", "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -250,4 +182,4 @@ } } } -} \ No newline at end of file +} From 0a001cd3180cb666e8c492996506d8e9df70234f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 12:36:28 +0200 Subject: [PATCH 018/275] fix lint --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index 2a63dfa9..747ad37f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) @praveenraj2018 +Copyright (c) Praveen Raj, Maxime U Garcia Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From a2856bd39b35374ea108de8b800f178f897bf831 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 14:23:47 +0200 Subject: [PATCH 019/275] fix path to file --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index dd25aa41..68f97def 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,7 @@ params { max_time = '6.h' // Input data - input = "https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet.csv" + input = "${projectDir}/tests/csv/1.0/fastq_single.csv" // Genome references genome = 'WBcel235' From c205c24ae64f0c4de72138fcadd089bf7ec86a9e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 14:55:48 +0200 Subject: [PATCH 020/275] add file --- tests/csv/1.0/fastq_single.csv | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 tests/csv/1.0/fastq_single.csv diff --git a/tests/csv/1.0/fastq_single.csv b/tests/csv/1.0/fastq_single.csv new file mode 100644 index 00000000..125f9bfd --- /dev/null +++ b/tests/csv/1.0/fastq_single.csv @@ -0,0 +1,2 @@ +sample,fastq_1,fastq_2,strandedness +GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,reverse From f7ae880151ac58cee924510c4835138e717c4b8f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 14:56:07 +0200 Subject: [PATCH 021/275] typo + code polish --- workflows/rnavar.nf | 144 +++++++++++++++++++------------------------- 1 file changed, 62 insertions(+), 82 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index f504b785..8a558bb1 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -32,11 +32,11 @@ def checkPathParamList = [ params.star_index, ] -for (param in checkPathParamList) {if (param) file(param, checkIfExists: true)} +for(param in checkPathParamList) {if (param) file(param, checkIfExists: true)} // Check mandatory parameters if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } -if(!params.star_index && !params.gtf && !params.gff){ exit 1, "GTF|GFF3 file is required to build a STAR reference index! Use option --gtf|--gff to provide a GTF|GFF file." } +if (!params.star_index && !params.gtf && !params.gff){ exit 1, "GTF|GFF3 file is required to build a STAR reference index! Use option --gtf|--gff to provide a GTF|GFF file." } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -55,9 +55,9 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { INPUT_CHECK } from '../subworkflows/local/input_check' // Validate the input samplesheet.csv and prepare input channels -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' // Build the genome index and other reference files -include { ANNOTATE } from '../subworkflows/local/annotate' // Annotate variants using snpEff or VEP or both +include { INPUT_CHECK } from '../subworkflows/local/input_check' // Validate the input samplesheet.csv and prepare input channels +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' // Build the genome index and other reference files +include { ANNOTATE } from '../subworkflows/local/annotate' // Annotate variants using snpEff or VEP or both /* ======================================================================================== @@ -88,7 +88,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/ ======================================================================================== */ -include { GTF2BED } from '../modules/local/gtf2bed' +include { GTF2BED } from '../modules/local/gtf2bed' /* ======================================================================================== @@ -96,10 +96,10 @@ include { GTF2BED } from '../modules/local/gtf2bed' ======================================================================================== */ -include { ALIGN_STAR } from '../subworkflows/nf-core/align_star' // Align reads to genome and sort and index the alignment file -include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' // Mark duplicates in the BAM file -include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string -include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' // Estimate and correct systematic bias +include { ALIGN_STAR } from '../subworkflows/nf-core/align_star' // Align reads to genome and sort and index the alignment file +include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' // Mark duplicates in the BAM file +include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string +include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' // Estimate and correct systematic bias /* ======================================================================================== @@ -109,8 +109,8 @@ include { RECALIBRATE } from '../subworkflows/nf-core/recalibr // Check STAR alignment parameters def prepareToolIndices = params.aligner -def seq_platform = params.seq_platform ? params.seq_platform : [] -def seq_center = params.seq_center ? params.seq_center : [] +def seq_platform = params.seq_platform ?: [] +def seq_center = params.seq_center ?: [] // Initialize file channels based on params ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() @@ -147,7 +147,7 @@ workflow RNAVAR { // SUBWORKFLOW: Uncompress and prepare reference genome files // - PREPARE_GENOME ( + PREPARE_GENOME( prepareToolIndices, params.feature_type ) @@ -157,25 +157,24 @@ workflow RNAVAR { // // SUBWORKFLOW: Read in samplesheet, validate and stage input files // - INPUT_CHECK ( - file(params.input) - ) - .reads - .map { - meta, fastq -> - def meta_clone = meta.clone() - meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') - [ meta_clone, fastq ] - } - .groupTuple(by: [0]) - .branch { - meta, fastq -> - single : fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - .set { ch_fastq } + INPUT_CHECK(file(params.input)) + .reads + .map { + meta, fastq -> + def meta_clone = meta.clone() + meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') + [ meta_clone, fastq ] + } + .groupTuple(by: [0]) + .branch { + meta, fastq -> + single : fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple: fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + .set { ch_fastq } + ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ @@ -184,20 +183,17 @@ workflow RNAVAR { // // MODULE: Concatenate FastQ files from same sample if required // - CAT_FASTQ ( - ch_fastq.multiple - ) - .reads - .mix(ch_fastq.single) - .set { ch_cat_fastq } + CAT_FASTQ(ch_fastq.multiple) + .reads + .mix(ch_fastq.single) + .set { ch_cat_fastq } + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) // // MODULE: Generate QC summary using FastQC // - FASTQC ( - ch_cat_fastq - ) + FASTQC(ch_cat_fastq) ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) @@ -205,10 +201,7 @@ workflow RNAVAR { // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList // ch_interval_list = Channel.empty() - GATK4_BEDTOINTERVALLIST( - ch_genome_bed, - PREPARE_GENOME.out.dict - ) + GATK4_BEDTOINTERVALLIST(ch_genome_bed, PREPARE_GENOME.out.dict) ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) @@ -217,9 +210,7 @@ workflow RNAVAR { // ch_interval_list_split = Channel.empty() if (!params.skip_intervallisttools) { - GATK4_INTERVALLISTTOOLS( - ch_interval_list - ) + GATK4_INTERVALLISTTOOLS(ch_interval_list) ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten() } else ch_interval_list_split = ch_interval_list @@ -237,7 +228,7 @@ workflow RNAVAR { ch_aligner_clustering_multiqc = Channel.empty() if (params.aligner == 'star') { - ALIGN_STAR ( + ALIGN_STAR( ch_cat_fastq, PREPARE_GENOME.out.star_index, PREPARE_GENOME.out.gtf, @@ -257,9 +248,7 @@ workflow RNAVAR { // // SUBWORKFLOW: Mark duplicates with GATK4 // - MARKDUPLICATES ( - ch_genome_bam - ) + MARKDUPLICATES(ch_genome_bam) ch_genome_bam = MARKDUPLICATES.out.bam_bai //Gather QC reports @@ -269,10 +258,10 @@ workflow RNAVAR { // // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals - // Splits reads that contain Ns in their cigar string (e.g. spanning splicing events in RNAseq data). + // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). // ch_splitncigar_bam_bai = Channel.empty() - SPLITNCIGAR ( + SPLITNCIGAR( ch_genome_bam, PREPARE_GENOME.out.fasta, PREPARE_GENOME.out.fai, @@ -287,7 +276,7 @@ workflow RNAVAR { // Generates a recalibration table based on various co-variates // ch_bam_variant_calling = Channel.empty() - if(!params.skip_baserecalibration) { + if (!params.skip_baserecalibration) { ch_bqsr_table = Channel.empty() // known_sites is made by grouping both the dbsnp and the known indels ressources // they can either or both be optional @@ -318,8 +307,8 @@ workflow RNAVAR { ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() ch_bam_applybqsr.combine(ch_interval_list_applybqsr) - .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval] - }.set{ch_applybqsr_bam_bai_interval} + .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} + .set{ch_applybqsr_bam_bai_interval} // // MODULE: ApplyBaseRecalibrator from GATK4 @@ -375,10 +364,10 @@ workflow RNAVAR { ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf - .map{ meta, vcf -> - meta.id = meta.sample - [meta, vcf]} - .groupTuple() + .map{ meta, vcf -> + meta.id = meta.sample + [meta, vcf]} + .groupTuple() ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) @@ -386,10 +375,7 @@ workflow RNAVAR { // MODULE: MergeVCFS from GATK4 // Merge multiple VCF files into one VCF // - GATK4_MERGEVCFS( - ch_haplotypecaller_raw, - PREPARE_GENOME.out.dict - ) + GATK4_MERGEVCFS(ch_haplotypecaller_raw, PREPARE_GENOME.out.dict) ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) @@ -414,15 +400,13 @@ workflow RNAVAR { // MODULE: IndexFeatureFile from GATK4 // Index the gVCF files // - GATK4_INDEXFEATUREFILE( - GATK4_HAPLOTYPECALLERGVCF.out.vcf - ) + GATK4_INDEXFEATUREFILE(GATK4_HAPLOTYPECALLERGVCF.out.vcf) ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index - .map{ meta, idx -> - meta.id = meta.sample - [meta, idx]} - .groupTuple() + .map{ meta, idx -> + meta.id = meta.sample + [meta, idx]} + .groupTuple() ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) @@ -452,9 +436,7 @@ workflow RNAVAR { // // MODULE: Index the VCF using TABIX // - TABIXGVCF( - ch_haplotypecaller_gvcf - ) + TABIXGVCF(ch_haplotypecaller_gvcf) ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf .join(TABIXGVCF.out.tbi, by: [0], remainder: true) @@ -471,9 +453,7 @@ workflow RNAVAR { // // MODULE: Index the VCF using TABIX // - TABIX( - ch_haplotypecaller_vcf - ) + TABIX(ch_haplotypecaller_vcf) ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf .join(TABIX.out.tbi, by: [0], remainder: true) @@ -507,7 +487,7 @@ workflow RNAVAR { // // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. // - if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { + if ((!params.skip_variantannotation) &&(params.annotate_tools) &&(params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { ANNOTATE( ch_final_vcf, params.annotate_tools, @@ -526,7 +506,7 @@ workflow RNAVAR { } ch_version_yaml = Channel.empty() - CUSTOM_DUMPSOFTWAREVERSIONS (ch_versions.unique().collectFile(name: 'collated_versions.yml')) + CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect() // @@ -549,9 +529,9 @@ workflow RNAVAR { ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect()) ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_config) - ch_multiqc_files = ch_multiqc_files.mix(ch_rnavar_logo)) + ch_multiqc_files = ch_multiqc_files.mix(ch_rnavar_logo) - MULTIQC ( + MULTIQC( ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), From 64a3dcd4012944759c1468f74fff95c0d2211816 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 14 Sep 2023 15:04:27 +0200 Subject: [PATCH 022/275] fix path to modules --- subworkflows/local/prepare_genome.nf | 32 ++++++++++----------- subworkflows/nf-core/align_star.nf | 2 +- subworkflows/nf-core/bam_sort_samtools.nf | 4 +-- subworkflows/nf-core/bam_stats_samtools.nf | 6 ++-- subworkflows/nf-core/ensemblvep_annotate.nf | 4 +-- subworkflows/nf-core/markduplicates.nf | 4 +-- subworkflows/nf-core/recalibrate.nf | 6 ++-- subworkflows/nf-core/snpeff_annotate.nf | 4 +-- subworkflows/nf-core/splitncigar.nf | 6 ++-- workflows/rnavar.nf | 32 ++++++++++----------- 10 files changed, 50 insertions(+), 50 deletions(-) diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf index 74acecc8..c9e1e417 100755 --- a/subworkflows/local/prepare_genome.nf +++ b/subworkflows/local/prepare_genome.nf @@ -2,18 +2,18 @@ // Uncompress and prepare reference genome files // -include { GATK4_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/modules/gatk4/createsequencedictionary/main' //addParams(options: params.genome_options) -include { GFFREAD } from '../../modules/nf-core/modules/gffread/main' //addParams(options: params.gffread_options) -include { GTF2BED } from '../../modules/local/gtf2bed' -include { BEDTOOLS_SORT } from '../../modules/nf-core/modules/bedtools/sort/main' -include { BEDTOOLS_MERGE } from '../../modules/nf-core/modules/bedtools/merge/main' -include { GUNZIP as GUNZIP_FASTA } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) -include { GUNZIP as GUNZIP_GENE_BED } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) -include { GUNZIP as GUNZIP_GFF } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) -include { GUNZIP as GUNZIP_GTF } from '../../modules/nf-core/modules/gunzip/main' //addParams(options: params.genome_options) -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/modules/samtools/faidx/main' //addParams(options: params.genome_options) -include { STAR_GENOMEGENERATE } from '../../modules/nf-core/modules/star/genomegenerate/main' //addParams(options: params.star_index_options) -include { UNTAR as UNTAR_STAR_INDEX } from '../../modules/nf-core/modules/untar/main' //addParams(options: params.star_untar_options) +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/gatk4/createsequencedictionary/main' //addParams(options: params.genome_options) +include { GFFREAD } from '../../modules/nf-core/gffread/main' //addParams(options: params.gffread_options) +include { GTF2BED } from '../../modules/local/gtf2bed' +include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/sort/main' +include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge/main' +include { GUNZIP as GUNZIP_FASTA } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) +include { GUNZIP as GUNZIP_GENE_BED } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) +include { GUNZIP as GUNZIP_GFF } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) +include { GUNZIP as GUNZIP_GTF } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) +include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' //addParams(options: params.genome_options) +include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate/main' //addParams(options: params.star_index_options) +include { UNTAR as UNTAR_STAR_INDEX } from '../../modules/nf-core/untar/main' //addParams(options: params.star_untar_options) workflow PREPARE_GENOME { @@ -89,19 +89,19 @@ workflow PREPARE_GENOME { ch_exon_bed = GTF2BED ( ch_gtf , feature_type).bed.collect() ch_versions = ch_versions.mix(GTF2BED.out.versions) } - + //ch_exon_bed.view() //ch_exon_bed.map{ it -> [[id:'exome'], it] } //ch_exon_bed.view() // Bedtools sort ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed.map{ it -> [[id:'exome'], it] }, 'sorted').sorted.collect() ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions) - - + + // Bedtools merge ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort).bed ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) - + // Index the genome fasta ch_fasta_fai = Channel.empty() diff --git a/subworkflows/nf-core/align_star.nf b/subworkflows/nf-core/align_star.nf index 2a4069fd..5f165e0d 100644 --- a/subworkflows/nf-core/align_star.nf +++ b/subworkflows/nf-core/align_star.nf @@ -2,7 +2,7 @@ // Alignment with STAR // -include { STAR_ALIGN } from '../../modules/nf-core/modules/star/align/main' +include { STAR_ALIGN } from '../../modules/nf-core/star/align/main' include { BAM_SORT_SAMTOOLS } from './bam_sort_samtools' workflow ALIGN_STAR { diff --git a/subworkflows/nf-core/bam_sort_samtools.nf b/subworkflows/nf-core/bam_sort_samtools.nf index f473b759..2e84fa95 100644 --- a/subworkflows/nf-core/bam_sort_samtools.nf +++ b/subworkflows/nf-core/bam_sort_samtools.nf @@ -2,8 +2,8 @@ // Sort, index BAM file and run samtools stats, flagstat and idxstats // -include { SAMTOOLS_SORT } from '../../modules/nf-core/modules/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/modules/samtools/index/main' +include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools' workflow BAM_SORT_SAMTOOLS { diff --git a/subworkflows/nf-core/bam_stats_samtools.nf b/subworkflows/nf-core/bam_stats_samtools.nf index 68d632c3..c45a91ae 100644 --- a/subworkflows/nf-core/bam_stats_samtools.nf +++ b/subworkflows/nf-core/bam_stats_samtools.nf @@ -2,9 +2,9 @@ // Run SAMtools stats, flagstat and idxstats // -include { SAMTOOLS_STATS } from '../../modules/nf-core/modules/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/modules/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/modules/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main' workflow BAM_STATS_SAMTOOLS { take: diff --git a/subworkflows/nf-core/ensemblvep_annotate.nf b/subworkflows/nf-core/ensemblvep_annotate.nf index 13dffee4..87cfc2b7 100644 --- a/subworkflows/nf-core/ensemblvep_annotate.nf +++ b/subworkflows/nf-core/ensemblvep_annotate.nf @@ -2,8 +2,8 @@ // Run VEP to annotate VCF files // -include { ENSEMBLVEP } from '../../modules/nf-core/modules/ensemblvep/main' -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' +include { ENSEMBLVEP_VEP } from '../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' workflow ENSEMBLVEP_ANNOTATE { take: diff --git a/subworkflows/nf-core/markduplicates.nf b/subworkflows/nf-core/markduplicates.nf index 85b724dd..18d3dc39 100644 --- a/subworkflows/nf-core/markduplicates.nf +++ b/subworkflows/nf-core/markduplicates.nf @@ -3,8 +3,8 @@ // include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools' -include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/modules/gatk4/markduplicates/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/modules/samtools/index/main' +include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/gatk4/markduplicates/main' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' workflow MARKDUPLICATES { take: diff --git a/subworkflows/nf-core/recalibrate.nf b/subworkflows/nf-core/recalibrate.nf index 664cf3f5..6d79257f 100644 --- a/subworkflows/nf-core/recalibrate.nf +++ b/subworkflows/nf-core/recalibrate.nf @@ -4,9 +4,9 @@ ======================================================================================== */ -include { GATK4_APPLYBQSR as APPLYBQSR } from '../../modules/nf-core/modules/gatk4/applybqsr/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/modules/samtools/index/main' -include { SAMTOOLS_STATS } from '../../modules/nf-core/modules/samtools/stats/main' +include { GATK4_APPLYBQSR as APPLYBQSR } from '../../modules/nf-core/gatk4/applybqsr/main' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' +include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' workflow RECALIBRATE { take: diff --git a/subworkflows/nf-core/snpeff_annotate.nf b/subworkflows/nf-core/snpeff_annotate.nf index 9a8b65bc..e3dd8f0f 100644 --- a/subworkflows/nf-core/snpeff_annotate.nf +++ b/subworkflows/nf-core/snpeff_annotate.nf @@ -2,8 +2,8 @@ // Run snpEff to annotate VCF files // -include { SNPEFF } from '../../modules/nf-core/modules/snpeff/main' -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/modules/tabix/bgziptabix/main' +include { SNPEFF_SNPEFF } from '../../modules/nf-core/snpeff/snpeff/main' +include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' workflow SNPEFF_ANNOTATE { take: diff --git a/subworkflows/nf-core/splitncigar.nf b/subworkflows/nf-core/splitncigar.nf index 1b1895f7..88c63a38 100644 --- a/subworkflows/nf-core/splitncigar.nf +++ b/subworkflows/nf-core/splitncigar.nf @@ -2,9 +2,9 @@ // Subworkflow: Run GATK4 SplitNCigarReads with intervals, merge and index BAM file. // -include { GATK4_SPLITNCIGARREADS } from '../../modules/nf-core/modules/gatk4/splitncigarreads/main' -include { SAMTOOLS_MERGE } from '../../modules/nf-core/modules/samtools/merge/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/modules/samtools/index/main' +include { GATK4_SPLITNCIGARREADS } from '../../modules/nf-core/gatk4/splitncigarreads/main' +include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' workflow SPLITNCIGAR { take: diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 8a558bb1..d33ddb57 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -65,22 +65,22 @@ include { ANNOTATE } from '../subworkflows/local/annotate' ======================================================================================== */ -include { FASTQC } from '../modules/nf-core/modules/fastqc/main' -include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' -include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main' -include { GATK4_BASERECALIBRATOR } from '../modules/nf-core/modules/gatk4/baserecalibrator/main' -include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/modules/gatk4/bedtointervallist/main' -include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/modules/gatk4/intervallisttools/main' -include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' -include { GATK4_HAPLOTYPECALLER as GATK4_HAPLOTYPECALLERGVCF } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' -include { GATK4_MERGEVCFS } from '../modules/nf-core/modules/gatk4/mergevcfs/main' -include { GATK4_COMBINEGVCFS } from '../modules/nf-core/modules/gatk4/combinegvcfs/main' -include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/modules/gatk4/indexfeaturefile/main' -include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/modules/gatk4/variantfiltration/main' -include { SAMTOOLS_INDEX } from '../modules/nf-core/modules/samtools/index/main' -include { TABIX_TABIX as TABIX } from '../modules/nf-core/modules/tabix/tabix/main' -include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/modules/tabix/tabix/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' +include { GATK4_BASERECALIBRATOR } from '../modules/nf-core/gatk4/baserecalibrator/main' +include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/gatk4/bedtointervallist/main' +include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/gatk4/intervallisttools/main' +include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/gatk4/haplotypecaller/main' +include { GATK4_HAPLOTYPECALLER as GATK4_HAPLOTYPECALLERGVCF } from '../modules/nf-core/gatk4/haplotypecaller/main' +include { GATK4_MERGEVCFS } from '../modules/nf-core/gatk4/mergevcfs/main' +include { GATK4_COMBINEGVCFS } from '../modules/nf-core/gatk4/combinegvcfs/main' +include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/gatk4/indexfeaturefile/main' +include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/gatk4/variantfiltration/main' +include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main' +include { TABIX_TABIX as TABIX } from '../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/tabix/tabix/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ======================================================================================== From 519f412b0b9fe8b4dcc7678cc065d6efbeeab24a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 18 Sep 2023 19:13:25 +0200 Subject: [PATCH 023/275] update all modules + fix path to subworkflows --- modules.json | 5 + modules/local/{gtf2bed.nf => gtf2bed/main.nf} | 0 modules/local/samplesheet_check.nf | 31 - modules/nf-core/mosdepth/main.nf | 80 ++ modules/nf-core/mosdepth/meta.yml | 109 +++ .../align_star/main.nf} | 4 +- .../local/{annotate.nf => annotate/main.nf} | 6 +- subworkflows/local/bam_markduplicates/main.nf | 43 + .../bam_sort_samtools/main.nf} | 6 +- .../bam_stats_samtools/main.nf} | 6 +- .../local/cram_qc_mosdepth_samtools/main.nf | 38 + .../ensemblvep_annotate/main.nf} | 4 +- subworkflows/local/input_check.nf | 46 - subworkflows/local/prepare_genome.nf | 175 ---- subworkflows/local/prepare_genome/main.nf | 136 +++ .../recalibrate/main.nf} | 6 +- .../snpeff_annotate/main.nf} | 4 +- .../splitncigar/main.nf} | 6 +- subworkflows/nf-core/markduplicates.nf | 54 -- workflows/rnavar.nf | 859 +++++++++--------- 20 files changed, 861 insertions(+), 757 deletions(-) rename modules/local/{gtf2bed.nf => gtf2bed/main.nf} (100%) delete mode 100644 modules/local/samplesheet_check.nf create mode 100644 modules/nf-core/mosdepth/main.nf create mode 100644 modules/nf-core/mosdepth/meta.yml rename subworkflows/{nf-core/align_star.nf => local/align_star/main.nf} (94%) rename subworkflows/local/{annotate.nf => annotate/main.nf} (87%) create mode 100644 subworkflows/local/bam_markduplicates/main.nf rename subworkflows/{nf-core/bam_sort_samtools.nf => local/bam_sort_samtools/main.nf} (87%) rename subworkflows/{nf-core/bam_stats_samtools.nf => local/bam_stats_samtools/main.nf} (78%) create mode 100644 subworkflows/local/cram_qc_mosdepth_samtools/main.nf rename subworkflows/{nf-core/ensemblvep_annotate.nf => local/ensemblvep_annotate/main.nf} (85%) delete mode 100644 subworkflows/local/input_check.nf delete mode 100755 subworkflows/local/prepare_genome.nf create mode 100755 subworkflows/local/prepare_genome/main.nf rename subworkflows/{nf-core/recalibrate.nf => local/recalibrate/main.nf} (85%) rename subworkflows/{nf-core/snpeff_annotate.nf => local/snpeff_annotate/main.nf} (82%) rename subworkflows/{nf-core/splitncigar.nf => local/splitncigar/main.nf} (87%) delete mode 100644 subworkflows/nf-core/markduplicates.nf diff --git a/modules.json b/modules.json index 1e399602..eb4ff72e 100755 --- a/modules.json +++ b/modules.json @@ -105,6 +105,11 @@ "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57", "installed_by": ["modules"] }, + "mosdepth": { + "branch": "master", + "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c", + "installed_by": ["modules"] + }, "multiqc": { "branch": "master", "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed/main.nf similarity index 100% rename from modules/local/gtf2bed.nf rename to modules/local/gtf2bed/main.nf diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 852dcbf9..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/rnavar/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf new file mode 100644 index 00000000..74db3a27 --- /dev/null +++ b/modules/nf-core/mosdepth/main.nf @@ -0,0 +1,80 @@ +process MOSDEPTH { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::mosdepth=0.3.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : + 'biocontainers/mosdepth:0.3.3--hdfd78af_1'}" + + input: + tuple val(meta), path(bam), path(bai), path(bed) + tuple val(meta2), path(fasta) + + output: + tuple val(meta), path('*.global.dist.txt') , emit: global_txt + tuple val(meta), path('*.summary.txt') , emit: summary_txt + tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt + tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 + tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed + tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi + tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed + tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi + tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed + tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi + tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed + tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--fasta ${fasta}" : "" + def interval = bed ? "--by ${bed}" : "" + if (bed && args.contains("--by")) { + error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" + } + if (!bed && args.contains("--thresholds")) { + error "'--thresholds' can only be specified in conjunction with '--by'" + } + + """ + mosdepth \\ + --threads $task.cpus \\ + $interval \\ + $reference \\ + $args \\ + $prefix \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.global.dist.txt + touch ${prefix}.region.dist.txt + touch ${prefix}.summary.txt + touch ${prefix}.per-base.d4 + touch ${prefix}.per-base.bed.gz + touch ${prefix}.per-base.bed.gz.csi + touch ${prefix}.regions.bed.gz + touch ${prefix}.regions.bed.gz.csi + touch ${prefix}.quantized.bed.gz + touch ${prefix}.quantized.bed.gz.csi + touch ${prefix}.thresholds.bed.gz + touch ${prefix}.thresholds.bed.gz.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml new file mode 100644 index 00000000..adf3893f --- /dev/null +++ b/modules/nf-core/mosdepth/meta.yml @@ -0,0 +1,109 @@ +name: mosdepth +description: Calculates genome-wide sequencing coverage. +keywords: + - mosdepth + - bam + - cram + - coverage +tools: + - mosdepth: + description: | + Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. + documentation: https://github.com/brentp/mosdepth + doi: 10.1093/bioinformatics/btx699 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index for BAM/CRAM file + pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'test' ] + - bed: + type: file + description: BED file with intersected intervals + pattern: "*.{bed}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - global_txt: + type: file + description: Text file with global cumulative coverage distribution + pattern: "*.{global.dist.txt}" + - regions_txt: + type: file + description: Text file with region cumulative coverage distribution + pattern: "*.{region.dist.txt}" + - summary_txt: + type: file + description: Text file with summary mean depths per chromosome and regions + pattern: "*.{summary.txt}" + - per_base_bed: + type: file + description: BED file with per-base coverage + pattern: "*.{per-base.bed.gz}" + - per_base_csi: + type: file + description: Index file for BED file with per-base coverage + pattern: "*.{per-base.bed.gz.csi}" + - per_base_d4: + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" + - regions_bed: + type: file + description: BED file with per-region coverage + pattern: "*.{regions.bed.gz}" + - regions_csi: + type: file + description: Index file for BED file with per-region coverage + pattern: "*.{regions.bed.gz.csi}" + - quantized_bed: + type: file + description: BED file with binned coverage + pattern: "*.{quantized.bed.gz}" + - quantized_csi: + type: file + description: Index file for BED file with binned coverage + pattern: "*.{quantized.bed.gz.csi}" + - thresholds_bed: + type: file + description: BED file with the number of bases in each region that are covered at or above each threshold + pattern: "*.{thresholds.bed.gz}" + - thresholds_csi: + type: file + description: Index file for BED file with threshold coverage + pattern: "*.{thresholds.bed.gz.csi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@ramprasadn" + - "@matthdsm" diff --git a/subworkflows/nf-core/align_star.nf b/subworkflows/local/align_star/main.nf similarity index 94% rename from subworkflows/nf-core/align_star.nf rename to subworkflows/local/align_star/main.nf index 5f165e0d..64ec6526 100644 --- a/subworkflows/nf-core/align_star.nf +++ b/subworkflows/local/align_star/main.nf @@ -2,8 +2,8 @@ // Alignment with STAR // -include { STAR_ALIGN } from '../../modules/nf-core/star/align/main' -include { BAM_SORT_SAMTOOLS } from './bam_sort_samtools' +include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main' +include { BAM_SORT_SAMTOOLS } from '../bam_sort_samtools/main' workflow ALIGN_STAR { take: diff --git a/subworkflows/local/annotate.nf b/subworkflows/local/annotate/main.nf similarity index 87% rename from subworkflows/local/annotate.nf rename to subworkflows/local/annotate/main.nf index 9555dddb..8f2b5104 100644 --- a/subworkflows/local/annotate.nf +++ b/subworkflows/local/annotate/main.nf @@ -2,9 +2,9 @@ // ANNOTATION // -include { SNPEFF_ANNOTATE } from '../nf-core/snpeff_annotate' -include { ENSEMBLVEP_ANNOTATE as MERGE_ANNOTATE } from '../nf-core/ensemblvep_annotate' -include { ENSEMBLVEP_ANNOTATE } from '../nf-core/ensemblvep_annotate' +include { SNPEFF_ANNOTATE } from '../snpeff_annotate/main' +include { ENSEMBLVEP_ANNOTATE as MERGE_ANNOTATE } from '../ensemblvep_annotate/main' +include { ENSEMBLVEP_ANNOTATE } from '../ensemblvep_annotate/main' workflow ANNOTATE { take: diff --git a/subworkflows/local/bam_markduplicates/main.nf b/subworkflows/local/bam_markduplicates/main.nf new file mode 100644 index 00000000..6ee53041 --- /dev/null +++ b/subworkflows/local/bam_markduplicates/main.nf @@ -0,0 +1,43 @@ +// +// MARKDUPLICATES AND QC after mapping +// +// For all modules here: +// A when clause condition is defined in the conf/modules.config to determine if the module should be run + +include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main' +include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main' + +workflow BAM_MARKDUPLICATES { + take: + bam // channel: [mandatory] [ meta, bam ] + fasta // channel: [mandatory] [ fasta ] + fasta_fai // channel: [mandatory] [ fasta_fai ] + intervals_bed_combined // channel: [optional] [ intervals_bed ] + + main: + versions = Channel.empty() + reports = Channel.empty() + + // RUN MARKDUPLICATES + GATK4_MARKDUPLICATES(bam, fasta, fasta_fai) + + // Join with the crai file + cram = GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true) + + // QC on CRAM + CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined) + + // Gather all reports generated + reports = reports.mix(GATK4_MARKDUPLICATES.out.metrics) + reports = reports.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.reports) + + // Gather versions of all tools used + versions = versions.mix(GATK4_MARKDUPLICATES.out.versions) + versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions) + + emit: + cram + reports + + versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/bam_sort_samtools.nf b/subworkflows/local/bam_sort_samtools/main.nf similarity index 87% rename from subworkflows/nf-core/bam_sort_samtools.nf rename to subworkflows/local/bam_sort_samtools/main.nf index 2e84fa95..9b4f6e31 100644 --- a/subworkflows/nf-core/bam_sort_samtools.nf +++ b/subworkflows/local/bam_sort_samtools/main.nf @@ -2,9 +2,9 @@ // Sort, index BAM file and run samtools stats, flagstat and idxstats // -include { SAMTOOLS_SORT } from '../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' workflow BAM_SORT_SAMTOOLS { take: diff --git a/subworkflows/nf-core/bam_stats_samtools.nf b/subworkflows/local/bam_stats_samtools/main.nf similarity index 78% rename from subworkflows/nf-core/bam_stats_samtools.nf rename to subworkflows/local/bam_stats_samtools/main.nf index c45a91ae..e94c1bd1 100644 --- a/subworkflows/nf-core/bam_stats_samtools.nf +++ b/subworkflows/local/bam_stats_samtools/main.nf @@ -2,9 +2,9 @@ // Run SAMtools stats, flagstat and idxstats // -include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../modules/nf-core/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' workflow BAM_STATS_SAMTOOLS { take: diff --git a/subworkflows/local/cram_qc_mosdepth_samtools/main.nf b/subworkflows/local/cram_qc_mosdepth_samtools/main.nf new file mode 100644 index 00000000..fd070a68 --- /dev/null +++ b/subworkflows/local/cram_qc_mosdepth_samtools/main.nf @@ -0,0 +1,38 @@ +// +// QC on CRAM +// +// For all modules here: +// A when clause condition is defined in the conf/modules.config to determine if the module should be run + +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' + +workflow CRAM_QC_MOSDEPTH_SAMTOOLS { + take: + cram // channel: [mandatory] [ meta, cram, crai ] + fasta // channel: [mandatory] [ fasta ] + intervals + + main: + versions = Channel.empty() + reports = Channel.empty() + + // Reports run on cram + SAMTOOLS_STATS(cram, fasta.map{ it -> [ [ id:'fasta' ], it ] }) + + MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed?:[] ] }), fasta.map{ it -> [ [ id:'fasta' ], it ] }) + + // Gather all reports generated + reports = reports.mix(SAMTOOLS_STATS.out.stats) + reports = reports.mix(MOSDEPTH.out.global_txt) + reports = reports.mix(MOSDEPTH.out.regions_txt) + + // Gather versions of all tools used + versions = versions.mix(MOSDEPTH.out.versions) + versions = versions.mix(SAMTOOLS_STATS.out.versions.first()) + + emit: + reports + + versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/ensemblvep_annotate.nf b/subworkflows/local/ensemblvep_annotate/main.nf similarity index 85% rename from subworkflows/nf-core/ensemblvep_annotate.nf rename to subworkflows/local/ensemblvep_annotate/main.nf index 87cfc2b7..83187150 100644 --- a/subworkflows/nf-core/ensemblvep_annotate.nf +++ b/subworkflows/local/ensemblvep_annotate/main.nf @@ -2,8 +2,8 @@ // Run VEP to annotate VCF files // -include { ENSEMBLVEP_VEP } from '../../modules/nf-core/ensemblvep/vep/main' -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' +include { ENSEMBLVEP_VEP } from '../../../modules/nf-core/ensemblvep/vep/main' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow ENSEMBLVEP_ANNOTATE { take: diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 95fc458e..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,46 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - SAMPLESHEET_CHECK ( - samplesheet - ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf deleted file mode 100755 index c9e1e417..00000000 --- a/subworkflows/local/prepare_genome.nf +++ /dev/null @@ -1,175 +0,0 @@ -// -// Uncompress and prepare reference genome files -// - -include { GATK4_CREATESEQUENCEDICTIONARY } from '../../modules/nf-core/gatk4/createsequencedictionary/main' //addParams(options: params.genome_options) -include { GFFREAD } from '../../modules/nf-core/gffread/main' //addParams(options: params.gffread_options) -include { GTF2BED } from '../../modules/local/gtf2bed' -include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/sort/main' -include { BEDTOOLS_MERGE } from '../../modules/nf-core/bedtools/merge/main' -include { GUNZIP as GUNZIP_FASTA } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) -include { GUNZIP as GUNZIP_GENE_BED } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) -include { GUNZIP as GUNZIP_GFF } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) -include { GUNZIP as GUNZIP_GTF } from '../../modules/nf-core/gunzip/main' //addParams(options: params.genome_options) -include { SAMTOOLS_FAIDX } from '../../modules/nf-core/samtools/faidx/main' //addParams(options: params.genome_options) -include { STAR_GENOMEGENERATE } from '../../modules/nf-core/star/genomegenerate/main' //addParams(options: params.star_index_options) -include { UNTAR as UNTAR_STAR_INDEX } from '../../modules/nf-core/untar/main' //addParams(options: params.star_untar_options) - - -workflow PREPARE_GENOME { - take: - prepare_tool_indices - feature_type - - main: - - ch_versions = Channel.empty() - - // - // Uncompress genome fasta file if required - // - if (params.fasta.endsWith('.gz')) { - GUNZIP_FASTA ( - Channel.fromPath(params.fasta).map{ it -> [[id:it[0].baseName], it] } - ) - ch_fasta = GUNZIP_FASTA.out.gunzip.map{ meta, fasta -> [fasta] }.collect() - ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) - } else { - ch_fasta = Channel.fromPath(params.fasta).collect() - } - - // - // Uncompress GTF annotation file or create from GFF3 if required - // - ch_gffread_version = Channel.empty() - if (params.gtf) { - if (params.gtf.endsWith('.gz')) { - GUNZIP_GTF ( - Channel.fromPath(params.gtf).map{ it -> [[id:it[0].baseName], it] } - ) - ch_gtf = GUNZIP_GTF.out.gunzip.map{ meta, gtf -> [gtf] }.collect() - ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) - } else { - ch_gtf = Channel.fromPath(params.gtf).collect() - } - } else if (params.gff) { - if (params.gff.endsWith('.gz')) { - GUNZIP_GFF ( - Channel.fromPath(params.gff).map{ it -> [[id:it[0].baseName], it] } - ) - ch_gff = GUNZIP_GFF.out.gunzip.map{ meta, gff -> [gff] }.collect() - ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions) - } else { - ch_gff = Channel.fromPath(params.gff).collect() - } - - GFFREAD ( - ch_gff - ) - .gtf - .set { ch_gtf } - - ch_versions = ch_versions.mix(GFFREAD.out.versions) - } - - // - // Uncompress exon BED annotation file or create from GTF if required - // - if (params.exon_bed) { - if (params.exon_bed.endsWith('.gz')) { - GUNZIP_GENE_BED ( - Channel.fromPath(params.exon_bed).map{ it -> [[id:it[0].baseName], it] } - ) - ch_gene_bed = GUNZIP_GENE_BED.out.gunzip.map{ meta, bed -> [bed] }.collect() - ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) - } else { - ch_gene_bed = Channel.fromPath(params.exon_bed).collect() - } - } else { - ch_exon_bed = GTF2BED ( ch_gtf , feature_type).bed.collect() - ch_versions = ch_versions.mix(GTF2BED.out.versions) - } - - //ch_exon_bed.view() - //ch_exon_bed.map{ it -> [[id:'exome'], it] } - //ch_exon_bed.view() - // Bedtools sort - ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed.map{ it -> [[id:'exome'], it] }, 'sorted').sorted.collect() - ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions) - - - // Bedtools merge - ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort).bed - ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) - - - // Index the genome fasta - ch_fasta_fai = Channel.empty() - if (params.fasta_fai) ch_fasta_fai = Channel.fromPath(params.fasta_fai).collect() - if (!params.fasta_fai) { - SAMTOOLS_FAIDX( - ch_fasta.map{ it -> [[id:it[0].getName()], it]} - ) - ch_fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] }.collect() - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) - } - - // Create dictionary file for the genome fasta - ch_fasta_dict = Channel.empty() - if (params.dict) ch_fasta_dict = Channel.fromPath(params.dict).collect() - else ch_fasta_dict = GATK4_CREATESEQUENCEDICTIONARY(ch_fasta).dict - - // - // Uncompress STAR index or generate from scratch if required - // - ch_star_index = Channel.empty() - if ('star' in prepare_tool_indices) { - if (params.star_index) { - if (params.star_index.endsWith('.tar.gz')) { - UNTAR_STAR_INDEX ( - Channel.fromPath(params.star_index).map{ it -> [[id:it[0].baseName], it] } - ) - ch_star_index = UNTAR_STAR_INDEX.out.untar.map{ meta, star_index -> [star_index] }.collect() - ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) - } else { - ch_star_index = Channel.fromPath(params.star_index).collect() - } - } - else { - STAR_GENOMEGENERATE ( - ch_fasta,ch_gtf - ) - .index - .set { ch_star_index } - ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) - } - - //if((!ch_star_index) || getIndexVersion(ch_star_index) != '2.7.4a'){ - // ch_star_index = STAR_GENOMEGENERATE(ch_fasta,ch_gtf).index - // ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) - //} - } - - - emit: - fasta = ch_fasta // path: genome.fasta - fai = ch_fasta_fai // path: genome.fasta.fai - dict = ch_fasta_dict // path: genome.fasta.dict - gtf = ch_gtf // path: genome.gtf - exon_bed = ch_exon_bed // path: exon.bed - bedtools_sort = ch_bedtools_sort // path: sort.bed - bedtools_merge = ch_bedtools_merge // path: merge.bed - star_index = ch_star_index // path: star/index/ - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] -} - -def getIndexVersion( index_path ) { - genomeParameters = new File("$index_path/genomeParameters.txt") - if ( genomeParameters.exists() ) { - for(line: genomeParameters.readLines()){ - if(line.startsWith("versionGenome")){ - return line.split("\t")[1].trim() - } - } - } -} diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf new file mode 100755 index 00000000..598dc4e4 --- /dev/null +++ b/subworkflows/local/prepare_genome/main.nf @@ -0,0 +1,136 @@ +// +// Uncompress and prepare reference genome files +// + +include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' +include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtools/sort/main' +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GFFREAD } from '../../../modules/nf-core/gffread/main' +include { GTF2BED } from '../../../modules/local/gtf2bed' +include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' +include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' +include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' +include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar/main' + +workflow PREPARE_GENOME { + take: + fasta // file: /path/to/genome.fasta + // gtf // file: /path/to/genome.gtf + // gff // file: /path/to/genome.gff + // exon_bed // file: /path/to/gene.bed + // prepare_tool_indices + // feature_type + + main: + ch_versions = Channel.empty() + + ch_fasta = fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } + + // + // Uncompress genome fasta file if required + // + // if (fasta.endsWith('.gz')) { + // ch_fasta = GUNZIP_FASTA([[:], fasta]).gunzip.map{ meta, fasta -> fasta } + // ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) + // } else { + // ch_fasta = Channel.value(file(fasta)) + // } + + // + // Uncompress GTF annotation file or create from GFF3 if required + // + // if (gtf) { + // if (gtf.endsWith('.gz')) { + // ch_gtf = GUNZIP_GTF([[:], gtf]).gunzip.map{ meta, gtf -> gtf } + // ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) + // } else ch_gtf = Channel.value(file(gtf)) + // } else if (gff) { + // if (gff.endsWith('.gz')) { + // ch_gff = GUNZIP_GFF([[:], gff]).gunzip.map{ meta, gff -> gff } + // ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions) + // } else ch_gff = Channel.value(file(gff)) + // ch_gtf = GFFREAD(ch_gff).gtf + // ch_versions = ch_versions.mix(GFFREAD.out.versions) + // } + + // + // Uncompress exon BED annotation file or create from GTF if required + // + // if (exon_bed) { + // if (exon_bed.endsWith('.gz')) { + // exonGENE_BED( + // Channel.fromPath(exon_bed).map{ it -> [[id:it[0].baseName], it] } + // ) + // ch_exon_bed = GUNZIP_GENE_BED.out.gunzip.map{ meta, bed -> [bed] }.collect() + // ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) + // } else { + // ch_exon_bed = Channel.fromPath(exon_bed).collect() + // } + // } else { + // ch_exon_bed = GTF2BED( ch_gtf , feature_type).bed.collect() + // ch_versions = ch_versions.mix(GTF2BED.out.versions) + // } + + //ch_exon_bed.view() + //ch_exon_bed.map{ it -> [[id:'exome'], it] } + //ch_exon_bed.view() + // Bedtools sort + // ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed.map{ it -> [[id:'exome'], it] }, 'sorted').sorted.collect() + // ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions) + + + // // Bedtools merge + // ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort).bed + // ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) + + + // Index the genome fasta + SAMTOOLS_FAIDX(ch_fasta, [['id':null], []]) + + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + + // Create dictionary file for the genome fasta + // ch_fasta_dict = Channel.empty() + // if (params.dict) ch_fasta_dict = Channel.fromPath(params.dict).collect() + // else ch_fasta_dict = GATK4_CREATESEQUENCEDICTIONARY(ch_fasta).dict + + // + // Uncompress STAR index or generate from scratch if required + // + // ch_star_index = Channel.empty() + // if ('star' in prepare_tool_indices) { + // if (params.star_index) { + // if (params.star_index.endsWith('.tar.gz')) { + // UNTAR_STAR_INDEX( + // Channel.fromPath(params.star_index).map{ it -> [[id:it[0].baseName], it] } + // ) + // ch_star_index = UNTAR_STAR_INDEX.out.untar.map{ meta, star_index -> [star_index] }.collect() + // ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) + // } else { + // ch_star_index = Channel.fromPath(params.star_index).collect() + // } + // } + // else { + // STAR_GENOMEGENERATE( + // ch_fasta,ch_gtf + // ) + // .index + // .set { ch_star_index } + // ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) + // } + // } + + + emit: + // fasta = ch_fasta // path: genome.fasta + fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai dict = ch_fasta_dict // path: genome.fasta.dict + // gtf = ch_gtf // path: genome.gtf + // exon_bed = ch_exon_bed // path: exon.bed + // bedtools_sort = ch_bedtools_sort // path: sort.bed + // bedtools_merge = ch_bedtools_merge // path: merge.bed + // star_index = ch_star_index // path: star/index/ + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/recalibrate.nf b/subworkflows/local/recalibrate/main.nf similarity index 85% rename from subworkflows/nf-core/recalibrate.nf rename to subworkflows/local/recalibrate/main.nf index 6d79257f..3b4ab0d8 100644 --- a/subworkflows/nf-core/recalibrate.nf +++ b/subworkflows/local/recalibrate/main.nf @@ -4,9 +4,9 @@ ======================================================================================== */ -include { GATK4_APPLYBQSR as APPLYBQSR } from '../../modules/nf-core/gatk4/applybqsr/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main' +include { GATK4_APPLYBQSR as APPLYBQSR } from '../../../modules/nf-core/gatk4/applybqsr/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' workflow RECALIBRATE { take: diff --git a/subworkflows/nf-core/snpeff_annotate.nf b/subworkflows/local/snpeff_annotate/main.nf similarity index 82% rename from subworkflows/nf-core/snpeff_annotate.nf rename to subworkflows/local/snpeff_annotate/main.nf index e3dd8f0f..241cb190 100644 --- a/subworkflows/nf-core/snpeff_annotate.nf +++ b/subworkflows/local/snpeff_annotate/main.nf @@ -2,8 +2,8 @@ // Run snpEff to annotate VCF files // -include { SNPEFF_SNPEFF } from '../../modules/nf-core/snpeff/snpeff/main' -include { TABIX_BGZIPTABIX } from '../../modules/nf-core/tabix/bgziptabix/main' +include { SNPEFF_SNPEFF } from '../../../modules/nf-core/snpeff/snpeff/main' +include { TABIX_BGZIPTABIX } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow SNPEFF_ANNOTATE { take: diff --git a/subworkflows/nf-core/splitncigar.nf b/subworkflows/local/splitncigar/main.nf similarity index 87% rename from subworkflows/nf-core/splitncigar.nf rename to subworkflows/local/splitncigar/main.nf index 88c63a38..9348a098 100644 --- a/subworkflows/nf-core/splitncigar.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -2,9 +2,9 @@ // Subworkflow: Run GATK4 SplitNCigarReads with intervals, merge and index BAM file. // -include { GATK4_SPLITNCIGARREADS } from '../../modules/nf-core/gatk4/splitncigarreads/main' -include { SAMTOOLS_MERGE } from '../../modules/nf-core/samtools/merge/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' +include { GATK4_SPLITNCIGARREADS } from '../../../modules/nf-core/gatk4/splitncigarreads/main' +include { SAMTOOLS_MERGE } from '../../../modules/nf-core/samtools/merge/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' workflow SPLITNCIGAR { take: diff --git a/subworkflows/nf-core/markduplicates.nf b/subworkflows/nf-core/markduplicates.nf deleted file mode 100644 index 18d3dc39..00000000 --- a/subworkflows/nf-core/markduplicates.nf +++ /dev/null @@ -1,54 +0,0 @@ -// -// GATK4 MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats -// - -include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools' -include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/gatk4/markduplicates/main' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main' - -workflow MARKDUPLICATES { - take: - bam // channel: [ val(meta), [ bam ] ] - - main: - - ch_versions = Channel.empty() - - GATK4_MARKDUPLICATES ( - bam - ) - ch_versions = ch_versions.mix(GATK4_MARKDUPLICATES.out.versions.first()) - - // - // Index BAM file and run samtools stats, flagstat and idxstats - // - SAMTOOLS_INDEX ( - GATK4_MARKDUPLICATES.out.bam - ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - - GATK4_MARKDUPLICATES.out.bam - .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) - .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) - .map{meta, bam, bai, csi -> - if (bai) [meta, bam, bai] - else [meta, bam, csi]} - .set{ch_bam_bai} - - BAM_STATS_SAMTOOLS ( - ch_bam_bai - ) - ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first()) - - emit: - bam = GATK4_MARKDUPLICATES.out.bam // channel: [ val(meta), [ bam ] ] - bam_bai = ch_bam_bai // channel: [ val(meta), [ bam ], [bai or csi] ] - metrics = GATK4_MARKDUPLICATES.out.metrics // channel: [ val(meta), [ metrics ] ] - - bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] - csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] - stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - versions = ch_versions // channel: [versions.yml] -} diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index d33ddb57..64264b44 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -55,9 +55,14 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { INPUT_CHECK } from '../subworkflows/local/input_check' // Validate the input samplesheet.csv and prepare input channels -include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' // Build the genome index and other reference files -include { ANNOTATE } from '../subworkflows/local/annotate' // Annotate variants using snpEff or VEP or both +include { GTF2BED } from '../modules/local/gtf2bed/main' + +include { ALIGN_STAR } from '../subworkflows/local/align_star/main' // Align reads to genome and sort and index the alignment file +include { ANNOTATE } from '../subworkflows/local/annotate/main' // Annotate variants using snpEff or VEP or both +include { BAM_MARKDUPLICATES } from '../subworkflows/local/bam_markduplicates/main' // Mark duplicates in the BAM file +include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome/main' // Build the genome index and other reference files +include { RECALIBRATE } from '../subworkflows/local/recalibrate/main' // Estimate and correct systematic bias +include { SPLITNCIGAR } from '../subworkflows/local/splitncigar/main' // Splits reads that contain Ns in their cigar string /* ======================================================================================== @@ -82,54 +87,38 @@ include { TABIX_TABIX as TABIX } from '../modules/ include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/tabix/tabix/main' include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' -/* -======================================================================================== - IMPORT LOCAL MODULES -======================================================================================== -*/ - -include { GTF2BED } from '../modules/local/gtf2bed' - -/* -======================================================================================== - IMPORT NF-CORE SUBWORKFLOWS -======================================================================================== -*/ - -include { ALIGN_STAR } from '../subworkflows/nf-core/align_star' // Align reads to genome and sort and index the alignment file -include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' // Mark duplicates in the BAM file -include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string -include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' // Estimate and correct systematic bias - /* ======================================================================================== VARIABLES ======================================================================================== */ -// Check STAR alignment parameters -def prepareToolIndices = params.aligner -def seq_platform = params.seq_platform ?: [] -def seq_center = params.seq_center ?: [] - -// Initialize file channels based on params -ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() -ch_dbsnp_tbi = params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : Channel.empty() -ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.empty() -ch_known_indels_tbi = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : Channel.empty() - -// Initialize variant annotation associated channels -ch_snpeff_db = params.snpeff_db ?: Channel.empty() -ch_vep_cache_version = params.vep_cache_version ?: Channel.empty() -ch_vep_genome = params.vep_genome ?: Channel.empty() -ch_vep_species = params.vep_species ?: Channel.empty() -ch_snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : [] -ch_vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : [] +// // Check STAR alignment parameters +// def prepareToolIndices = params.aligner +// def seq_platform = params.seq_platform ?: [] +// def seq_center = params.seq_center ?: [] + +// // Initialize file channels based on params +// ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() +// ch_dbsnp_tbi = params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : Channel.empty() +// ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.empty() +// ch_known_indels_tbi = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : Channel.empty() + +// // Initialize variant annotation associated channels +// ch_snpeff_db = params.snpeff_db ?: Channel.empty() +// ch_vep_cache_version = params.vep_cache_version ?: Channel.empty() +// ch_vep_genome = params.vep_genome ?: Channel.empty() +// ch_vep_species = params.vep_species ?: Channel.empty() +// ch_snpeff_cache = params.snpeff_cache ? Channel.fromPath(params.snpeff_cache).collect() : [] +// ch_vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cache).collect() : [] // MultiQC reporting -def multiqc_report = [] +// def multiqc_report = [] +// Initialize file channels based on params, defined in the params.genomes[params.genome] scope +ch_fasta = params.fasta ? Channel.fromPath(params.fasta).first() : Channel.empty() + /* ======================================================================================== RUN MAIN WORKFLOW RNAVAR @@ -148,397 +137,407 @@ workflow RNAVAR { // PREPARE_GENOME( - prepareToolIndices, - params.feature_type + ch_fasta + // params.gtf, + // params.gff, + // params.gene_bed, + // params.aligner, + // params.feature_type ) - ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) - ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) - - // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files - // - INPUT_CHECK(file(params.input)) - .reads - .map { - meta, fastq -> - def meta_clone = meta.clone() - meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') - [ meta_clone, fastq ] - } - .groupTuple(by: [0]) - .branch { - meta, fastq -> - single : fastq.size() == 1 - return [ meta, fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - .set { ch_fastq } - - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema - - // - // MODULE: Concatenate FastQ files from same sample if required - // - CAT_FASTQ(ch_fastq.multiple) - .reads - .mix(ch_fastq.single) - .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) - - // - // MODULE: Generate QC summary using FastQC - // - FASTQC(ch_cat_fastq) - ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - - // - // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList - // - ch_interval_list = Channel.empty() - GATK4_BEDTOINTERVALLIST(ch_genome_bed, PREPARE_GENOME.out.dict) - ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list - ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) - - // - // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools - // - ch_interval_list_split = Channel.empty() - if (!params.skip_intervallisttools) { - GATK4_INTERVALLISTTOOLS(ch_interval_list) - ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten() - } - else ch_interval_list_split = ch_interval_list - - // - // SUBWORKFLOW: Perform read alignment using STAR aligner - // - ch_genome_bam = Channel.empty() - ch_genome_bam_index = Channel.empty() - ch_samtools_stats = Channel.empty() - ch_samtools_flagstat = Channel.empty() - ch_samtools_idxstats = Channel.empty() - ch_star_multiqc = Channel.empty() - ch_aligner_pca_multiqc = Channel.empty() - ch_aligner_clustering_multiqc = Channel.empty() - - if (params.aligner == 'star') { - ALIGN_STAR( - ch_cat_fastq, - PREPARE_GENOME.out.star_index, - PREPARE_GENOME.out.gtf, - params.star_ignore_sjdbgtf, - seq_platform, - seq_center - ) - ch_genome_bam = ALIGN_STAR.out.bam - ch_genome_bam_index = ALIGN_STAR.out.bai - ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript - - // Gather QC reports - ch_reports = ch_reports.mix(ALIGN_STAR.out.stats.collect{it[1]}.ifEmpty([])) - ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(ALIGN_STAR.out.versions.first().ifEmpty(null)) - - // - // SUBWORKFLOW: Mark duplicates with GATK4 - // - MARKDUPLICATES(ch_genome_bam) - ch_genome_bam = MARKDUPLICATES.out.bam_bai - - //Gather QC reports - ch_reports = ch_reports.mix(MARKDUPLICATES.out.stats.collect{it[1]}.ifEmpty([])) - ch_reports = ch_reports.mix(MARKDUPLICATES.out.metrics.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(MARKDUPLICATES.out.versions.first().ifEmpty(null)) - - // - // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals - // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). - // - ch_splitncigar_bam_bai = Channel.empty() - SPLITNCIGAR( - ch_genome_bam, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict, - ch_interval_list_split - ) - ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai - ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions.first().ifEmpty(null)) - - // - // MODULE: BaseRecalibrator from GATK4 - // Generates a recalibration table based on various co-variates - // - ch_bam_variant_calling = Channel.empty() - if (!params.skip_baserecalibration) { - ch_bqsr_table = Channel.empty() - // known_sites is made by grouping both the dbsnp and the known indels ressources - // they can either or both be optional - ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() - ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() - - ch_interval_list_recalib = ch_interval_list.map{ meta, bed -> [bed] }.flatten() - ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) - .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] - }.set{ch_splitncigar_bam_bai_interval} - - GATK4_BASERECALIBRATOR( - ch_splitncigar_bam_bai_interval, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict, - ch_known_sites, - ch_known_sites_tbi - ) - ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table - - // Gather QC reports - ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) - ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions.first().ifEmpty(null)) - - ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table, by: [0]) - ch_bam_recalibrated_qc = Channel.empty() - - ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() - ch_bam_applybqsr.combine(ch_interval_list_applybqsr) - .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} - .set{ch_applybqsr_bam_bai_interval} - - // - // MODULE: ApplyBaseRecalibrator from GATK4 - // Recalibrates the base qualities of the input reads based on the recalibration table produced by the GATK BaseRecalibrator tool. - // - RECALIBRATE( - params.skip_multiqc, - ch_applybqsr_bam_bai_interval, - PREPARE_GENOME.out.dict, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.fasta - ) - - ch_bam_variant_calling = RECALIBRATE.out.bam - ch_bam_recalibrated_qc = RECALIBRATE.out.qc - - // Gather QC reports - ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) - } else { - ch_bam_variant_calling = ch_splitncigar_bam_bai - } - - interval_flag = params.no_intervals - // Run haplotyper even in the absence of dbSNP files - if (!params.dbsnp){ - ch_dbsnp = [] - ch_dbsnp_tbi = [] - } - - ch_haplotypecaller_vcf = Channel.empty() - ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) - .map{ meta, bam, bai, interval_list -> - new_meta = meta.clone() - new_meta.id = meta.id + "_" + interval_list.baseName - new_meta.sample = meta.id - [new_meta, bam, bai, interval_list] - } - - // - // MODULE: HaplotypeCaller from GATK4 - // Calls germline SNPs and indels via local re-assembly of haplotypes. - // - - GATK4_HAPLOTYPECALLER( - ch_haplotypecaller_interval_bam, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict, - ch_dbsnp, - ch_dbsnp_tbi - ) - - - ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf - .map{ meta, vcf -> - meta.id = meta.sample - [meta, vcf]} - .groupTuple() - - ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) - - // - // MODULE: MergeVCFS from GATK4 - // Merge multiple VCF files into one VCF - // - GATK4_MERGEVCFS(ch_haplotypecaller_raw, PREPARE_GENOME.out.dict) - ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf - ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) - - if (params.generate_gvcf){ - GATK4_HAPLOTYPECALLERGVCF( - ch_haplotypecaller_interval_bam, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict, - ch_dbsnp, - ch_dbsnp_tbi - ) - - ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf - .map{ meta, vcf -> - meta.id = meta.sample - [meta, vcf]} - .groupTuple() - - ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) - // - // MODULE: IndexFeatureFile from GATK4 - // Index the gVCF files - // - GATK4_INDEXFEATUREFILE(GATK4_HAPLOTYPECALLERGVCF.out.vcf) - - ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index - .map{ meta, idx -> - meta.id = meta.sample - [meta, idx]} - .groupTuple() - - ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) - - // - // MODULE: CombineGVCFS from GATK4 - // Merge multiple GVCF files into one GVCF - // - - //ch_haplotypecallergvcf_raw_tbi = ch_haplotypecallergvcf_raw - // .join(ch_haplotypecallergvcf_raw_index, by: [0], remainder: true) - // .map{meta, vcf, tbi -> - // [meta, vcf, tbi] - // } - - - - GATK4_COMBINEGVCFS( - ch_haplotypecallergvcf_raw, - ch_haplotypecallergvcf_raw_index, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict - ) - ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf - ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) - - // - // MODULE: Index the VCF using TABIX - // - TABIXGVCF(ch_haplotypecaller_gvcf) - - ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf - .join(TABIXGVCF.out.tbi, by: [0], remainder: true) - .join(TABIXGVCF.out.csi, by: [0], remainder: true) - .map{meta, vcf, tbi, csi -> - if (tbi) [meta, vcf, tbi] - else [meta, vcf, csi] - } - - ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) - - } - - // - // MODULE: Index the VCF using TABIX - // - TABIX(ch_haplotypecaller_vcf) - - ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf - .join(TABIX.out.tbi, by: [0], remainder: true) - .join(TABIX.out.csi, by: [0], remainder: true) - .map{meta, vcf, tbi, csi -> - if (tbi) [meta, vcf, tbi] - else [meta, vcf, csi] - } - - ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) - ch_final_vcf = ch_haplotypecaller_vcf - - // - // MODULE: VariantFiltration from GATK4 - // Filter variant calls based on certain criteria - // - if (!params.skip_variantfiltration && !params.bam_csi_index ) { - - GATK4_VARIANTFILTRATION( - ch_haplotypecaller_vcf_tbi, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict - ) - - ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf - ch_final_vcf = ch_filtered_vcf - ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) - } - - // - // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. - // - if ((!params.skip_variantannotation) &&(params.annotate_tools) &&(params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { - ANNOTATE( - ch_final_vcf, - params.annotate_tools, - ch_snpeff_db, - ch_snpeff_cache, - ch_vep_genome, - ch_vep_species, - ch_vep_cache_version, - ch_vep_cache) - - // Gather QC reports - ch_reports = ch_reports.mix(ANNOTATE.out.reports) - ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) - } - - } - - ch_version_yaml = Channel.empty() - CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) - ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect() - - // - // MODULE: MultiQC - // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report - // - if (!params.skip_multiqc){ - workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_version_yaml) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect()) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_config) - ch_multiqc_files = ch_multiqc_files.mix(ch_rnavar_logo) - - MULTIQC( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() - ) - multiqc_report = MULTIQC.out.report.toList() - } + // ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) + // ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + + // // + // // SUBWORKFLOW: Read in samplesheet, validate and stage input files + // // + // INPUT_CHECK(file(params.input)) + // .reads + // .map { + // meta, fastq -> + // def meta_clone = meta.clone() + // meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') + // [ meta_clone, fastq ] + // } + // .groupTuple(by: [0]) + // .branch { + // meta, fastq -> + // single : fastq.size() == 1 + // return [ meta, fastq.flatten() ] + // multiple: fastq.size() > 1 + // return [ meta, fastq.flatten() ] + // } + // .set { ch_fastq } + + // ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // // ! There is currently no tooling to help you write a sample sheet schema + + // // + // // MODULE: Concatenate FastQ files from same sample if required + // // + // CAT_FASTQ(ch_fastq.multiple) + // .reads + // .mix(ch_fastq.single) + // .set { ch_cat_fastq } + + // ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + + // // + // // MODULE: Generate QC summary using FastQC + // // + // FASTQC(ch_cat_fastq) + // ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + + // // + // // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList + // // + // ch_interval_list = Channel.empty() + // GATK4_BEDTOINTERVALLIST(ch_genome_bed, PREPARE_GENOME.out.dict) + // ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list + // ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) + + // // + // // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools + // // + // ch_interval_list_split = Channel.empty() + // if (!params.skip_intervallisttools) { + // GATK4_INTERVALLISTTOOLS(ch_interval_list) + // ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten() + // } + // else ch_interval_list_split = ch_interval_list + + // // + // // SUBWORKFLOW: Perform read alignment using STAR aligner + // // + // ch_genome_bam = Channel.empty() + // ch_genome_bam_index = Channel.empty() + // ch_samtools_stats = Channel.empty() + // ch_samtools_flagstat = Channel.empty() + // ch_samtools_idxstats = Channel.empty() + // ch_star_multiqc = Channel.empty() + // ch_aligner_pca_multiqc = Channel.empty() + // ch_aligner_clustering_multiqc = Channel.empty() + + // if (params.aligner == 'star') { + // ALIGN_STAR( + // ch_cat_fastq, + // PREPARE_GENOME.out.star_index, + // PREPARE_GENOME.out.gtf, + // params.star_ignore_sjdbgtf, + // seq_platform, + // seq_center + // ) + // ch_genome_bam = ALIGN_STAR.out.bam + // ch_genome_bam_index = ALIGN_STAR.out.bai + // ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript + + // // Gather QC reports + // ch_reports = ch_reports.mix(ALIGN_STAR.out.stats.collect{it[1]}.ifEmpty([])) + // ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) + // ch_versions = ch_versions.mix(ALIGN_STAR.out.versions.first().ifEmpty(null)) + + // // + // // SUBWORKFLOW: Mark duplicates with GATK4 + // // + // BAM_MARKDUPLICATES( + // ch_genome_bam, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // []) + + // ch_genome_bam = BAM_MARKDUPLICATES.out.bam_bai + + // //Gather QC reports + // ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.stats.collect{it[1]}.ifEmpty([])) + // ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.metrics.collect{it[1]}.ifEmpty([])) + // ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions.first().ifEmpty(null)) + + // // + // // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals + // // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). + // // + // ch_splitncigar_bam_bai = Channel.empty() + // SPLITNCIGAR( + // ch_genome_bam, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.dict, + // ch_interval_list_split + // ) + // ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai + // ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions.first().ifEmpty(null)) + + // // + // // MODULE: BaseRecalibrator from GATK4 + // // Generates a recalibration table based on various co-variates + // // + // ch_bam_variant_calling = Channel.empty() + // if (!params.skip_baserecalibration) { + // ch_bqsr_table = Channel.empty() + // // known_sites is made by grouping both the dbsnp and the known indels ressources + // // they can either or both be optional + // ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() + // ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() + + // ch_interval_list_recalib = ch_interval_list.map{ meta, bed -> [bed] }.flatten() + // ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) + // .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] + // }.set{ch_splitncigar_bam_bai_interval} + + // GATK4_BASERECALIBRATOR( + // ch_splitncigar_bam_bai_interval, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.dict, + // ch_known_sites, + // ch_known_sites_tbi + // ) + // ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table + + // // Gather QC reports + // ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) + // ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions.first().ifEmpty(null)) + + // ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table, by: [0]) + // ch_bam_recalibrated_qc = Channel.empty() + + // ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() + // ch_bam_applybqsr.combine(ch_interval_list_applybqsr) + // .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} + // .set{ch_applybqsr_bam_bai_interval} + + // // + // // MODULE: ApplyBaseRecalibrator from GATK4 + // // Recalibrates the base qualities of the input reads based on the recalibration table produced by the GATK BaseRecalibrator tool. + // // + // RECALIBRATE( + // params.skip_multiqc, + // ch_applybqsr_bam_bai_interval, + // PREPARE_GENOME.out.dict, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.fasta + // ) + + // ch_bam_variant_calling = RECALIBRATE.out.bam + // ch_bam_recalibrated_qc = RECALIBRATE.out.qc + + // // Gather QC reports + // ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) + // ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) + // } else { + // ch_bam_variant_calling = ch_splitncigar_bam_bai + // } + + // interval_flag = params.no_intervals + // // Run haplotyper even in the absence of dbSNP files + // if (!params.dbsnp){ + // ch_dbsnp = [] + // ch_dbsnp_tbi = [] + // } + + // ch_haplotypecaller_vcf = Channel.empty() + // ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) + // .map{ meta, bam, bai, interval_list -> + // new_meta = meta.clone() + // new_meta.id = meta.id + "_" + interval_list.baseName + // new_meta.sample = meta.id + // [new_meta, bam, bai, interval_list] + // } + + // // + // // MODULE: HaplotypeCaller from GATK4 + // // Calls germline SNPs and indels via local re-assembly of haplotypes. + // // + + // GATK4_HAPLOTYPECALLER( + // ch_haplotypecaller_interval_bam, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.dict, + // ch_dbsnp, + // ch_dbsnp_tbi + // ) + + + // ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf + // .map{ meta, vcf -> + // meta.id = meta.sample + // [meta, vcf]} + // .groupTuple() + + // ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) + + // // + // // MODULE: MergeVCFS from GATK4 + // // Merge multiple VCF files into one VCF + // // + // GATK4_MERGEVCFS(ch_haplotypecaller_raw, PREPARE_GENOME.out.dict) + // ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf + // ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) + + // if (params.generate_gvcf){ + // GATK4_HAPLOTYPECALLERGVCF( + // ch_haplotypecaller_interval_bam, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.dict, + // ch_dbsnp, + // ch_dbsnp_tbi + // ) + + // ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf + // .map{ meta, vcf -> + // meta.id = meta.sample + // [meta, vcf]} + // .groupTuple() + + // ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) + // // + // // MODULE: IndexFeatureFile from GATK4 + // // Index the gVCF files + // // + // GATK4_INDEXFEATUREFILE(GATK4_HAPLOTYPECALLERGVCF.out.vcf) + + // ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index + // .map{ meta, idx -> + // meta.id = meta.sample + // [meta, idx]} + // .groupTuple() + + // ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) + + // // + // // MODULE: CombineGVCFS from GATK4 + // // Merge multiple GVCF files into one GVCF + // // + + // //ch_haplotypecallergvcf_raw_tbi = ch_haplotypecallergvcf_raw + // // .join(ch_haplotypecallergvcf_raw_index, by: [0], remainder: true) + // // .map{meta, vcf, tbi -> + // // [meta, vcf, tbi] + // // } + + + + // GATK4_COMBINEGVCFS( + // ch_haplotypecallergvcf_raw, + // ch_haplotypecallergvcf_raw_index, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.dict + // ) + // ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf + // ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) + + // // + // // MODULE: Index the VCF using TABIX + // // + // TABIXGVCF(ch_haplotypecaller_gvcf) + + // ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf + // .join(TABIXGVCF.out.tbi, by: [0], remainder: true) + // .join(TABIXGVCF.out.csi, by: [0], remainder: true) + // .map{meta, vcf, tbi, csi -> + // if (tbi) [meta, vcf, tbi] + // else [meta, vcf, csi] + // } + + // ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) + + // } + + // // + // // MODULE: Index the VCF using TABIX + // // + // TABIX(ch_haplotypecaller_vcf) + + // ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf + // .join(TABIX.out.tbi, by: [0], remainder: true) + // .join(TABIX.out.csi, by: [0], remainder: true) + // .map{meta, vcf, tbi, csi -> + // if (tbi) [meta, vcf, tbi] + // else [meta, vcf, csi] + // } + + // ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) + // ch_final_vcf = ch_haplotypecaller_vcf + + // // + // // MODULE: VariantFiltration from GATK4 + // // Filter variant calls based on certain criteria + // // + // if (!params.skip_variantfiltration && !params.bam_csi_index ) { + + // GATK4_VARIANTFILTRATION( + // ch_haplotypecaller_vcf_tbi, + // PREPARE_GENOME.out.fasta, + // PREPARE_GENOME.out.fai, + // PREPARE_GENOME.out.dict + // ) + + // ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf + // ch_final_vcf = ch_filtered_vcf + // ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) + // } + + // // + // // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. + // // + // if ((!params.skip_variantannotation) &&(params.annotate_tools) &&(params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { + // ANNOTATE( + // ch_final_vcf, + // params.annotate_tools, + // ch_snpeff_db, + // ch_snpeff_cache, + // ch_vep_genome, + // ch_vep_species, + // ch_vep_cache_version, + // ch_vep_cache) + + // // Gather QC reports + // ch_reports = ch_reports.mix(ANNOTATE.out.reports) + // ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) + // } + + // } + + // ch_version_yaml = Channel.empty() + // CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) + // ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect() + + // // + // // MODULE: MultiQC + // // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report + // // + // if (!params.skip_multiqc){ + // workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) + // ch_workflow_summary = Channel.value(workflow_summary) + + // methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) + // ch_methods_description = Channel.value(methods_description) + + // ch_multiqc_files = Channel.empty() + // ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + // ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) + // ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) + // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + // ch_multiqc_files = ch_multiqc_files.mix(ch_version_yaml) + // ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) + // ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect()) + // ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_config) + // ch_multiqc_files = ch_multiqc_files.mix(ch_rnavar_logo) + + // MULTIQC( + // ch_multiqc_files.collect(), + // ch_multiqc_config.toList(), + // ch_multiqc_custom_config.toList(), + // ch_multiqc_logo.toList() + // ) + // multiqc_report = MULTIQC.out.report.toList() + // } } /* From b3427dfc391c3040c3fbda1baa8e4d999975890f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 19 Sep 2023 16:45:57 +0200 Subject: [PATCH 024/275] improve prepare_genome subworkflow --- modules/local/gtf2bed/main.nf | 3 +- subworkflows/local/prepare_genome/main.nf | 131 ++++------------------ workflows/rnavar.nf | 18 +-- 3 files changed, 35 insertions(+), 117 deletions(-) diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf index b0c7e42a..b18a63d4 100755 --- a/modules/local/gtf2bed/main.nf +++ b/modules/local/gtf2bed/main.nf @@ -8,8 +8,9 @@ process GTF2BED { 'biocontainers/r-base:3.5.0'}" input: - path gtf + tuple val(meta), path(gtf) val feature_type + output: path '*.bed' , emit: bed path "versions.yml", emit: versions diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 598dc4e4..d3cde79e 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -1,5 +1,5 @@ // -// Uncompress and prepare reference genome files +// Prepare reference genome files // include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' @@ -7,130 +7,43 @@ include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtoo include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' include { GFFREAD } from '../../../modules/nf-core/gffread/main' include { GTF2BED } from '../../../modules/local/gtf2bed' -include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' -include { UNTAR as UNTAR_STAR_INDEX } from '../../../modules/nf-core/untar/main' workflow PREPARE_GENOME { take: - fasta // file: /path/to/genome.fasta - // gtf // file: /path/to/genome.gtf - // gff // file: /path/to/genome.gff - // exon_bed // file: /path/to/gene.bed + ch_exon_bed // file: /path/to/gene.bed + ch_fasta // file: /path/to/genome.fasta + ch_gff // file: /path/to/genome.gff + ch_gtf // file: /path/to/genome.gtf + feature_type // prepare_tool_indices - // feature_type main: ch_versions = Channel.empty() - ch_fasta = fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } - - // - // Uncompress genome fasta file if required - // - // if (fasta.endsWith('.gz')) { - // ch_fasta = GUNZIP_FASTA([[:], fasta]).gunzip.map{ meta, fasta -> fasta } - // ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) - // } else { - // ch_fasta = Channel.value(file(fasta)) - // } - - // - // Uncompress GTF annotation file or create from GFF3 if required - // - // if (gtf) { - // if (gtf.endsWith('.gz')) { - // ch_gtf = GUNZIP_GTF([[:], gtf]).gunzip.map{ meta, gtf -> gtf } - // ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) - // } else ch_gtf = Channel.value(file(gtf)) - // } else if (gff) { - // if (gff.endsWith('.gz')) { - // ch_gff = GUNZIP_GFF([[:], gff]).gunzip.map{ meta, gff -> gff } - // ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions) - // } else ch_gff = Channel.value(file(gff)) - // ch_gtf = GFFREAD(ch_gff).gtf - // ch_versions = ch_versions.mix(GFFREAD.out.versions) - // } - - // - // Uncompress exon BED annotation file or create from GTF if required - // - // if (exon_bed) { - // if (exon_bed.endsWith('.gz')) { - // exonGENE_BED( - // Channel.fromPath(exon_bed).map{ it -> [[id:it[0].baseName], it] } - // ) - // ch_exon_bed = GUNZIP_GENE_BED.out.gunzip.map{ meta, bed -> [bed] }.collect() - // ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions) - // } else { - // ch_exon_bed = Channel.fromPath(exon_bed).collect() - // } - // } else { - // ch_exon_bed = GTF2BED( ch_gtf , feature_type).bed.collect() - // ch_versions = ch_versions.mix(GTF2BED.out.versions) - // } - - //ch_exon_bed.view() - //ch_exon_bed.map{ it -> [[id:'exome'], it] } - //ch_exon_bed.view() - // Bedtools sort - // ch_bedtools_sort = BEDTOOLS_SORT(ch_exon_bed.map{ it -> [[id:'exome'], it] }, 'sorted').sorted.collect() - // ch_versions = ch_versions.mix(BEDTOOLS_SORT.out.versions) - - - // // Bedtools merge - // ch_bedtools_merge = BEDTOOLS_MERGE(ch_bedtools_sort).bed - // ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions) - - - // Index the genome fasta + GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) + GFFREAD(ch_gff) SAMTOOLS_FAIDX(ch_fasta, [['id':null], []]) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + ch_gtf = ch_gtf.mix(GFFREAD.out.gtf) - // Create dictionary file for the genome fasta - // ch_fasta_dict = Channel.empty() - // if (params.dict) ch_fasta_dict = Channel.fromPath(params.dict).collect() - // else ch_fasta_dict = GATK4_CREATESEQUENCEDICTIONARY(ch_fasta).dict - - // - // Uncompress STAR index or generate from scratch if required - // - // ch_star_index = Channel.empty() - // if ('star' in prepare_tool_indices) { - // if (params.star_index) { - // if (params.star_index.endsWith('.tar.gz')) { - // UNTAR_STAR_INDEX( - // Channel.fromPath(params.star_index).map{ it -> [[id:it[0].baseName], it] } - // ) - // ch_star_index = UNTAR_STAR_INDEX.out.untar.map{ meta, star_index -> [star_index] }.collect() - // ch_versions = ch_versions.mix(UNTAR_STAR_INDEX.out.versions) - // } else { - // ch_star_index = Channel.fromPath(params.star_index).collect() - // } - // } - // else { - // STAR_GENOMEGENERATE( - // ch_fasta,ch_gtf - // ) - // .index - // .set { ch_star_index } - // ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) - // } - // } + GTF2BED(ch_gtf, feature_type) + STAR_GENOMEGENERATE(ch_fasta, ch_gtf) + ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) + ch_versions = ch_versions.mix(GFFREAD.out.versions) + ch_versions = ch_versions.mix(GTF2BED.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) emit: - // fasta = ch_fasta // path: genome.fasta - fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai dict = ch_fasta_dict // path: genome.fasta.dict - // gtf = ch_gtf // path: genome.gtf - // exon_bed = ch_exon_bed // path: exon.bed + dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict + exon_bed = GTF2BED.out.bed.collect() // path: exon.bed + fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai + gtf = ch_gtf // path: genome.gtf + star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ + versions = ch_versions // channel: [ versions.yml ] // bedtools_sort = ch_bedtools_sort // path: sort.bed // bedtools_merge = ch_bedtools_merge // path: merge.bed - // star_index = ch_star_index // path: star/index/ - versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 64264b44..b2796ae2 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -117,7 +117,10 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/ // Initialize file channels based on params, defined in the params.genomes[params.genome] scope -ch_fasta = params.fasta ? Channel.fromPath(params.fasta).first() : Channel.empty() +ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed) : Channel.empty() +ch_fasta = params.fasta ? Channel.fromPath(params.fasta).map{ fasta -> [ [ id:fasta.baseName ], fasta ] }.first() : Channel.empty() +ch_gff = params.gff ? Channel.fromPath(params.gff).first() : Channel.empty() +ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.first() : Channel.empty() /* ======================================================================================== @@ -129,20 +132,21 @@ workflow RNAVAR { // To gather all QC reports for MultiQC ch_reports = Channel.empty() + // To gather used softwares versions for MultiQC ch_versions = Channel.empty() // - // SUBWORKFLOW: Uncompress and prepare reference genome files + // Prepare reference genome files // PREPARE_GENOME( - ch_fasta - // params.gtf, - // params.gff, - // params.gene_bed, + ch_exon_bed, + ch_fasta, + ch_gff, + ch_gtf, // params.aligner, - // params.feature_type + params.feature_type ) // ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) From 3663ecbff77e440f39d39c45e0a63e20b30294c5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 11:45:11 +0200 Subject: [PATCH 025/275] use samplesheet from nf-validation --- assets/schema_input.json | 27 +++++++--- conf/modules.config | 8 --- nextflow_schema.json | 9 ++-- subworkflows/local/prepare_genome/main.nf | 1 - workflows/rnavar.nf | 66 +++++++++-------------- 5 files changed, 50 insertions(+), 61 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 6fd501da..dc7fcba6 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,15 +10,27 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample ID must be provided and cannot contain spaces", + "meta": ["sample"] }, "fastq_1": { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" + "errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+\\.f(ast)?q\\.gz$" + }, + { + "type": "string", + "maxLength": 0 + } + ], + "format": "file-path", + "exists": true }, "fastq_2": { "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "dependentRequired": ["fastq_1"], "anyOf": [ { "type": "string", @@ -28,12 +40,15 @@ "type": "string", "maxLength": 0 } - ] + ], + "format": "file-path", + "exists": true }, "strandedness": { "type": "string", "errorMessage": "Strandedness must be provided and be one of 'forward', 'reverse' or 'unstranded'", - "enum": ["forward", "reverse", "unstranded"] + "enum": ["forward", "reverse", "unstranded"], + "meta": ["strandedness"] } }, "required": ["sample", "fastq_1", "strandedness"] diff --git a/conf/modules.config b/conf/modules.config index f05b3322..d5e4f84e 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: 'NFCORE_RNAVAR:RNAVAR:INPUT_CHECK:SAMPLESHEET_CHECK' { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { publishDir = [ path: { "${params.outdir}/pipeline_info" }, diff --git a/nextflow_schema.json b/nextflow_schema.json index 7fb6d183..7ce1ee3d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -13,14 +13,15 @@ "required": ["input", "outdir"], "properties": { "input": { + "description": "Path to comma-separated file containing information about the samples in the experiment.", + "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory. If no input should be supplied, i.e. when --step is supplied or --build_from_index, then set --input false", + "fa_icon": "fas fa-file-csv", + "schema": "assets/schema_input.json", "type": "string", "format": "file-path", "exists": true, "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", - "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/rnavar/usage#samplesheet-input).", - "fa_icon": "fas fa-file-csv" + "pattern": "^\\S+\\.csv$" }, "outdir": { "type": "string", diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index d3cde79e..d20d8fe6 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -17,7 +17,6 @@ workflow PREPARE_GENOME { ch_gff // file: /path/to/genome.gff ch_gtf // file: /path/to/genome.gtf feature_type - // prepare_tool_indices main: ch_versions = Channel.empty() diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index b2796ae2..94c2cff8 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation' def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' @@ -116,6 +116,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/ // def multiqc_report = [] + // Initialize file channels based on params, defined in the params.genomes[params.genome] scope ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed) : Channel.empty() ch_fasta = params.fasta ? Channel.fromPath(params.fasta).map{ fasta -> [ [ id:fasta.baseName ], fasta ] }.first() : Channel.empty() @@ -129,71 +130,52 @@ ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id: */ workflow RNAVAR { - // To gather all QC reports for MultiQC ch_reports = Channel.empty() // To gather used softwares versions for MultiQC ch_versions = Channel.empty() - // + ch_from_samplesheet = Channel.empty() + + if (params.input) ch_from_samplesheet = Channel.fromSamplesheet("input") + + ch_fastq = ch_from_samplesheet.map{ meta, fastq_1, fastq_2 -> + if (fastq_2) return [ meta + [id: meta.sample], [ fastq_1, fastq_2 ] ] + else return [ meta + [id: meta.sample], [ fastq_1 ] ] + }.groupTuple() + .branch { meta, fastq -> + single : fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple: fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + // Prepare reference genome files - // PREPARE_GENOME( ch_exon_bed, ch_fasta, ch_gff, ch_gtf, - // params.aligner, params.feature_type ) // ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) // ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) - // // - // // SUBWORKFLOW: Read in samplesheet, validate and stage input files - // // - // INPUT_CHECK(file(params.input)) - // .reads - // .map { - // meta, fastq -> - // def meta_clone = meta.clone() - // meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') - // [ meta_clone, fastq ] - // } - // .groupTuple(by: [0]) - // .branch { - // meta, fastq -> - // single : fastq.size() == 1 - // return [ meta, fastq.flatten() ] - // multiple: fastq.size() > 1 - // return [ meta, fastq.flatten() ] - // } - // .set { ch_fastq } + // // MODULE: Concatenate FastQ files from same sample if required - // ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // // ! There is currently no tooling to help you write a sample sheet schema + CAT_FASTQ(ch_fastq.multiple) - // // - // // MODULE: Concatenate FastQ files from same sample if required - // // - // CAT_FASTQ(ch_fastq.multiple) - // .reads - // .mix(ch_fastq.single) - // .set { ch_cat_fastq } + ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_fastq.single) - // ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) - // // // // MODULE: Generate QC summary using FastQC - // // - // FASTQC(ch_cat_fastq) - // ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - // ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + FASTQC(ch_cat_fastq) + ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // // // // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList From 4e44c19ba915d4f0f11cb19aeee165d389a14ea1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 11:59:35 +0200 Subject: [PATCH 026/275] one more step --- subworkflows/local/prepare_genome/main.nf | 13 ++++++------- workflows/rnavar.nf | 18 +++++++++++------- 2 files changed, 17 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index d20d8fe6..efb649ae 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -12,7 +12,6 @@ include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/g workflow PREPARE_GENOME { take: - ch_exon_bed // file: /path/to/gene.bed ch_fasta // file: /path/to/genome.fasta ch_gff // file: /path/to/genome.gff ch_gtf // file: /path/to/genome.gtf @@ -37,12 +36,12 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) emit: - dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict - exon_bed = GTF2BED.out.bed.collect() // path: exon.bed - fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai - gtf = ch_gtf // path: genome.gtf - star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ - versions = ch_versions // channel: [ versions.yml ] + dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict + exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed + fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai + gtf = ch_gtf // path: genome.gtf + star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ + versions = ch_versions // channel: [ versions.yml ] // bedtools_sort = ch_bedtools_sort // path: sort.bed // bedtools_merge = ch_bedtools_merge // path: merge.bed } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 94c2cff8..ab429c34 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -154,15 +154,19 @@ workflow RNAVAR { // Prepare reference genome files PREPARE_GENOME( - ch_exon_bed, ch_fasta, ch_gff, ch_gtf, params.feature_type ) + ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) - // ch_genome_bed = Channel.from([id:'genome.bed']).combine(PREPARE_GENOME.out.exon_bed) - // ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + ch_genome_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() + : PREPARE_GENOME.out.exon_bed + ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() + : PREPARE_GENOME.out.dict + ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() + : PREPARE_GENOME.out.fasta_fai // // MODULE: Concatenate FastQ files from same sample if required @@ -180,10 +184,10 @@ workflow RNAVAR { // // // // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList // // - // ch_interval_list = Channel.empty() - // GATK4_BEDTOINTERVALLIST(ch_genome_bed, PREPARE_GENOME.out.dict) - // ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list - // ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) + + GATK4_BEDTOINTERVALLIST(ch_genome_bed, ch_dict) + ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list + ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) // // // // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools From 65b3343a0554e06b617444222d428f3f5a65f219 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 12:23:00 +0200 Subject: [PATCH 027/275] markduplicates --- subworkflows/local/bam_markduplicates/main.nf | 8 +- subworkflows/local/bam_stats_samtools/main.nf | 16 +- workflows/rnavar.nf | 169 +++++++++--------- 3 files changed, 92 insertions(+), 101 deletions(-) diff --git a/subworkflows/local/bam_markduplicates/main.nf b/subworkflows/local/bam_markduplicates/main.nf index 6ee53041..fac00488 100644 --- a/subworkflows/local/bam_markduplicates/main.nf +++ b/subworkflows/local/bam_markduplicates/main.nf @@ -18,22 +18,22 @@ workflow BAM_MARKDUPLICATES { versions = Channel.empty() reports = Channel.empty() - // RUN MARKDUPLICATES + // RUN MARKUPDUPLICATES GATK4_MARKDUPLICATES(bam, fasta, fasta_fai) // Join with the crai file cram = GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true) // QC on CRAM - CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined) + // CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined) // Gather all reports generated reports = reports.mix(GATK4_MARKDUPLICATES.out.metrics) - reports = reports.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.reports) + // reports = reports.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.reports) // Gather versions of all tools used versions = versions.mix(GATK4_MARKDUPLICATES.out.versions) - versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions) + // versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions) emit: cram diff --git a/subworkflows/local/bam_stats_samtools/main.nf b/subworkflows/local/bam_stats_samtools/main.nf index e94c1bd1..94bb2037 100644 --- a/subworkflows/local/bam_stats_samtools/main.nf +++ b/subworkflows/local/bam_stats_samtools/main.nf @@ -13,21 +13,13 @@ workflow BAM_STATS_SAMTOOLS { main: ch_versions = Channel.empty() - SAMTOOLS_STATS ( - ch_bam_bai, - [] - ) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) + SAMTOOLS_FLAGSTAT(ch_bam_bai) + SAMTOOLS_IDXSTATS(ch_bam_bai) + SAMTOOLS_STATS(ch_bam_bai, [[],[]]) - SAMTOOLS_FLAGSTAT ( - ch_bam_bai - ) ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first()) - - SAMTOOLS_IDXSTATS ( - ch_bam_bai - ) ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first()) + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) emit: stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ] diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index ab429c34..7f84af92 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -95,8 +95,8 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/ // // Check STAR alignment parameters // def prepareToolIndices = params.aligner -// def seq_platform = params.seq_platform ?: [] -// def seq_center = params.seq_center ?: [] +def seq_platform = params.seq_platform ?: [] +def seq_center = params.seq_center ?: [] // // Initialize file channels based on params // ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() @@ -164,11 +164,11 @@ workflow RNAVAR { ch_genome_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() - : PREPARE_GENOME.out.dict + : ch_dict ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : PREPARE_GENOME.out.fasta_fai - // // MODULE: Concatenate FastQ files from same sample if required + // MODULE: Concatenate FastQ files from same sample if required CAT_FASTQ(ch_fastq.multiple) @@ -176,74 +176,73 @@ workflow RNAVAR { ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) - // // MODULE: Generate QC summary using FastQC + // MODULE: Generate QC summary using FastQC FASTQC(ch_cat_fastq) ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - // // - // // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList - // // + // + // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList + // GATK4_BEDTOINTERVALLIST(ch_genome_bed, ch_dict) ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) - // // - // // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools - // // - // ch_interval_list_split = Channel.empty() - // if (!params.skip_intervallisttools) { - // GATK4_INTERVALLISTTOOLS(ch_interval_list) - // ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten() - // } - // else ch_interval_list_split = ch_interval_list - - // // - // // SUBWORKFLOW: Perform read alignment using STAR aligner - // // - // ch_genome_bam = Channel.empty() - // ch_genome_bam_index = Channel.empty() - // ch_samtools_stats = Channel.empty() - // ch_samtools_flagstat = Channel.empty() - // ch_samtools_idxstats = Channel.empty() - // ch_star_multiqc = Channel.empty() - // ch_aligner_pca_multiqc = Channel.empty() - // ch_aligner_clustering_multiqc = Channel.empty() - - // if (params.aligner == 'star') { - // ALIGN_STAR( - // ch_cat_fastq, - // PREPARE_GENOME.out.star_index, - // PREPARE_GENOME.out.gtf, - // params.star_ignore_sjdbgtf, - // seq_platform, - // seq_center - // ) - // ch_genome_bam = ALIGN_STAR.out.bam - // ch_genome_bam_index = ALIGN_STAR.out.bai - // ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript - - // // Gather QC reports - // ch_reports = ch_reports.mix(ALIGN_STAR.out.stats.collect{it[1]}.ifEmpty([])) - // ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) - // ch_versions = ch_versions.mix(ALIGN_STAR.out.versions.first().ifEmpty(null)) - - // // - // // SUBWORKFLOW: Mark duplicates with GATK4 - // // - // BAM_MARKDUPLICATES( - // ch_genome_bam, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // []) - - // ch_genome_bam = BAM_MARKDUPLICATES.out.bam_bai - - // //Gather QC reports - // ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.stats.collect{it[1]}.ifEmpty([])) - // ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.metrics.collect{it[1]}.ifEmpty([])) - // ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions.first().ifEmpty(null)) + // + // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools + // + ch_interval_list_split = Channel.empty() + if (!params.skip_intervallisttools) { + GATK4_INTERVALLISTTOOLS(ch_interval_list) + ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten() + } + else ch_interval_list_split = ch_interval_list + + // + // SUBWORKFLOW: Perform read alignment using STAR aligner + // + ch_genome_bam = Channel.empty() + ch_genome_bam_index = Channel.empty() + ch_samtools_stats = Channel.empty() + ch_samtools_flagstat = Channel.empty() + ch_samtools_idxstats = Channel.empty() + ch_star_multiqc = Channel.empty() + ch_aligner_pca_multiqc = Channel.empty() + ch_aligner_clustering_multiqc = Channel.empty() + + if (params.aligner == 'star') { + ALIGN_STAR( + ch_cat_fastq, + PREPARE_GENOME.out.star_index, + PREPARE_GENOME.out.gtf, + params.star_ignore_sjdbgtf, + seq_platform, + seq_center + ) + ch_genome_bam = ALIGN_STAR.out.bam + ch_genome_bam_index = ALIGN_STAR.out.bai + ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript + + // Gather QC reports + ch_reports = ch_reports.mix(ALIGN_STAR.out.stats.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) + ch_versions = ch_versions.mix(ALIGN_STAR.out.versions.first().ifEmpty(null)) + + // + // SUBWORKFLOW: Mark duplicates with GATK4 + // + BAM_MARKDUPLICATES( + ch_genome_bam, + ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta_fai, + []) + + ch_genome_bam = BAM_MARKDUPLICATES.out.cram + + //Gather QC reports + ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.reports.collect{it[1]}.ifEmpty([])) + ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions.first().ifEmpty(null)) // // // // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals @@ -252,9 +251,9 @@ workflow RNAVAR { // ch_splitncigar_bam_bai = Channel.empty() // SPLITNCIGAR( // ch_genome_bam, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // PREPARE_GENOME.out.dict, + // ch_fasta, + // ch_fasta_fai, + // ch_dict, // ch_interval_list_split // ) // ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai @@ -279,9 +278,9 @@ workflow RNAVAR { // GATK4_BASERECALIBRATOR( // ch_splitncigar_bam_bai_interval, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // PREPARE_GENOME.out.dict, + // ch_fasta, + // ch_fasta_fai, + // ch_dict, // ch_known_sites, // ch_known_sites_tbi // ) @@ -306,8 +305,8 @@ workflow RNAVAR { // RECALIBRATE( // params.skip_multiqc, // ch_applybqsr_bam_bai_interval, - // PREPARE_GENOME.out.dict, - // PREPARE_GENOME.out.fai, + // ch_dict, + // ch_fasta_fai, // PREPARE_GENOME.out.fasta // ) @@ -319,7 +318,7 @@ workflow RNAVAR { // ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) // } else { // ch_bam_variant_calling = ch_splitncigar_bam_bai - // } + } // interval_flag = params.no_intervals // // Run haplotyper even in the absence of dbSNP files @@ -344,9 +343,9 @@ workflow RNAVAR { // GATK4_HAPLOTYPECALLER( // ch_haplotypecaller_interval_bam, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // PREPARE_GENOME.out.dict, + // ch_fasta, + // ch_fasta_fai, + // ch_dict, // ch_dbsnp, // ch_dbsnp_tbi // ) @@ -364,16 +363,16 @@ workflow RNAVAR { // // MODULE: MergeVCFS from GATK4 // // Merge multiple VCF files into one VCF // // - // GATK4_MERGEVCFS(ch_haplotypecaller_raw, PREPARE_GENOME.out.dict) + // GATK4_MERGEVCFS(ch_haplotypecaller_raw, ch_dict) // ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf // ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) // if (params.generate_gvcf){ // GATK4_HAPLOTYPECALLERGVCF( // ch_haplotypecaller_interval_bam, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // PREPARE_GENOME.out.dict, + // ch_fasta, + // ch_fasta_fai, + // ch_dict, // ch_dbsnp, // ch_dbsnp_tbi // ) @@ -415,9 +414,9 @@ workflow RNAVAR { // GATK4_COMBINEGVCFS( // ch_haplotypecallergvcf_raw, // ch_haplotypecallergvcf_raw_index, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // PREPARE_GENOME.out.dict + // ch_fasta, + // ch_fasta_fai, + // ch_dict // ) // ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf // ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) @@ -463,9 +462,9 @@ workflow RNAVAR { // GATK4_VARIANTFILTRATION( // ch_haplotypecaller_vcf_tbi, - // PREPARE_GENOME.out.fasta, - // PREPARE_GENOME.out.fai, - // PREPARE_GENOME.out.dict + // ch_fasta, + // ch_fasta_fai, + // ch_dict // ) // ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf From fc9cbc2b45abe22ce4c21465b94cbff7a895f830 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 13:14:47 +0200 Subject: [PATCH 028/275] splitncigar --- conf/modules.config | 8 ++-- subworkflows/local/align_star/main.nf | 5 +-- subworkflows/local/bam_markduplicates/main.nf | 38 ++++++++++------- subworkflows/local/bam_sort_samtools/main.nf | 4 +- subworkflows/local/bam_stats_samtools/main.nf | 5 +-- subworkflows/local/splitncigar/main.nf | 41 +++++++++---------- workflows/rnavar.nf | 32 +++++++-------- 7 files changed, 65 insertions(+), 68 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index d5e4f84e..b536b83f 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -204,19 +204,19 @@ process { publishDir = [ enabled: false ] } - withName: '.*:MARKDUPLICATES:GATK4_MARKDUPLICATES' { + withName: 'GATK4_MARKDUPLICATES' { ext.args = [ '--ASSUME_SORTED true', '--VALIDATION_STRINGENCY LENIENT', params.remove_duplicates ? '--REMOVE_DUPLICATES true' : '' ].join(' ').trim() - ext.prefix = {"${meta.id}.markdup.sorted"} + ext.prefix = {"${meta.id}.md.bam"} publishDir = [ [ path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, enabled: true, - pattern: "*.{bam}" + pattern: "*.{bam,bai}" ], [ path: { "${params.outdir}/reports/stats/${meta.id}" }, @@ -229,7 +229,7 @@ process { withName: '.*:MARKDUPLICATES:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' - ext.prefix = {"${meta.id}.markdup.sorted"} + ext.prefix = {"${meta.id}.md"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf index 64ec6526..4949686f 100644 --- a/subworkflows/local/align_star/main.nf +++ b/subworkflows/local/align_star/main.nf @@ -52,10 +52,7 @@ workflow ALIGN_STAR { bam = BAM_SORT_SAMTOOLS.out.bam // channel: [ val(meta), [ bam ] ] bai = BAM_SORT_SAMTOOLS.out.bai // channel: [ val(meta), [ bai ] ] csi = BAM_SORT_SAMTOOLS.out.csi // channel: [ val(meta), [ csi ] ] - stats = BAM_SORT_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = BAM_SORT_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = BAM_SORT_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - + reports = BAM_SORT_SAMTOOLS.out.reports versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/bam_markduplicates/main.nf b/subworkflows/local/bam_markduplicates/main.nf index fac00488..37d901b9 100644 --- a/subworkflows/local/bam_markduplicates/main.nf +++ b/subworkflows/local/bam_markduplicates/main.nf @@ -4,8 +4,9 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main' -include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main' +include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' +include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' workflow BAM_MARKDUPLICATES { take: @@ -15,29 +16,36 @@ workflow BAM_MARKDUPLICATES { intervals_bed_combined // channel: [optional] [ intervals_bed ] main: - versions = Channel.empty() - reports = Channel.empty() + ch_versions = Channel.empty() + ch_reports = Channel.empty() // RUN MARKUPDUPLICATES GATK4_MARKDUPLICATES(bam, fasta, fasta_fai) - // Join with the crai file - cram = GATK4_MARKDUPLICATES.out.cram.join(GATK4_MARKDUPLICATES.out.crai, failOnDuplicate: true, failOnMismatch: true) + SAMTOOLS_INDEX(GATK4_MARKDUPLICATES.out.bam) - // QC on CRAM - // CRAM_QC_MOSDEPTH_SAMTOOLS(cram, fasta, intervals_bed_combined) + ch_bam_index = GATK4_MARKDUPLICATES.out.bam + .join(SAMTOOLS_INDEX.out.bai, remainder: true) + .join(SAMTOOLS_INDEX.out.csi, remainder: true) + .map{meta, bam, bai, csi -> + if (bai) [meta, bam, bai] + else [meta, bam, csi] + } + + BAM_STATS_SAMTOOLS(ch_bam_index) // Gather all reports generated - reports = reports.mix(GATK4_MARKDUPLICATES.out.metrics) - // reports = reports.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.reports) + ch_reports = ch_reports.mix(GATK4_MARKDUPLICATES.out.metrics) + ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.reports) // Gather versions of all tools used - versions = versions.mix(GATK4_MARKDUPLICATES.out.versions) - // versions = versions.mix(CRAM_QC_MOSDEPTH_SAMTOOLS.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_MARKDUPLICATES.out.versions) + ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: - cram - reports + bam = ch_bam_index + reports = ch_reports - versions // channel: [ versions.yml ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/bam_sort_samtools/main.nf b/subworkflows/local/bam_sort_samtools/main.nf index 9b4f6e31..2680e618 100644 --- a/subworkflows/local/bam_sort_samtools/main.nf +++ b/subworkflows/local/bam_sort_samtools/main.nf @@ -47,8 +47,6 @@ workflow BAM_SORT_SAMTOOLS { bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] - stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + reports = BAM_STATS_SAMTOOLS.out.reports versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/bam_stats_samtools/main.nf b/subworkflows/local/bam_stats_samtools/main.nf index 94bb2037..6b664686 100644 --- a/subworkflows/local/bam_stats_samtools/main.nf +++ b/subworkflows/local/bam_stats_samtools/main.nf @@ -22,9 +22,6 @@ workflow BAM_STATS_SAMTOOLS { ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) emit: - stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), [ stats ] ] - flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), [ flagstat ] ] - idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), [ idxstats ] ] - + reports = SAMTOOLS_STATS.out.stats.mix(SAMTOOLS_FLAGSTAT.out.flagstat, SAMTOOLS_IDXSTATS.out.idxstats) versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 9348a098..cbc30618 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -9,52 +9,49 @@ include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index workflow SPLITNCIGAR { take: bam // channel: [ val(meta), [ bam ], [bai] ] - fasta // channel: [ fasta ] - fasta_fai // channel: [ fai ] - fasta_dict // channel: [ dict ] + ch_fasta // channel: [ fasta ] + ch_fai // channel: [ fai ] + ch_dict // channel: [ dict ] intervals // channel: [ interval_list] main: - ch_versions = Channel.empty() - bam.combine(intervals) - .map{ meta, bam, bai, intervals -> + bam_interval = bam.combine(intervals).map{ meta, bam, bai, intervals -> new_meta = meta.clone() new_meta.id = meta.id + "_" + intervals.baseName new_meta.sample = meta.id [new_meta, bam, bai, intervals] - }.set{bam_interval} + } - GATK4_SPLITNCIGARREADS ( + GATK4_SPLITNCIGARREADS( bam_interval, - fasta, - fasta_fai, - fasta_dict + ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fai, + ch_dict.map{ meta, dict -> [dict] }, ) bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions.first()) - bam_splitncigar + bam_splitncigar_interval = bam_splitncigar .map{ meta, bam -> new_meta = meta.clone() new_meta.id = meta.sample [new_meta, bam] - }.groupTuple().set{bam_splitncigar_interval} + }.groupTuple() + + SAMTOOLS_MERGE(bam_splitncigar_interval, + ch_fasta, + ch_fai.map{ fai -> [[id:fai.baseName], fai] }) - SAMTOOLS_MERGE ( - bam_splitncigar_interval, - fasta - ) splitncigar_bam = SAMTOOLS_MERGE.out.bam ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions.first()) - SAMTOOLS_INDEX ( - splitncigar_bam - ) + SAMTOOLS_INDEX(splitncigar_bam) + splitncigar_bam_bai = splitncigar_bam - .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) - .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) + .join(SAMTOOLS_INDEX.out.bai, remainder: true) + .join(SAMTOOLS_INDEX.out.csi, remainder: true) .map{meta, bam, bai, csi -> if (bai) [meta, bam, bai] else [meta, bam, csi] diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 7f84af92..0cbbb699 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -225,7 +225,7 @@ workflow RNAVAR { ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript // Gather QC reports - ch_reports = ch_reports.mix(ALIGN_STAR.out.stats.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(ALIGN_STAR.out.reports) ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(ALIGN_STAR.out.versions.first().ifEmpty(null)) @@ -238,26 +238,26 @@ workflow RNAVAR { ch_fasta_fai, []) - ch_genome_bam = BAM_MARKDUPLICATES.out.cram + ch_genome_bam = BAM_MARKDUPLICATES.out.bam //Gather QC reports ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.reports.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions.first().ifEmpty(null)) - // // - // // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals - // // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). - // // - // ch_splitncigar_bam_bai = Channel.empty() - // SPLITNCIGAR( - // ch_genome_bam, - // ch_fasta, - // ch_fasta_fai, - // ch_dict, - // ch_interval_list_split - // ) - // ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai - // ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions.first().ifEmpty(null)) + // + // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals + // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). + // + ch_splitncigar_bam_bai = Channel.empty() + SPLITNCIGAR( + ch_genome_bam, + ch_fasta, + ch_fasta_fai, + ch_dict, + ch_interval_list_split + ) + ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai + ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions.first().ifEmpty(null)) // // // // MODULE: BaseRecalibrator from GATK4 From d8e927f01e011787a13cae89d90647a3c74b3226 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 13:24:50 +0200 Subject: [PATCH 029/275] baserecalibrator --- workflows/rnavar.nf | 61 ++++++++++++++++++++++----------------------- 1 file changed, 30 insertions(+), 31 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 0cbbb699..694357e1 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -99,10 +99,10 @@ def seq_platform = params.seq_platform ?: [] def seq_center = params.seq_center ?: [] // // Initialize file channels based on params -// ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() -// ch_dbsnp_tbi = params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : Channel.empty() -// ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.empty() -// ch_known_indels_tbi = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : Channel.empty() +ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.empty() +ch_dbsnp_tbi = params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : Channel.empty() +ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.empty() +ch_known_indels_tbi = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : Channel.empty() // // Initialize variant annotation associated channels // ch_snpeff_db = params.snpeff_db ?: Channel.empty() @@ -259,32 +259,31 @@ workflow RNAVAR { ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions.first().ifEmpty(null)) - // // - // // MODULE: BaseRecalibrator from GATK4 - // // Generates a recalibration table based on various co-variates - // // - // ch_bam_variant_calling = Channel.empty() - // if (!params.skip_baserecalibration) { - // ch_bqsr_table = Channel.empty() - // // known_sites is made by grouping both the dbsnp and the known indels ressources - // // they can either or both be optional - // ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() - // ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() - - // ch_interval_list_recalib = ch_interval_list.map{ meta, bed -> [bed] }.flatten() - // ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) - // .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] - // }.set{ch_splitncigar_bam_bai_interval} - - // GATK4_BASERECALIBRATOR( - // ch_splitncigar_bam_bai_interval, - // ch_fasta, - // ch_fasta_fai, - // ch_dict, - // ch_known_sites, - // ch_known_sites_tbi - // ) - // ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table + // + // MODULE: BaseRecalibrator from GATK4 + // Generates a recalibration table based on various co-variates + // + ch_bam_variant_calling = Channel.empty() + if (!params.skip_baserecalibration) { + ch_bqsr_table = Channel.empty() + // known_sites is made by grouping both the dbsnp and the known indels ressources + // they can either or both be optional + ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() + ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() + + ch_interval_list_recalib = ch_interval_list.map{ meta, bed -> [bed] }.flatten() + ch_splitncigar_bam_bai_interval = ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) + .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] } + + GATK4_BASERECALIBRATOR( + ch_splitncigar_bam_bai_interval, + ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta_fai, + ch_dict.map{ meta, dict -> [dict] }, + ch_known_sites, + ch_known_sites_tbi + ) + ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table // // Gather QC reports // ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) @@ -491,7 +490,7 @@ workflow RNAVAR { // ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) // } - // } + } // ch_version_yaml = Channel.empty() // CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) From 1ce336931d53c33551d23dd284bddb76e8e8cc54 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 13:32:17 +0200 Subject: [PATCH 030/275] recalibrate --- subworkflows/local/recalibrate/main.nf | 7 ++-- workflows/rnavar.nf | 46 +++++++++++++------------- 2 files changed, 26 insertions(+), 27 deletions(-) diff --git a/subworkflows/local/recalibrate/main.nf b/subworkflows/local/recalibrate/main.nf index 3b4ab0d8..518e9fb2 100644 --- a/subworkflows/local/recalibrate/main.nf +++ b/subworkflows/local/recalibrate/main.nf @@ -33,9 +33,8 @@ workflow RECALIBRATE { bam_recalibrated = APPLYBQSR.out.bam ch_versions = ch_versions.mix(APPLYBQSR.out.versions.first()) - SAMTOOLS_INDEX ( - bam_recalibrated - ) + SAMTOOLS_INDEX(bam_recalibrated) + bam_recalibrated_index = bam_recalibrated .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) @@ -49,7 +48,7 @@ workflow RECALIBRATE { samtools_stats = Channel.empty() if (!skip_samtools) { - SAMTOOLS_STATS(bam_recalibrated_index, []) + SAMTOOLS_STATS(bam_recalibrated_index, [[], []]) samtools_stats = SAMTOOLS_STATS.out.stats ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 694357e1..ce32bc22 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -285,29 +285,29 @@ workflow RNAVAR { ) ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table - // // Gather QC reports - // ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) - // ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions.first().ifEmpty(null)) - - // ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table, by: [0]) - // ch_bam_recalibrated_qc = Channel.empty() - - // ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() - // ch_bam_applybqsr.combine(ch_interval_list_applybqsr) - // .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} - // .set{ch_applybqsr_bam_bai_interval} - - // // - // // MODULE: ApplyBaseRecalibrator from GATK4 - // // Recalibrates the base qualities of the input reads based on the recalibration table produced by the GATK BaseRecalibrator tool. - // // - // RECALIBRATE( - // params.skip_multiqc, - // ch_applybqsr_bam_bai_interval, - // ch_dict, - // ch_fasta_fai, - // PREPARE_GENOME.out.fasta - // ) + // Gather QC reports + ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) + ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions.first().ifEmpty(null)) + + ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table, by: [0]) + ch_bam_recalibrated_qc = Channel.empty() + + ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() + ch_bam_applybqsr.combine(ch_interval_list_applybqsr) + .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} + .set{ch_applybqsr_bam_bai_interval} + + // + // MODULE: ApplyBaseRecalibrator from GATK4 + // Recalibrates the base qualities of the input reads based on the recalibration table produced by the GATK BaseRecalibrator tool. + // + RECALIBRATE( + params.skip_multiqc, + ch_applybqsr_bam_bai_interval, + ch_dict.map{ meta, dict -> [dict] }, + ch_fasta_fai, + ch_fasta.map{ meta, fasta -> [fasta] } + ) // ch_bam_variant_calling = RECALIBRATE.out.bam // ch_bam_recalibrated_qc = RECALIBRATE.out.qc From 6669292e6a2c5e3459946d944d90222c87828856 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 13:38:31 +0200 Subject: [PATCH 031/275] haplotypecaller --- workflows/rnavar.nf | 89 ++++++++++++++++++++++----------------------- 1 file changed, 43 insertions(+), 46 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index ce32bc22..90d1b825 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -309,62 +309,59 @@ workflow RNAVAR { ch_fasta.map{ meta, fasta -> [fasta] } ) - // ch_bam_variant_calling = RECALIBRATE.out.bam - // ch_bam_recalibrated_qc = RECALIBRATE.out.qc + ch_bam_variant_calling = RECALIBRATE.out.bam + ch_bam_recalibrated_qc = RECALIBRATE.out.qc - // // Gather QC reports - // ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) - // ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) - // } else { - // ch_bam_variant_calling = ch_splitncigar_bam_bai + // Gather QC reports + ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) + ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) + } else { + ch_bam_variant_calling = ch_splitncigar_bam_bai } - // interval_flag = params.no_intervals - // // Run haplotyper even in the absence of dbSNP files - // if (!params.dbsnp){ - // ch_dbsnp = [] - // ch_dbsnp_tbi = [] - // } + interval_flag = params.no_intervals + // Run haplotyper even in the absence of dbSNP files + if (!params.dbsnp){ + ch_dbsnp = [] + ch_dbsnp_tbi = [] + } - // ch_haplotypecaller_vcf = Channel.empty() - // ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) - // .map{ meta, bam, bai, interval_list -> - // new_meta = meta.clone() - // new_meta.id = meta.id + "_" + interval_list.baseName - // new_meta.sample = meta.id - // [new_meta, bam, bai, interval_list] - // } + ch_haplotypecaller_vcf = Channel.empty() + ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) + .map{ meta, bam, bai, interval_list -> + [meta + [id:meta.id + "_" + interval_list.baseName], bam, bai, interval_list, []] + } - // // - // // MODULE: HaplotypeCaller from GATK4 - // // Calls germline SNPs and indels via local re-assembly of haplotypes. - // // + // + // MODULE: HaplotypeCaller from GATK4 + // Calls germline SNPs and indels via local re-assembly of haplotypes. + // - // GATK4_HAPLOTYPECALLER( - // ch_haplotypecaller_interval_bam, - // ch_fasta, - // ch_fasta_fai, - // ch_dict, - // ch_dbsnp, - // ch_dbsnp_tbi - // ) + GATK4_HAPLOTYPECALLER( + ch_haplotypecaller_interval_bam, + ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta_fai, + ch_dict.map{ meta, dict -> [dict] }, + ch_dbsnp, + ch_dbsnp_tbi + ) - // ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf - // .map{ meta, vcf -> - // meta.id = meta.sample - // [meta, vcf]} - // .groupTuple() + ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf + .map{ meta, vcf -> + meta.id = meta.sample + [meta, vcf]} + .groupTuple() - // ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) - // // - // // MODULE: MergeVCFS from GATK4 - // // Merge multiple VCF files into one VCF - // // - // GATK4_MERGEVCFS(ch_haplotypecaller_raw, ch_dict) - // ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf - // ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) + // + // MODULE: MergeVCFS from GATK4 + // Merge multiple VCF files into one VCF + // + GATK4_MERGEVCFS(ch_haplotypecaller_raw, ch_dict) + ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf + ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) // if (params.generate_gvcf){ // GATK4_HAPLOTYPECALLERGVCF( From 40128c7fd876c83c84960f624a186905e78565ce Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 13:50:29 +0200 Subject: [PATCH 032/275] HAPLOTYPECALLERGVCF --- workflows/rnavar.nf | 116 +++++++++++++++++++++----------------------- 1 file changed, 54 insertions(+), 62 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 90d1b825..9d7e8aac 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -289,7 +289,7 @@ workflow RNAVAR { ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions.first().ifEmpty(null)) - ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table, by: [0]) + ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table) ch_bam_recalibrated_qc = Channel.empty() ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() @@ -363,76 +363,68 @@ workflow RNAVAR { ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) - // if (params.generate_gvcf){ - // GATK4_HAPLOTYPECALLERGVCF( - // ch_haplotypecaller_interval_bam, - // ch_fasta, - // ch_fasta_fai, - // ch_dict, - // ch_dbsnp, - // ch_dbsnp_tbi - // ) - - // ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf - // .map{ meta, vcf -> - // meta.id = meta.sample - // [meta, vcf]} - // .groupTuple() - - // ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) - // // - // // MODULE: IndexFeatureFile from GATK4 - // // Index the gVCF files - // // - // GATK4_INDEXFEATUREFILE(GATK4_HAPLOTYPECALLERGVCF.out.vcf) + if (params.generate_gvcf){ + GATK4_HAPLOTYPECALLERGVCF( + ch_haplotypecaller_interval_bam, + ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta_fai, + ch_dict.map{ meta, dict -> [dict] }, + ch_dbsnp, + ch_dbsnp_tbi + ) - // ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index - // .map{ meta, idx -> - // meta.id = meta.sample - // [meta, idx]} - // .groupTuple() + ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf + .map{ meta, vcf -> + meta.id = meta.sample + [meta, vcf] + }.groupTuple() - // ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) + // + // MODULE: IndexFeatureFile from GATK4 + // Index the gVCF files + // + GATK4_INDEXFEATUREFILE(GATK4_HAPLOTYPECALLERGVCF.out.vcf) - // // - // // MODULE: CombineGVCFS from GATK4 - // // Merge multiple GVCF files into one GVCF - // // + ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index + .map{ meta, idx -> + meta.id = meta.sample + [meta, idx] + }.groupTuple() - // //ch_haplotypecallergvcf_raw_tbi = ch_haplotypecallergvcf_raw - // // .join(ch_haplotypecallergvcf_raw_index, by: [0], remainder: true) - // // .map{meta, vcf, tbi -> - // // [meta, vcf, tbi] - // // } + ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) + // MODULE: CombineGVCFS from GATK4 + // Merge multiple GVCF files into one GVCF + ch_haplotypecallergvcf_raw_tbi = ch_haplotypecallergvcf_raw + .join(ch_haplotypecallergvcf_raw_index, remainder: true) - // GATK4_COMBINEGVCFS( - // ch_haplotypecallergvcf_raw, - // ch_haplotypecallergvcf_raw_index, - // ch_fasta, - // ch_fasta_fai, - // ch_dict - // ) - // ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf - // ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) + GATK4_COMBINEGVCFS( + ch_haplotypecallergvcf_raw_tbi, + ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta_fai, + ch_dict.map{ meta, dict -> [dict] } + ) + ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf + ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) - // // - // // MODULE: Index the VCF using TABIX - // // - // TABIXGVCF(ch_haplotypecaller_gvcf) + // + // MODULE: Index the VCF using TABIX + // + TABIXGVCF(ch_haplotypecaller_gvcf) - // ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf - // .join(TABIXGVCF.out.tbi, by: [0], remainder: true) - // .join(TABIXGVCF.out.csi, by: [0], remainder: true) - // .map{meta, vcf, tbi, csi -> - // if (tbi) [meta, vcf, tbi] - // else [meta, vcf, csi] - // } + ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf + .join(TABIXGVCF.out.tbi, remainder: true) + .join(TABIXGVCF.out.csi, remainder: true) + .map{meta, vcf, tbi, csi -> + if (tbi) [meta, vcf, tbi] + else [meta, vcf, csi] + } - // ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) - // } + } // // // // MODULE: Index the VCF using TABIX @@ -440,8 +432,8 @@ workflow RNAVAR { // TABIX(ch_haplotypecaller_vcf) // ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf - // .join(TABIX.out.tbi, by: [0], remainder: true) - // .join(TABIX.out.csi, by: [0], remainder: true) + // .join(TABIX.out.tbi, remainder: true) + // .join(TABIX.out.csi, remainder: true) // .map{meta, vcf, tbi, csi -> // if (tbi) [meta, vcf, tbi] // else [meta, vcf, csi] From 0bf28e0d18bdf1af119fcfcd03807ddb7d997880 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 14:13:29 +0200 Subject: [PATCH 033/275] multiqc --- subworkflows/local/bam_sort_samtools/main.nf | 9 +- subworkflows/local/bam_stats_samtools/main.nf | 7 +- workflows/rnavar.nf | 124 +++++++++--------- 3 files changed, 70 insertions(+), 70 deletions(-) diff --git a/subworkflows/local/bam_sort_samtools/main.nf b/subworkflows/local/bam_sort_samtools/main.nf index 2680e618..feabd8c9 100644 --- a/subworkflows/local/bam_sort_samtools/main.nf +++ b/subworkflows/local/bam_sort_samtools/main.nf @@ -37,9 +37,10 @@ workflow BAM_SORT_SAMTOOLS { } .set { ch_bam_bai } - BAM_STATS_SAMTOOLS ( - ch_bam_bai - ) + BAM_STATS_SAMTOOLS(ch_bam_bai) + + reports = BAM_STATS_SAMTOOLS.out.reports.map{meta, logs -> [logs] } + ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first()) emit: @@ -47,6 +48,6 @@ workflow BAM_SORT_SAMTOOLS { bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] - reports = BAM_STATS_SAMTOOLS.out.reports + reports versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/bam_stats_samtools/main.nf b/subworkflows/local/bam_stats_samtools/main.nf index 6b664686..09fdd265 100644 --- a/subworkflows/local/bam_stats_samtools/main.nf +++ b/subworkflows/local/bam_stats_samtools/main.nf @@ -12,6 +12,7 @@ workflow BAM_STATS_SAMTOOLS { main: ch_versions = Channel.empty() + ch_reports = Channel.empty() SAMTOOLS_FLAGSTAT(ch_bam_bai) SAMTOOLS_IDXSTATS(ch_bam_bai) @@ -21,7 +22,11 @@ workflow BAM_STATS_SAMTOOLS { ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first()) ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) + ch_reports = ch_reports.mix(SAMTOOLS_STATS.out.stats) + ch_reports = ch_reports.mix(SAMTOOLS_FLAGSTAT.out.flagstat) + ch_reports = ch_reports.mix(SAMTOOLS_IDXSTATS.out.idxstats) + emit: - reports = SAMTOOLS_STATS.out.stats.mix(SAMTOOLS_FLAGSTAT.out.flagstat, SAMTOOLS_IDXSTATS.out.idxstats) + reports = ch_reports versions = ch_versions // channel: [ versions.yml ] } diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 9d7e8aac..d72839cd 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -178,7 +178,7 @@ workflow RNAVAR { // MODULE: Generate QC summary using FastQC FASTQC(ch_cat_fastq) - ch_reports = ch_reports.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ meta, logs -> logs }) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // @@ -426,39 +426,39 @@ workflow RNAVAR { } - // // - // // MODULE: Index the VCF using TABIX - // // - // TABIX(ch_haplotypecaller_vcf) + // + // MODULE: Index the VCF using TABIX + // + TABIX(ch_haplotypecaller_vcf) + + ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf + .join(TABIX.out.tbi, remainder: true) + .join(TABIX.out.csi, remainder: true) + .map{meta, vcf, tbi, csi -> + if (tbi) [meta, vcf, tbi] + else [meta, vcf, csi] + } - // ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf - // .join(TABIX.out.tbi, remainder: true) - // .join(TABIX.out.csi, remainder: true) - // .map{meta, vcf, tbi, csi -> - // if (tbi) [meta, vcf, tbi] - // else [meta, vcf, csi] - // } + ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) + ch_final_vcf = ch_haplotypecaller_vcf - // ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) - // ch_final_vcf = ch_haplotypecaller_vcf + // + // MODULE: VariantFiltration from GATK4 + // Filter variant calls based on certain criteria + // + if (!params.skip_variantfiltration && !params.bam_csi_index ) { - // // - // // MODULE: VariantFiltration from GATK4 - // // Filter variant calls based on certain criteria - // // - // if (!params.skip_variantfiltration && !params.bam_csi_index ) { - - // GATK4_VARIANTFILTRATION( - // ch_haplotypecaller_vcf_tbi, - // ch_fasta, - // ch_fasta_fai, - // ch_dict - // ) - - // ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf - // ch_final_vcf = ch_filtered_vcf - // ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) - // } + GATK4_VARIANTFILTRATION( + ch_haplotypecaller_vcf_tbi, + ch_fasta, + ch_fasta_fai.map{ it -> [ [id:'fai'], it ] }, + ch_dict + ) + + ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf + ch_final_vcf = ch_filtered_vcf + ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) + } // // // // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. @@ -481,40 +481,34 @@ workflow RNAVAR { } - // ch_version_yaml = Channel.empty() - // CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) - // ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect() - - // // - // // MODULE: MultiQC - // // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report - // // - // if (!params.skip_multiqc){ - // workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) - // ch_workflow_summary = Channel.value(workflow_summary) - - // methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - // ch_methods_description = Channel.value(methods_description) - - // ch_multiqc_files = Channel.empty() - // ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - // ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - // ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - // ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - // ch_multiqc_files = ch_multiqc_files.mix(ch_version_yaml) - // ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) - // ch_multiqc_files = ch_multiqc_files.mix(ch_reports.collect()) - // ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_config) - // ch_multiqc_files = ch_multiqc_files.mix(ch_rnavar_logo) - - // MULTIQC( - // ch_multiqc_files.collect(), - // ch_multiqc_config.toList(), - // ch_multiqc_custom_config.toList(), - // ch_multiqc_logo.toList() - // ) - // multiqc_report = MULTIQC.out.report.toList() - // } + ch_version_yaml = Channel.empty() + CUSTOM_DUMPSOFTWAREVERSIONS(ch_versions.unique().collectFile(name: 'collated_versions.yml')) + ch_version_yaml = CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect() + + // + // MODULE: MultiQC + // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report + // + if (!params.skip_multiqc){ + workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) + ch_workflow_summary = Channel.value(workflow_summary) + + methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) + ch_methods_description = Channel.value(methods_description) + + ch_reports.view() + + multiqc_files = Channel.empty() + multiqc_files = multiqc_files.mix(ch_version_yaml) + multiqc_files = multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + multiqc_files = multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) + multiqc_files = multiqc_files.mix(ch_reports.collect().ifEmpty([])) + + MULTIQC(multiqc_files.collect(), ch_multiqc_config.collect().ifEmpty([]), ch_multiqc_custom_config.collect().ifEmpty([]), ch_multiqc_logo.collect().ifEmpty([])) + + multiqc_report = MULTIQC.out.report.toList() + ch_versions = ch_versions.mix(MULTIQC.out.versions) + } } /* From 90600fe72e7f302b91f47dd54420ed469f220f27 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 14:15:17 +0200 Subject: [PATCH 034/275] update tests --- tests/test_annotation.yml | 54 ++++++++++++++++----------------- tests/test_bamcsiindex.yml | 2 +- tests/test_default.yml | 2 +- tests/test_removeduplicates.yml | 2 +- tests/test_skipbasecalib.yml | 2 +- 5 files changed, 31 insertions(+), 31 deletions(-) diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml index b6fb529d..80bdadf3 100644 --- a/tests/test_annotation.yml +++ b/tests/test_annotation.yml @@ -1,27 +1,27 @@ -- name: Run snpEff - command: nextflow run main.nf -profile test,docker --annotate_tools snpeff - tags: - - annotation - - snpeff - files: - - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz - - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz.tbi - - path: results/reports/multiqc_report.html -- name: Run VEP - command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc - tags: - - annotation - - vep - files: - - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz - - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz.tbi -- name: Run snpEff followed by VEP - command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc - tags: - - annotation - - merge - - snpeff - - vep - files: - - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz - - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz.tbi +# - name: Run snpEff +# command: nextflow run main.nf -profile test,docker --annotate_tools snpeff --outdir results +# tags: +# - annotation +# - snpeff +# files: +# - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz +# - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz.tbi +# - path: results/reports/multiqc_report.html +# - name: Run VEP +# command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results +# tags: +# - annotation +# - vep +# files: +# - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz +# - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz.tbi +# - name: Run snpEff followed by VEP +# command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results +# tags: +# - annotation +# - merge +# - snpeff +# - vep +# files: +# - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz +# - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz.tbi diff --git a/tests/test_bamcsiindex.yml b/tests/test_bamcsiindex.yml index 06fb817f..a06de700 100644 --- a/tests/test_bamcsiindex.yml +++ b/tests/test_bamcsiindex.yml @@ -1,5 +1,5 @@ - name: Run pipeline with bam_csi_index for large genomes - command: nextflow run main.nf -profile test,docker --bam_csi_index + command: nextflow run main.nf -profile test,docker --bam_csi_index --outdir results tags: - bamcsiindex files: diff --git a/tests/test_default.yml b/tests/test_default.yml index 36cb35fa..776ec6f3 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -1,5 +1,5 @@ - name: Run default pipeline - command: nextflow run main.nf -profile test,docker + command: nextflow run main.nf -profile test,docker --outdir results tags: - default - preprocessing diff --git a/tests/test_removeduplicates.yml b/tests/test_removeduplicates.yml index 8889ad6a..d0650728 100644 --- a/tests/test_removeduplicates.yml +++ b/tests/test_removeduplicates.yml @@ -1,5 +1,5 @@ - name: Run pipeline with duplicate reads removed - command: nextflow run main.nf -profile test,docker --remove_duplicates true + command: nextflow run main.nf -profile test,docker --remove_duplicates true --outdir results tags: - removeduplicates - preprocessing diff --git a/tests/test_skipbasecalib.yml b/tests/test_skipbasecalib.yml index 7b5b2132..67f1c463 100644 --- a/tests/test_skipbasecalib.yml +++ b/tests/test_skipbasecalib.yml @@ -1,5 +1,5 @@ - name: Run pipeline without base calibration step - command: nextflow run main.nf -profile test,docker --skip_baserecalibration true + command: nextflow run main.nf -profile test,docker --skip_baserecalibration true --outdir results tags: - skipbasecalib - preprocessing From 1cd7988ecfa283d587f6b5576f92d6ea788b44d0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 14:17:45 +0200 Subject: [PATCH 035/275] remove annotation tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f3319d00..cc8f7dfa 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ jobs: - "latest-everything" test: - "default" - - "annotation" + # - "annotation" - "removeduplicates" - "skipbasecalib" - "bamcsiindex" From 05cb821e582e7c4faf4af43c07a7573e1b0e2f22 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 14:29:27 +0200 Subject: [PATCH 036/275] fix test csi --- conf/modules.config | 1 - workflows/rnavar.nf | 2 -- 2 files changed, 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b536b83f..16dd423b 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -326,7 +326,6 @@ process { withName: GATK4_MERGEVCFS { ext.prefix = {"${meta.id}.haplotypecaller"} - ext.args = params.bam_csi_index ? '--CREATE_INDEX false' : '' publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index d72839cd..698e0c25 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -496,8 +496,6 @@ workflow RNAVAR { methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) - ch_reports.view() - multiqc_files = Channel.empty() multiqc_files = multiqc_files.mix(ch_version_yaml) multiqc_files = multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) From e32e8e894075ceb5b134ae0869158c3832b58095 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 14:37:28 +0200 Subject: [PATCH 037/275] fix tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cc8f7dfa..fc55fff3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,4 +50,4 @@ jobs: run: python -m pip install --upgrade pip pytest-workflow - name: Run pipeline with tests settings - run: pytest --tag ${{matrix.test}} --kwdof + run: TMPDIR=~ PROFILE=docker pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes From 8858819e1d21090ec95307c4665a2a4fa9f58793 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 14:44:02 +0200 Subject: [PATCH 038/275] uncomment --- tests/test_annotation.yml | 54 +++++++++++++++++++-------------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml index 80bdadf3..28ef4322 100644 --- a/tests/test_annotation.yml +++ b/tests/test_annotation.yml @@ -1,27 +1,27 @@ -# - name: Run snpEff -# command: nextflow run main.nf -profile test,docker --annotate_tools snpeff --outdir results -# tags: -# - annotation -# - snpeff -# files: -# - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz -# - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz.tbi -# - path: results/reports/multiqc_report.html -# - name: Run VEP -# command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results -# tags: -# - annotation -# - vep -# files: -# - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz -# - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz.tbi -# - name: Run snpEff followed by VEP -# command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results -# tags: -# - annotation -# - merge -# - snpeff -# - vep -# files: -# - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz -# - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz.tbi +- name: Run snpEff + command: nextflow run main.nf -profile test,docker --annotate_tools snpeff --outdir results + tags: + - annotation + - snpeff + files: + - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz + - path: results/variant_annotation/GM12878/GM12878_snpEff.ann.vcf.gz.tbi + - path: results/reports/multiqc_report.html +- name: Run VEP + command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results + tags: + - annotation + - vep + files: + - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz + - path: results/variant_annotation/GM12878/GM12878_VEP.ann.vcf.gz.tbi +- name: Run snpEff followed by VEP + command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results + tags: + - annotation + - merge + - snpeff + - vep + files: + - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz + - path: results/variant_annotation/GM12878/GM12878_snpEff_VEP.ann.vcf.gz.tbi From 80503cce89e7de4c44a3de598214f84608f40d42 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 15:46:12 +0200 Subject: [PATCH 039/275] fix csi tests --- conf/modules.config | 4 ++-- tests/test_bamcsiindex.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 16dd423b..55f7dcc9 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -216,7 +216,7 @@ process { path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, enabled: true, - pattern: "*.{bam,bai}" + pattern: "*.{bam,bai,csi}" ], [ path: { "${params.outdir}/reports/stats/${meta.id}" }, @@ -227,7 +227,7 @@ process { ] } - withName: '.*:MARKDUPLICATES:SAMTOOLS_INDEX' { + withName: '.*:BAM_MARKDUPLICATES:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.md"} publishDir = [ diff --git a/tests/test_bamcsiindex.yml b/tests/test_bamcsiindex.yml index a06de700..7235d9f9 100644 --- a/tests/test_bamcsiindex.yml +++ b/tests/test_bamcsiindex.yml @@ -4,7 +4,7 @@ - bamcsiindex files: - path: results/reports/multiqc_report.html - - path: results/preprocessing/GM12878/GM12878.markdup.sorted.bam - - path: results/preprocessing/GM12878/GM12878.markdup.sorted.bam.csi + - path: results/preprocessing/GM12878/GM12878.md.bam + - path: results/preprocessing/GM12878/GM12878.md.bam.csi - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.csi From cfeeeb4c66f1d2eed435032dc2368e795a721e26 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 20 Sep 2023 18:04:05 +0200 Subject: [PATCH 040/275] fix comments from review --- assets/schema_input.json | 14 +-- bin/check_samplesheet.py | 259 --------------------------------------- 2 files changed, 3 insertions(+), 270 deletions(-) delete mode 100755 bin/check_samplesheet.py diff --git a/assets/schema_input.json b/assets/schema_input.json index dc7fcba6..7cbc45b8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -14,17 +14,9 @@ "meta": ["sample"] }, "fastq_1": { - "errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ], + "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "type": "string", + "pattern": "^\\S+\\.f(ast)?q\\.gz$", "format": "file-path", "exists": true }, diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 9f85605d..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,259 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `rnavar test samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _rnavar test samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="WARNING", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) From a23a895f4af79c528c4815f949d2d5f5ad6501ca Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 21 Sep 2023 08:59:27 +0200 Subject: [PATCH 041/275] update schema --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7ce1ee3d..36d0136e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -14,7 +14,7 @@ "properties": { "input": { "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory. If no input should be supplied, i.e. when --step is supplied or --build_from_index, then set --input false", + "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/rnavar/usage#input).", "fa_icon": "fas fa-file-csv", "schema": "assets/schema_input.json", "type": "string", From a4bea80113042e9d64633d6a143412ef1bc708bc Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 26 Sep 2023 08:09:03 +0000 Subject: [PATCH 042/275] Template update for nf-core/tools version 2.10 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcments.yml | 68 +++++++++ CITATIONS.md | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++---- LICENSE | 2 +- README.md | 23 +-- assets/multiqc_config.yml | 4 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowRnavar.groovy | 2 +- main.nf | 3 + modules.json | 6 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 9 +- nextflow_schema.json | 15 -- workflows/rnavar.nf | 1 + 22 files changed, 254 insertions(+), 79 deletions(-) create mode 100644 .github/workflows/release-announcments.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a584..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 90bd1ebb..60cb4b0a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -> If you need help using or modifying nf-core/rnavar then the best place to ask is on the nf-core Slack [#rnavar](https://nfcore.slack.com/channels/rnavar) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/rnavar then the best place to ask is on the nf-core Slack [#rnavar](https://nfcore.slack.com/channels/rnavar) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 00000000..6ad33927 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/CITATIONS.md b/CITATIONS.md index 27fb294e..20cd17cf 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f..c089ec78 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/LICENSE b/LICENSE index 2a63dfa9..747ad37f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) @praveenraj2018 +Copyright (c) Praveen Raj, Maxime U Garcia Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 5c7f0b4f..674fdac1 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_light.png#gh-light-mode-only) ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -29,10 +30,11 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +with `-profile test` before running the workflow on actual data. +::: - + diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c13e471c..15689f51 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rnavar + This report has been generated by the nf-core/rnavar analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: diff --git a/assets/slackreport.json b/assets/slackreport.json index 6ab75715..e3b5eeaf 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/rnavar v${version} - ${runName}", + "author_name": "nf-core/rnavar ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules.config b/conf/modules.config index 39e81386..d91c6aba 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -39,7 +39,7 @@ process { } withName: 'MULTIQC' { - ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, mode: params.publish_dir_mode, diff --git a/docs/usage.md b/docs/usage.md index e75b5d12..fc3321a7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -20,7 +20,7 @@ You will need to create a samplesheet with information about the samples you wou The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz @@ -33,7 +33,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..e248e4c3 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -4,6 +4,7 @@ import org.yaml.snakeyaml.Yaml import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -141,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -155,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -227,15 +232,14 @@ class NfcoreTemplate { // Dump pipeline parameters in a json file // public static void dump_parameters(workflow, params) { - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def output_pf = new File(output_d, "params_${timestamp}.json") + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() } // diff --git a/modules.json b/modules.json index f8b9ac2f..f3fdaddd 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..f0c63f69 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..eec1db10 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..4274ed57 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ], + "1": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "2": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "versions": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "yml": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ] + } + ], + "timestamp": "2023-11-03T14:43:22.157011" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..1787b38a --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..9e19a74c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..b9e8f926 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process FASTQC" + script "../main.nf" + process "FASTQC" + tag "modules" + tag "modules_nfcore" + tag "fastqc" + + test("Single-Read") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) + } + } +// TODO +// // +// // Test with paired-end data +// // +// workflow test_fastqc_paired_end { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with interleaved data +// // +// workflow test_fastqc_interleaved { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with bam data +// // +// workflow test_fastqc_bam { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with multiple samples +// // +// workflow test_fastqc_multiple { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with custom prefix +// // +// workflow test_fastqc_custom_prefix { +// input = [ +// [ id:'mysample', single_end:true ], // meta map +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } +} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..636a32ce --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 00000000..7834294b --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..bc0bdb5b --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..c2dad217 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } + + test("MULTIQC: FASTQC and a config file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index e081196e..bdfbb7fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { input = null // References genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false @@ -82,6 +82,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -104,13 +105,13 @@ profiles { } docker { docker.enabled = true - docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -181,7 +182,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -204,6 +205,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true From 1b14283057411836cfd6013a356673fca1c89d9c Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 20 Dec 2023 15:57:52 +0000 Subject: [PATCH 067/275] Template update for nf-core/tools version 2.11.1 --- .../{release-announcments.yml => release-announcements.yml} | 0 nextflow.config | 4 ++-- 2 files changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{release-announcments.yml => release-announcements.yml} (100%) diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcements.yml similarity index 100% rename from .github/workflows/release-announcments.yml rename to .github/workflows/release-announcements.yml diff --git a/nextflow.config b/nextflow.config index bdfbb7fb..2fd2a3fc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -111,10 +111,10 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true From 310dbe2fa4115122195b5a978f87c0a7bf46e44f Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 28 Dec 2023 14:59:39 +0000 Subject: [PATCH 068/275] Added unzip feature --- modules.json | 5 +++ modules/nf-core/unzip/environment.yml | 7 ++++ modules/nf-core/unzip/main.nf | 37 ++++++++++++++++++++ modules/nf-core/unzip/meta.yml | 42 +++++++++++++++++++++++ subworkflows/local/prepare_genome/main.nf | 42 +++++++++++++++++++++-- workflows/rnavar.nf | 25 +++++++++----- 6 files changed, 146 insertions(+), 12 deletions(-) create mode 100644 modules/nf-core/unzip/environment.yml create mode 100644 modules/nf-core/unzip/main.nf create mode 100644 modules/nf-core/unzip/meta.yml diff --git a/modules.json b/modules.json index 96700193..4224b367 100755 --- a/modules.json +++ b/modules.json @@ -204,6 +204,11 @@ "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] + }, + "unzip": { + "branch": "master", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules"] } } }, diff --git a/modules/nf-core/unzip/environment.yml b/modules/nf-core/unzip/environment.yml new file mode 100644 index 00000000..d3a535f1 --- /dev/null +++ b/modules/nf-core/unzip/environment.yml @@ -0,0 +1,7 @@ +name: unzip +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::p7zip=16.02 diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf new file mode 100644 index 00000000..08cfc3c4 --- /dev/null +++ b/modules/nf-core/unzip/main.nf @@ -0,0 +1,37 @@ +process UNZIP { + tag "$archive" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/p7zip:16.02' : + 'biocontainers/p7zip:16.02' }" + + input: + tuple val(meta), path(archive) + + output: + tuple val(meta), path("${prefix}/"), emit: unzipped_archive + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } + + prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName) + """ + 7za \\ + x \\ + -o"${prefix}"/ \\ + $args \\ + $archive + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + 7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml new file mode 100644 index 00000000..e8e377e2 --- /dev/null +++ b/modules/nf-core/unzip/meta.yml @@ -0,0 +1,42 @@ +name: unzip +description: Unzip ZIP archive files +keywords: + - unzip + - decompression + - zip + - archiving +tools: + - unzip: + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + homepage: https://sourceforge.net/projects/p7zip/ + documentation: https://sourceforge.net/projects/p7zip/ + tool_dev_url: https://sourceforge.net/projects/p7zip" + licence: ["LGPL-2.1-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: ZIP file + pattern: "*.zip" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - unzipped_archive: + type: directory + description: Directory contents of the unzipped archive + pattern: "${archive.baseName}/" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jfy133" +maintainers: + - "@jfy133" diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index efb649ae..130c96cc 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -9,17 +9,52 @@ include { GFFREAD } from '../../../modules/nf-core/gffrea include { GTF2BED } from '../../../modules/local/gtf2bed' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' +include { UNZIP as UNZIP_FASTA } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_GTF } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_GFF } from '../../../modules/nf-core/unzip/main' workflow PREPARE_GENOME { take: - ch_fasta // file: /path/to/genome.fasta - ch_gff // file: /path/to/genome.gff - ch_gtf // file: /path/to/genome.gtf + ch_fasta_raw // file: /path/to/genome.fasta + ch_gff // file: /path/to/genome.gff + ch_gtf_raw // file: /path/to/genome.gtf feature_type main: ch_versions = Channel.empty() + //Unzip reference genome files if needed + + if (params.fasta.endsWith('.gz')) { + UNZIP_FASTA(ch_fasta_raw) + + ch_fasta = + UNZIP_FASTA.out.unzipped_archive + .map{ meta,file -> //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder + def file_name = file.baseName + def full_file_path = file.toString() + '/' + file_name + '.fa' + + [meta,full_file_path] + } + } else { + ch_fasta = ch_fasta_raw + } + + if (params.gtf.endsWith('.gz')) { + UNZIP_GTF(ch_gtf_raw) + + ch_gtf = + UNZIP_GTF.out.unzipped_archive + .map{ meta,file -> //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder + def file_name = file.baseName + def full_file_path = file.toString() + '/' + file_name + '.gtf' + + [meta,full_file_path] + } + } else { + ch_gtf = ch_gtf_raw + } + GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) GFFREAD(ch_gff) SAMTOOLS_FAIDX(ch_fasta, [['id':null], []]) @@ -38,6 +73,7 @@ workflow PREPARE_GENOME { emit: dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed + fasta = ch_fasta fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai gtf = ch_gtf // path: genome.gtf star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 6674386a..c3d96d41 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -188,10 +188,10 @@ if (params.spliceai_snv && params.spliceai_snv_tbi && params.spliceai_indel && p // def multiqc_report = [] // Initialize file channels based on params, defined in the params.genomes[params.genome] scope -ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed) : Channel.empty() -ch_fasta = params.fasta ? Channel.fromPath(params.fasta).map{ fasta -> [ [ id:fasta.baseName ], fasta ] }.first() : Channel.empty() -ch_gff = params.gff ? Channel.fromPath(params.gff).first() : Channel.empty() -ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.first() : Channel.empty() +ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed) : Channel.empty() +ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ fasta -> [ [ id:fasta.baseName ], fasta ] }.first() : Channel.empty() +ch_gff = params.gff ? Channel.fromPath(params.gff).first() : Channel.empty() +ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.first() : Channel.empty() /* ======================================================================================== @@ -237,20 +237,27 @@ workflow RNAVAR { // Prepare reference genome files PREPARE_GENOME( - ch_fasta, + ch_fasta_raw, ch_gff, - ch_gtf, + ch_gtf_raw, params.feature_type ) ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) - ch_genome_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() + ch_genome_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed - ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() + ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict - ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() + + ch_fasta = params.fasta.endsWith('.gz') ? PREPARE_GENOME.out.fasta + : ch_fasta_raw + + ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() : PREPARE_GENOME.out.fasta_fai + ch_gtf = params.gtf.endsWith('.gz') ? PREPARE_GENOME.out.gtf + : ch_gtf_raw + // MODULE: Concatenate FastQ files from same sample if required CAT_FASTQ(ch_input.multiple) From ed755f36e81ffba147da69a8f07bbc26958724c1 Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 28 Dec 2023 15:05:06 +0000 Subject: [PATCH 069/275] Fixed linting issues --- .github/CONTRIBUTING.md | 3 +++ .github/PULL_REQUEST_TEMPLATE.md | 1 + .github/workflows/linting.yml | 12 ++++++------ lib/NfcoreTemplate.groovy | 32 ++++++++++++++++++-------------- 4 files changed, 28 insertions(+), 20 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 60cb4b0a..04afaff2 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to +receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. + When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 80d8e275..866f5cb1 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnav - [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b8bdd214..905c58e4 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -27,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @@ -40,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Check code lints with Black uses: psf/black@stable @@ -71,7 +71,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..e248e4c3 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -4,6 +4,7 @@ import org.yaml.snakeyaml.Yaml import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -141,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -155,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -227,15 +232,14 @@ class NfcoreTemplate { // Dump pipeline parameters in a json file // public static void dump_parameters(workflow, params) { - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def output_pf = new File(output_d, "params_${timestamp}.json") + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() } // From 12d209bd8b4866bed70e72d0d244a2f796e22c14 Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 28 Dec 2023 15:12:05 +0000 Subject: [PATCH 070/275] Updated changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 084197e7..c25cab1d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,9 +6,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [1.1.0dev] nfcore/rnavar ### Added +- Added`unzip` from nf-core modules for working with unzipped fasta and gtf files ### Changed - - [#95](https://github.com/nf-core/rnavar/pull/95) - Template update from nf-core/tools 2.5 -> 2.9 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules From 57b6abbaae53f18c9da076f9689b9dc92bbf856f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 29 Dec 2023 09:38:44 +0100 Subject: [PATCH 071/275] forgot to fix conflicts --- modules.json | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/modules.json b/modules.json index 945d32e9..1eaaf409 100755 --- a/modules.json +++ b/modules.json @@ -37,11 +37,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", -<<<<<<< HEAD "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", -======= - "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f", ->>>>>>> dev "installed_by": ["modules"] }, "ensemblvep/download": { @@ -56,10 +52,7 @@ }, "fastqc": { "branch": "master", -<<<<<<< HEAD "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", -======= - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", "installed_by": ["modules"] }, "gatk4/applybqsr": { @@ -135,16 +128,11 @@ "mosdepth": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", ->>>>>>> dev "installed_by": ["modules"] }, "multiqc": { "branch": "master", -<<<<<<< HEAD "git_sha": "4ab13872435962dadc239979554d13709e20bf29", -======= - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", ->>>>>>> dev "installed_by": ["modules"] }, "samtools/faidx": { From 898040305530f6e3faf90a8a60a5c3bbc383b522 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 29 Dec 2023 09:44:04 +0100 Subject: [PATCH 072/275] update all modules --- modules.json | 80 +- .../nf-core/bcftools/concat/environment.yml | 3 +- modules/nf-core/bcftools/concat/main.nf | 4 +- modules/nf-core/bcftools/concat/meta.yml | 4 +- .../bcftools/concat/tests/main.nf.test | 108 ++ .../bcftools/concat/tests/main.nf.test.snap | 43 + .../bcftools/concat/tests/nextflow.config | 3 + .../nf-core/bcftools/concat/tests/tags.yml | 2 + .../bcftools/pluginscatter/environment.yml | 3 +- .../nf-core/bcftools/pluginscatter/main.nf | 4 +- modules/nf-core/bcftools/sort/environment.yml | 3 +- modules/nf-core/bcftools/sort/main.nf | 4 +- .../nf-core/bedtools/merge/environment.yml | 3 +- modules/nf-core/bedtools/merge/main.nf | 4 +- modules/nf-core/bedtools/sort/environment.yml | 3 +- modules/nf-core/bedtools/sort/main.nf | 4 +- modules/nf-core/cat/fastq/environment.yml | 1 + .../ensemblvep/download/environment.yml | 1 + modules/nf-core/ensemblvep/download/meta.yml | 2 +- .../nf-core/ensemblvep/vep/environment.yml | 1 + modules/nf-core/ensemblvep/vep/meta.yml | 2 +- .../nf-core/gatk4/applybqsr/environment.yml | 1 + .../gatk4/applybqsr/tests/main.nf.test | 95 ++ .../gatk4/applybqsr/tests/main.nf.test.snap | 86 ++ .../nf-core/gatk4/applybqsr/tests/tags.yml | 2 + .../gatk4/baserecalibrator/environment.yml | 1 + .../nf-core/gatk4/baserecalibrator/main.nf | 10 + .../gatk4/baserecalibrator/tests/main.nf.test | 166 +++ .../baserecalibrator/tests/main.nf.test.snap | 147 +++ .../gatk4/baserecalibrator/tests/tags.yml | 2 + .../gatk4/bedtointervallist/environment.yml | 1 + .../gatk4/combinegvcfs/environment.yml | 1 + .../createsequencedictionary/environment.yml | 1 + .../gatk4/haplotypecaller/environment.yml | 1 + modules/nf-core/gatk4/haplotypecaller/main.nf | 12 +- .../nf-core/gatk4/haplotypecaller/meta.yml | 25 + .../gatk4/haplotypecaller/tests/main.nf.test | 146 +++ .../haplotypecaller/tests/main.nf.test.snap | 20 + .../gatk4/haplotypecaller/tests/tags.yml | 2 + .../gatk4/indexfeaturefile/environment.yml | 1 + .../gatk4/intervallisttools/environment.yml | 1 + .../gatk4/markduplicates/environment.yml | 3 +- modules/nf-core/gatk4/markduplicates/main.nf | 4 +- .../gatk4/markduplicates/tests/bam.config | 8 + .../gatk4/markduplicates/tests/cram.config | 8 + .../gatk4/markduplicates/tests/main.nf.test | 126 ++ .../markduplicates/tests/main.nf.test.snap | 112 ++ .../gatk4/markduplicates/tests/tags.yml | 2 + .../nf-core/gatk4/mergevcfs/environment.yml | 1 + .../gatk4/splitncigarreads/environment.yml | 1 + .../gatk4/variantfiltration/environment.yml | 1 + modules/nf-core/gffread/environment.yml | 1 + modules/nf-core/gffread/main.nf | 10 +- modules/nf-core/gffread/meta.yml | 6 +- modules/nf-core/gffread/tests/main.nf.test | 33 +- .../nf-core/gffread/tests/main.nf.test.snap | 39 +- modules/nf-core/gffread/tests/nextflow.config | 5 + modules/nf-core/gunzip/environment.yml | 1 + modules/nf-core/mosdepth/environment.yml | 4 +- modules/nf-core/mosdepth/main.nf | 4 +- modules/nf-core/mosdepth/meta.yml | 9 +- modules/nf-core/mosdepth/tests/main.nf.test | 260 ++++ .../nf-core/mosdepth/tests/main.nf.test.snap | 1145 +++++++++++++++++ .../nf-core/mosdepth/tests/quantized.config | 3 + modules/nf-core/mosdepth/tests/tags.yml | 2 + .../nf-core/mosdepth/tests/threshold.config | 3 + modules/nf-core/mosdepth/tests/window.config | 3 + .../nf-core/samtools/faidx/environment.yml | 3 +- modules/nf-core/samtools/faidx/main.nf | 4 +- .../nf-core/samtools/flagstat/environment.yml | 3 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test | 36 + .../samtools/flagstat/tests/main.nf.test.snap | 16 + .../nf-core/samtools/flagstat/tests/tags.yml | 2 + .../nf-core/samtools/idxstats/environment.yml | 3 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test | 36 + .../samtools/idxstats/tests/main.nf.test.snap | 16 + .../nf-core/samtools/idxstats/tests/tags.yml | 2 + .../nf-core/samtools/index/environment.yml | 3 +- modules/nf-core/samtools/index/main.nf | 4 +- .../samtools/index/tests/csi.nextflow.config | 7 + .../nf-core/samtools/index/tests/main.nf.test | 87 ++ .../samtools/index/tests/main.nf.test.snap | 28 + modules/nf-core/samtools/index/tests/tags.yml | 2 + .../nf-core/samtools/merge/environment.yml | 3 +- modules/nf-core/samtools/merge/main.nf | 8 +- .../nf-core/samtools/merge/tests/index.config | 3 + .../nf-core/samtools/merge/tests/main.nf.test | 156 +++ .../samtools/merge/tests/main.nf.test.snap | 68 + modules/nf-core/samtools/merge/tests/tags.yml | 2 + modules/nf-core/samtools/sort/environment.yml | 3 +- modules/nf-core/samtools/sort/main.nf | 4 +- .../nf-core/samtools/sort/tests/main.nf.test | 5 +- .../samtools/sort/tests/main.nf.test.snap | 19 +- .../nf-core/samtools/stats/environment.yml | 3 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../nf-core/samtools/stats/tests/main.nf.test | 2 +- .../samtools/stats/tests/main.nf.test.snap | 20 +- .../nf-core/snpeff/download/environment.yml | 1 + modules/nf-core/snpeff/download/meta.yml | 2 +- modules/nf-core/snpeff/snpeff/environment.yml | 1 + modules/nf-core/snpeff/snpeff/meta.yml | 2 +- modules/nf-core/star/align/environment.yml | 3 +- modules/nf-core/star/align/main.nf | 4 +- modules/nf-core/star/align/tests/main.nf.test | 339 +++++ .../star/align/tests/main.nf.test.snap | 769 +++++++++++ .../star/align/tests/nextflow.arriba.config | 14 + .../nf-core/star/align/tests/nextflow.config | 14 + .../align/tests/nextflow.starfusion.config | 14 + modules/nf-core/star/align/tests/tags.yml | 2 + .../star/genomegenerate/environment.yml | 5 +- modules/nf-core/star/genomegenerate/main.nf | 87 +- .../star/genomegenerate/tests/main.nf.test | 117 ++ .../genomegenerate/tests/main.nf.test.snap | 22 + .../star/genomegenerate/tests/tags.yml | 2 + .../nf-core/tabix/bgziptabix/environment.yml | 1 + modules/nf-core/tabix/tabix/environment.yml | 1 + modules/nf-core/untar/environment.yml | 1 + modules/nf-core/untar/tests/main.nf.test | 77 ++ modules/nf-core/untar/tests/main.nf.test.snap | 513 ++++++++ modules/nf-core/untar/tests/tags.yml | 2 + 122 files changed, 5185 insertions(+), 165 deletions(-) create mode 100644 modules/nf-core/bcftools/concat/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/concat/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/concat/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/concat/tests/tags.yml create mode 100644 modules/nf-core/gatk4/applybqsr/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/applybqsr/tests/tags.yml create mode 100644 modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/baserecalibrator/tests/tags.yml create mode 100644 modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/haplotypecaller/tests/tags.yml create mode 100644 modules/nf-core/gatk4/markduplicates/tests/bam.config create mode 100644 modules/nf-core/gatk4/markduplicates/tests/cram.config create mode 100644 modules/nf-core/gatk4/markduplicates/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/markduplicates/tests/tags.yml create mode 100644 modules/nf-core/gffread/tests/nextflow.config create mode 100644 modules/nf-core/mosdepth/tests/main.nf.test create mode 100644 modules/nf-core/mosdepth/tests/main.nf.test.snap create mode 100644 modules/nf-core/mosdepth/tests/quantized.config create mode 100644 modules/nf-core/mosdepth/tests/tags.yml create mode 100644 modules/nf-core/mosdepth/tests/threshold.config create mode 100644 modules/nf-core/mosdepth/tests/window.config create mode 100644 modules/nf-core/samtools/flagstat/tests/main.nf.test create mode 100644 modules/nf-core/samtools/flagstat/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/flagstat/tests/tags.yml create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test create mode 100644 modules/nf-core/samtools/idxstats/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/idxstats/tests/tags.yml create mode 100644 modules/nf-core/samtools/index/tests/csi.nextflow.config create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/index/tests/tags.yml create mode 100644 modules/nf-core/samtools/merge/tests/index.config create mode 100644 modules/nf-core/samtools/merge/tests/main.nf.test create mode 100644 modules/nf-core/samtools/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/merge/tests/tags.yml create mode 100644 modules/nf-core/star/align/tests/main.nf.test create mode 100644 modules/nf-core/star/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/align/tests/nextflow.arriba.config create mode 100644 modules/nf-core/star/align/tests/nextflow.config create mode 100644 modules/nf-core/star/align/tests/nextflow.starfusion.config create mode 100644 modules/nf-core/star/align/tests/tags.yml create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/genomegenerate/tests/tags.yml create mode 100644 modules/nf-core/untar/tests/main.nf.test create mode 100644 modules/nf-core/untar/tests/main.nf.test.snap create mode 100644 modules/nf-core/untar/tests/tags.yml diff --git a/modules.json b/modules.json index 1eaaf409..0c0b37ea 100755 --- a/modules.json +++ b/modules.json @@ -7,32 +7,32 @@ "nf-core": { "bcftools/concat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/pluginscatter": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/sort": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bedtools/merge": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { @@ -42,13 +42,13 @@ }, "ensemblvep/download": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "214d575774c172062924ad3564b4f66655600730", "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["vcf_annotate_ensemblvep", "modules", "vcf_annotate_ensemblvep_snpeff"] + "git_sha": "214d575774c172062924ad3564b4f66655600730", + "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] }, "fastqc": { "branch": "master", @@ -57,77 +57,77 @@ }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "f1b92874e0de01dd82fe1bf7c6a7409673578065", "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "85561f483acc3bc6a885667ea431b3bb3fccdecb", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/combinegvcfs": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "eab2bd29e589bd05da2b47c9bf95ef10b9508699", "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "bc93a4b8904472ce64c6bb50b1fb0a1659b9cf78", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/splitncigarreads": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gffread": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65", "installed_by": ["modules"] }, "multiqc": { @@ -137,72 +137,72 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "e7ce60acc8a33fa17429e966364657a63016e870", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "snpeff/download": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "214d575774c172062924ad3564b4f66655600730", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["vcf_annotate_ensemblvep_snpeff", "modules", "vcf_annotate_snpeff"] + "git_sha": "214d575774c172062924ad3564b4f66655600730", + "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff", "vcf_annotate_snpeff"] }, "star/align": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["vcf_annotate_ensemblvep", "modules", "vcf_annotate_ensemblvep_snpeff"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 57631f42..ff0200df 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,6 +1,7 @@ +name: bcftools_concat channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bcftools=1.17 + - bioconda::bcftools=1.18 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index 2ff690b1..a5830a25 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_CONCAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': - 'biocontainers/bcftools:1.17--haef29d1_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': + 'biocontainers/bcftools:1.18--h8b25389_0' }" input: tuple val(meta), path(vcfs), path(tbi) diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index 8731b17b..91cb54d5 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -20,12 +20,12 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcfs: - type: files + type: list description: | List containing 2 or more vcf files e.g. [ 'file1.vcf', 'file2.vcf' ] - tbi: - type: files + type: list description: | List containing 2 or more index files (optional) e.g. [ 'file1.tbi', 'file2.tbi' ] diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test new file mode 100644 index 00000000..bf1a5f3f --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_process { + + name "Test Process BCFTOOLS_CONCAT" + script "../main.nf" + process "BCFTOOLS_CONCAT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/concat" + + config "./nextflow.config" + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") { + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], []]") { + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + ], + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap new file mode 100644 index 00000000..7344e6e3 --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -0,0 +1,43 @@ +{ + "sarscov2 - [[vcf1, vcf2], []]": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + ] + ], + [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ] + ], + "timestamp": "2023-11-29T13:52:27.03724666" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + ] + ], + [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ] + ], + "timestamp": "2023-11-29T13:52:21.468988293" + }, + "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "content": [ + "test3.vcf.gz", + [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ] + ], + "timestamp": "2023-11-29T13:41:04.716017811" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/nextflow.config b/modules/nf-core/bcftools/concat/tests/nextflow.config new file mode 100644 index 00000000..f3e1e98c --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = "--no-version" +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/tags.yml b/modules/nf-core/bcftools/concat/tests/tags.yml new file mode 100644 index 00000000..21710d4e --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/concat: + - "modules/nf-core/bcftools/concat/**" diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 57631f42..42e97daa 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -1,6 +1,7 @@ +name: bcftools_pluginscatter channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bcftools=1.17 + - bioconda::bcftools=1.18 diff --git a/modules/nf-core/bcftools/pluginscatter/main.nf b/modules/nf-core/bcftools/pluginscatter/main.nf index 96c11254..9f52e947 100644 --- a/modules/nf-core/bcftools/pluginscatter/main.nf +++ b/modules/nf-core/bcftools/pluginscatter/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSCATTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': - 'biocontainers/bcftools:1.17--haef29d1_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': + 'biocontainers/bcftools:1.18--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 57631f42..89cf911d 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,6 +1,7 @@ +name: bcftools_sort channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bcftools=1.17 + - bioconda::bcftools=1.18 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index c842daf2..c982944c 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.17--haef29d1_0': - 'biocontainers/bcftools:1.17--haef29d1_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': + 'biocontainers/bcftools:1.18--h8b25389_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml index ee820940..99707878 100644 --- a/modules/nf-core/bedtools/merge/environment.yml +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -1,6 +1,7 @@ +name: bedtools_merge channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.31.0 + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/main.nf b/modules/nf-core/bedtools/merge/main.nf index 3fa08d19..5310647d 100644 --- a/modules/nf-core/bedtools/merge/main.nf +++ b/modules/nf-core/bedtools/merge/main.nf @@ -4,8 +4,8 @@ process BEDTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' : - 'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }" + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml index ee820940..87b2e425 100644 --- a/modules/nf-core/bedtools/sort/environment.yml +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -1,6 +1,7 @@ +name: bedtools_sort channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::bedtools=2.31.0 + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/sort/main.nf b/modules/nf-core/bedtools/sort/main.nf index 5b748903..b833150a 100644 --- a/modules/nf-core/bedtools/sort/main.nf +++ b/modules/nf-core/bedtools/sort/main.nf @@ -4,8 +4,8 @@ process BEDTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bedtools:2.31.0--hf5e1c6e_2' : - 'biocontainers/bedtools:2.31.0--hf5e1c6e_2' }" + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 222b301f..bff93add 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,3 +1,4 @@ +name: cat_fastq channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index d3805c0c..beebaca6 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -1,3 +1,4 @@ +name: ensemblvep_download channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index 0183a435..a4277ad7 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP_DOWNLOAD +name: ensemblvep_download description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. keywords: - annotation diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index d3805c0c..7a127746 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,3 +1,4 @@ +name: ensemblvep_vep channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index 61d29d3f..d8ff8d14 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,4 +1,4 @@ -name: ENSEMBLVEP_VEP +name: ensemblvep_vep description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. keywords: - annotation diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 16241b6d..a6900991 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_applybqsr channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test new file mode 100644 index 00000000..5ee53d5c --- /dev/null +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test @@ -0,0 +1,95 @@ +nextflow_process { + + name "Test Process GATK4_APPLYBQSR" + script "../main.nf" + process "GATK4_APPLYBQSR" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/applybqsr" + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true), + [] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - intervals") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - cram") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert snapshot(file(process.out.cram[0][1]).name).match("test.cram") } + ) + } + } + +} diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap new file mode 100644 index 00000000..1473d66a --- /dev/null +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -0,0 +1,86 @@ +{ + "sarscov2 - bam - intervals": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,13f8358467c9cda8a95194a1498ce605" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,13f8358467c9cda8a95194a1498ce605" + ] + ], + "cram": [ + + ], + "versions": [ + "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + ] + } + ], + "timestamp": "2023-12-09T03:10:32.612468954" + }, + "sarscov2 - cram": { + "content": [ + [ + "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + ] + ], + "timestamp": "2023-12-09T03:10:46.692732651" + }, + "test.cram": { + "content": [ + "test.cram" + ], + "timestamp": "2023-12-09T03:10:46.70859771" + }, + "sarscov2 - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,e025e4351c5a3ff426bb5521cb353e0f" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,e025e4351c5a3ff426bb5521cb353e0f" + ] + ], + "cram": [ + + ], + "versions": [ + "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + ] + } + ], + "timestamp": "2023-12-09T03:10:19.704738169" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/applybqsr/tests/tags.yml b/modules/nf-core/gatk4/applybqsr/tests/tags.yml new file mode 100644 index 00000000..8da9292d --- /dev/null +++ b/modules/nf-core/gatk4/applybqsr/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/applybqsr: + - "modules/nf-core/gatk4/applybqsr/**" diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 16241b6d..6863fb17 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_baserecalibrator channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index e893b650..b4af1f33 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -50,4 +50,14 @@ process GATK4_BASERECALIBRATOR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.table + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test new file mode 100644 index 00000000..1262b694 --- /dev/null +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -0,0 +1,166 @@ +nextflow_process { + + name "Test Process GATK4_BASERECALIBRATOR" + script "../main.nf" + process "GATK4_BASERECALIBRATOR" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/baserecalibrator" + + test("sarscov2 - bam") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - intervals") { + when { + process { + """ + + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - multiple sites") { + when { + process { + """ + + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[4] = [ + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) + ] + input[5] = [ + file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [], + [], + [] + ] + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - cram ") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [] + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[4] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) + input[5] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap new file mode 100644 index 00000000..0d96f660 --- /dev/null +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -0,0 +1,147 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ] + } + ], + "timestamp": "2023-12-14T20:42:32.991100186" + }, + "sarscov2 - bam - intervals": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + ] + ], + "1": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,9ecb5f00a2229291705addc09c0ec231" + ] + ], + "versions": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ] + } + ], + "timestamp": "2023-12-14T20:42:07.697600853" + }, + "sarscov2 - bam - multiple sites": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "1": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "versions": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ] + } + ], + "timestamp": "2023-12-14T20:42:21.374942189" + }, + "homo_sapiens - cram ": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + ] + ], + "1": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + ] + ], + "versions": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ] + } + ], + "timestamp": "2023-12-14T20:42:49.148196543" + }, + "sarscov2 - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "1": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,e2e43abdc0c943c1a54dae816d0b9ea7" + ] + ], + "versions": [ + "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + ] + } + ], + "timestamp": "2023-12-14T20:41:53.870942331" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/tags.yml b/modules/nf-core/gatk4/baserecalibrator/tests/tags.yml new file mode 100644 index 00000000..648b4626 --- /dev/null +++ b/modules/nf-core/gatk4/baserecalibrator/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/baserecalibrator: + - "modules/nf-core/gatk4/baserecalibrator/**" diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index 16241b6d..e7cb4280 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_bedtointervallist channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index 16241b6d..c1205a35 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_combinegvcfs channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 16241b6d..db663e14 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_createsequencedictionary channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 16241b6d..0c8f32fa 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_haplotypecaller channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index fdecf5f8..a6a71d56 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -8,12 +8,12 @@ process GATK4_HAPLOTYPECALLER { 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: - tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) - path fasta - path fai - path dict - path dbsnp - path dbsnp_tbi + tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(dbsnp) + tuple val(meta6), path(dbsnp_tbi) output: tuple val(meta), path("*.vcf.gz") , emit: vcf diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index f38dc37d..2085c2db 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -35,21 +35,46 @@ input: type: file description: Text file containing the DragSTR model of the used BAM/CRAM file (optional) pattern: "*.txt" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] - fasta: type: file description: The reference fasta file pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] - fai: type: file description: Index of reference fasta file pattern: "fasta.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] - dict: type: file description: GATK sequence dictionary pattern: "*.dict" + - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test', single_end:false ] - dbsnp: type: file description: VCF file containing known sites (optional) + - meta6: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test', single_end:false ] - dbsnp_tbi: type: file description: VCF index of dbsnp (optional) diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test new file mode 100644 index 00000000..8d6ed4cf --- /dev/null +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test @@ -0,0 +1,146 @@ +// nf-core modules test gatk4/haplotypecaller +nextflow_process { + + name "Test Process GATK4_HAPLOTYPECALLER" + script "../main.nf" + process "GATK4_HAPLOTYPECALLER" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/haplotypecaller" + + test("homo_sapiens - [bam, bai] - fasta - fai - dict") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [], + [] + ] + input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + // { assert snapshot(process.out).match() }, // Unstable hashes + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, + { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + ) + } + + } + + test("homo_sapiens - [cram, crai] - fasta - fai - dict") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [], + [] + ] + input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [], [] ] + input[5] = [ [], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + // { assert snapshot(process.out).match() }, // Unstable hashes + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, + { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + ) + } + + } + + test("homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [], + [] + ] + input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + // { assert snapshot(process.out).match() }, // Unstable hashes + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, + { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + ) + } + + } + + test("homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true) + ] + input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + // { assert snapshot(process.out).match() }, // Unstable hashes + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, + { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap new file mode 100644 index 00000000..e5349c2d --- /dev/null +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -0,0 +1,20 @@ +{ + "output/gatk4/versions.yml": { + "content": [ + "versions.yml" + ], + "timestamp": "2023-11-24T12:59:29.843116" + }, + "output/gatk4/test.vcf.gz.tbi": { + "content": [ + "test.vcf.gz.tbi" + ], + "timestamp": "2023-11-24T12:59:29.840834" + }, + "output/gatk4/test.vcf.gz": { + "content": [ + "test.vcf.gz" + ], + "timestamp": "2023-11-24T12:59:29.832106" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/tags.yml b/modules/nf-core/gatk4/haplotypecaller/tests/tags.yml new file mode 100644 index 00000000..d05bb655 --- /dev/null +++ b/modules/nf-core/gatk4/haplotypecaller/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/haplotypecaller: + - "modules/nf-core/gatk4/haplotypecaller/**" diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 16241b6d..95beac68 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_indexfeaturefile channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index 16241b6d..b70e5e14 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_intervallisttools channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 8c0c6bb2..9af4f568 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,7 +1,8 @@ +name: gatk4_markduplicates channels: - conda-forge - bioconda - defaults dependencies: - bioconda::gatk4=4.4.0.0 - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 564b86d3..790af889 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -4,8 +4,8 @@ process GATK4_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0': - 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-13342043031ce2dd38cd19135a0754154f3d5dcf:5b8e58304eeed40565ed7894b208444fc5c852fa-0': + 'biocontainers/mulled-v2-13342043031ce2dd38cd19135a0754154f3d5dcf:5b8e58304eeed40565ed7894b208444fc5c852fa-0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/markduplicates/tests/bam.config b/modules/nf-core/gatk4/markduplicates/tests/bam.config new file mode 100644 index 00000000..0bbfbac3 --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/tests/bam.config @@ -0,0 +1,8 @@ +process { + + withName: GATK4_MARKDUPLICATES { + ext.args = '--CREATE_INDEX true' + ext.prefix = { "${meta.id}.bam" } + } + +} diff --git a/modules/nf-core/gatk4/markduplicates/tests/cram.config b/modules/nf-core/gatk4/markduplicates/tests/cram.config new file mode 100644 index 00000000..04a9b074 --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/tests/cram.config @@ -0,0 +1,8 @@ +process { + + withName: GATK4_MARKDUPLICATES { + ext.args = '--CREATE_INDEX true' + ext.prefix = { "${meta.id}.cram" } + } + +} diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test new file mode 100644 index 00000000..d243b19a --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test @@ -0,0 +1,126 @@ +nextflow_process { + + name "Test Process GATK4_MARKDUPLICATES" + script "../main.nf" + process "GATK4_MARKDUPLICATES" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/markduplicates" + + test("sarscov2 - bam") { + config "./bam.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.bam).match("bam") }, + { assert snapshot(process.out.bai).match("bai") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert snapshot(file(process.out.metrics[0][1]).name).match("test.metrics") } + ) + } + } + + test("homo_sapiens - multiple bam") { + config "./bam.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + ] + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.bam).match("multi bam") }, + { assert snapshot(process.out.bai).match("multi bai") }, + { assert snapshot(process.out.versions).match("multi versions") }, + { assert snapshot(file(process.out.metrics[0][1]).name).match("multi test.metrics") } + ) + } + + } + + test("homo_sapiens - multiple cram") { + config "./cram.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + ] + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.cram[0][1]).name).match("multi cram")}, + { assert snapshot(file(process.out.crai[0][1]).name).match("multi crai") }, + { assert snapshot(process.out.versions).match("multi cram versions") }, + { assert snapshot(file(process.out.metrics[0][1]).name).match("multi cram test.metrics") } + ) + } + + } + + test("stub") { + config "./bam.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + [] + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap new file mode 100644 index 00000000..a89fe989 --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap @@ -0,0 +1,112 @@ +{ + "multi bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,f178378cbc335ab2447f49f32b767083" + ] + ] + ], + "timestamp": "2023-12-12T17:43:11.703789701" + }, + "multi crai": { + "content": [ + "test.cram.crai" + ], + "timestamp": "2023-12-12T17:43:37.780426007" + }, + "multi bai": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bai:md5,529fbbad54edf512a1249c9be4258fba" + ] + ] + ], + "timestamp": "2023-12-12T17:43:11.71311291" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,ea27c5dfbc6df51aff34d5bf4b7a0eca" + ] + ], + "timestamp": "2023-12-12T17:42:39.657705497" + }, + "multi test.metrics": { + "content": [ + "test.bam.metrics" + ], + "timestamp": "2023-12-12T17:43:11.732892667" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bai:md5,26001bcdbce12e9f07557d8f7b8d360e" + ] + ] + ], + "timestamp": "2023-12-12T17:42:39.651888758" + }, + "multi cram versions": { + "content": [ + [ + "versions.yml:md5,ea27c5dfbc6df51aff34d5bf4b7a0eca" + ] + ], + "timestamp": "2023-12-12T17:43:37.789135196" + }, + "multi versions": { + "content": [ + [ + "versions.yml:md5,ea27c5dfbc6df51aff34d5bf4b7a0eca" + ] + ], + "timestamp": "2023-12-12T17:43:11.722133619" + }, + "multi cram test.metrics": { + "content": [ + "test.cram.metrics" + ], + "timestamp": "2023-12-12T17:43:37.798977444" + }, + "multi cram": { + "content": [ + "test.cram" + ], + "timestamp": "2023-12-12T17:43:37.771137858" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,2e17dfa6db576fd87be8b36fa2133c73" + ] + ] + ], + "timestamp": "2023-12-12T17:42:39.64008431" + }, + "test.metrics": { + "content": [ + "test.bam.metrics" + ], + "timestamp": "2023-12-12T17:42:39.672508385" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/markduplicates/tests/tags.yml b/modules/nf-core/gatk4/markduplicates/tests/tags.yml new file mode 100644 index 00000000..8632e32b --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/markduplicates: + - "modules/nf-core/gatk4/markduplicates/**" diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index 16241b6d..d6c3e51a 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_mergevcfs channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 16241b6d..50b79217 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_splitncigarreads channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 16241b6d..cc16bc0e 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -1,3 +1,4 @@ +name: gatk4_variantfiltration channels: - conda-forge - bioconda diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index d127cae3..5398f71c 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -1,3 +1,4 @@ +name: gffread channels: - conda-forge - bioconda diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index 68f8045b..d8a473e0 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -11,20 +11,22 @@ process GFFREAD { path gff output: - path "*.gtf" , emit: gtf + path "*.gtf" , emit: gtf , optional: true + path "*.gff3" , emit: gffread_gff , optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${gff.baseName}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${gff.baseName}" + def extension = args.contains("-T") ? 'gtf' : 'gffread.gff3' """ gffread \\ $gff \\ $args \\ - -o ${prefix}.gtf + -o ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": gffread: \$(gffread --version 2>&1) diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index f486f8bb..27ac3105 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -20,8 +20,12 @@ input: output: - gtf: type: file - description: GTF file resulting from the conversion of the GFF input file + description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present pattern: "*.{gtf}" + - gffread_gff: + type: file + description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent + pattern: "*.{gff3}" - versions: type: file description: File containing software versions diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index 67d47ecb..3c064b31 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -3,11 +3,38 @@ nextflow_process { name "Test Process GFFREAD" script "../main.nf" process "GFFREAD" + tag "gffread" tag "modules_nfcore" tag "modules" - test("Should run without failures") { + test("sarscov2-gff3-gtf") { + + config "./nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf != null }, + { assert process.out.gffread_gff == [] } + ) + } + + } + + test("sarscov2-gff3-gff3") { when { params { @@ -23,7 +50,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match() }, + { assert process.out.gtf == [] }, + { assert process.out.gffread_gff != null }, ) } diff --git a/modules/nf-core/gffread/tests/main.nf.test.snap b/modules/nf-core/gffread/tests/main.nf.test.snap index fb5460cf..1f1342e1 100644 --- a/modules/nf-core/gffread/tests/main.nf.test.snap +++ b/modules/nf-core/gffread/tests/main.nf.test.snap @@ -1,21 +1,52 @@ { - "Should run without failures": { + "sarscov2-gff3-gtf": { "content": [ { "0": [ - "genome.gtf:md5,f184f856b7fe3e159d21b052b5dd3954" + "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3" ], "1": [ + + ], + "2": [ + "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + ], + "gffread_gff": [ + + ], + "gtf": [ + "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3" + ], + "versions": [ + "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + ] + } + ], + "timestamp": "2023-11-29T15:39:30.006985" + }, + "sarscov2-gff3-gff3": { + "content": [ + { + "0": [ + + ], + "1": [ + "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d" + ], + "2": [ "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" ], + "gffread_gff": [ + "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d" + ], "gtf": [ - "genome.gtf:md5,f184f856b7fe3e159d21b052b5dd3954" + ], "versions": [ "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" ] } ], - "timestamp": "2023-10-17T10:00:08.542490523" + "timestamp": "2023-11-29T15:39:34.636061" } } \ No newline at end of file diff --git a/modules/nf-core/gffread/tests/nextflow.config b/modules/nf-core/gffread/tests/nextflow.config new file mode 100644 index 00000000..74b25094 --- /dev/null +++ b/modules/nf-core/gffread/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GFFREAD { + ext.args = '-T' + } +} diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 222b301f..25910b34 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,3 +1,4 @@ +name: gunzip channels: - conda-forge - bioconda diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index f1521e08..88c7126c 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,6 +1,8 @@ +name: mosdepth channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::mosdepth=0.3.3 + # renovate: datasource=conda depName=bioconda/mosdepth + - mosdepth=0.3.6 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 7dd13ffb..c7e24303 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : - 'biocontainers/mosdepth:0.3.3--hdfd78af_1'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' : + 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}" input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index 76263b5a..9caaf2cd 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -26,19 +26,14 @@ input: type: file description: Index for BAM/CRAM file pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'test' ] - bed: type: file description: BED file with intersected intervals pattern: "*.{bed}" - - meta3: + - meta2: type: map description: | - Groovy Map containing reference information + Groovy Map containing bed information e.g. [ id:'test' ] - fasta: type: file diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test new file mode 100644 index 00000000..d991f819 --- /dev/null +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -0,0 +1,260 @@ +nextflow_process { + + name "Test Process MOSDEPTH" + script "../main.nf" + process "MOSDEPTH" + + tag "modules" + tag "modules_nfcore" + tag "mosdepth" + + test("homo_sapiens - bam, bai, []") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - bam, bai, bed") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - cram, crai, []") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + [] + ] + input[1] = [ + [ id:'test' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - cram, crai, bed") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [ + [ id:'test' ], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - bam, bai, [] - window") { + + config "./window.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - bam, bai, [] - quantized") { + + config "./quantized.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + [] + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - bam, bai, bed - thresholds") { + + config "./threshold.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - bam, bai, bed - fail") { + + config "./window.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.failed } + ) + } + + } + + test("homo_sapiens - bam, bai, [] - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.global_txt[0][1]).name, + file(process.out.summary_txt[0][1]).name, + file(process.out.regions_txt[0][1]).name, + file(process.out.per_base_d4[0][1]).name, + file(process.out.per_base_bed[0][1]).name, + file(process.out.per_base_csi[0][1]).name, + file(process.out.regions_bed[0][1]).name, + file(process.out.regions_csi[0][1]).name, + file(process.out.quantized_bed[0][1]).name, + file(process.out.quantized_csi[0][1]).name, + file(process.out.thresholds_bed[0][1]).name, + file(process.out.thresholds_csi[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap new file mode 100644 index 00000000..dc4d9508 --- /dev/null +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -0,0 +1,1145 @@ +{ + "homo_sapiens - bam, bai, [] - stub": { + "content": [ + "test.global.dist.txt", + "test.summary.txt", + "test.region.dist.txt", + "test.per-base.d4", + "test.per-base.bed.gz", + "test.per-base.bed.gz.csi", + "test.regions.bed.gz", + "test.regions.bed.gz.csi", + "test.quantized.bed.gz", + "test.quantized.bed.gz.csi", + "test.thresholds.bed.gz", + "test.thresholds.bed.gz.csi", + [ + "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + ] + ], + "timestamp": "2023-11-27T15:14:34.897155161" + }, + "homo_sapiens - cram, crai, bed": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.mosdepth.global.dist.txt:md5,e82e90c7d508a135b5a8a7cd6933452e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.mosdepth.summary.txt:md5,96c037f769974b904beb53edc4f56d82" + ] + ], + "10": [ + + ], + "11": [ + + ], + "12": [ + "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.mosdepth.region.dist.txt:md5,e82e90c7d508a135b5a8a7cd6933452e" + ] + ], + "3": [ + + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + ] + ], + "8": [ + + ], + "9": [ + + ], + "global_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.mosdepth.global.dist.txt:md5,e82e90c7d508a135b5a8a7cd6933452e" + ] + ], + "per_base_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + ] + ], + "per_base_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + ] + ], + "per_base_d4": [ + + ], + "quantized_bed": [ + + ], + "quantized_csi": [ + + ], + "regions_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + ] + ], + "regions_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + ] + ], + "regions_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.mosdepth.region.dist.txt:md5,e82e90c7d508a135b5a8a7cd6933452e" + ] + ], + "summary_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.mosdepth.summary.txt:md5,96c037f769974b904beb53edc4f56d82" + ] + ], + "thresholds_bed": [ + + ], + "thresholds_csi": [ + + ], + "versions": [ + "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + ] + } + ], + "timestamp": "2023-11-27T14:47:18.171150781" + }, + "homo_sapiens - 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"modules/nf-core/mosdepth/**" diff --git a/modules/nf-core/mosdepth/tests/threshold.config b/modules/nf-core/mosdepth/tests/threshold.config new file mode 100644 index 00000000..9b014ddf --- /dev/null +++ b/modules/nf-core/mosdepth/tests/threshold.config @@ -0,0 +1,3 @@ +process { + ext.args = "--thresholds 1,10,20,30" +} \ No newline at end of file diff --git a/modules/nf-core/mosdepth/tests/window.config b/modules/nf-core/mosdepth/tests/window.config new file mode 100644 index 00000000..7a0f755c --- /dev/null +++ b/modules/nf-core/mosdepth/tests/window.config @@ -0,0 +1,3 @@ +process { + ext.args = "--by 100" +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 04c82f14..01ccbcc7 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,6 +1,7 @@ +name: samtools_faidx channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 3aa98822..d3461627 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 04c82f14..5efae053 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,6 +1,7 @@ +name: samtools_flagstat channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 9dee35a5..f1893d7c 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test new file mode 100644 index 00000000..c8dd8dc9 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FLAGSTAT" + script "../main.nf" + process "SAMTOOLS_FLAGSTAT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/flagstat" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.flagstat).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap new file mode 100644 index 00000000..880019f2 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "timestamp": "2023-11-14T15:49:22.577133" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/tests/tags.yml b/modules/nf-core/samtools/flagstat/tests/tags.yml new file mode 100644 index 00000000..2d2b7255 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/flagstat: + - modules/nf-core/samtools/flagstat/** diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 04c82f14..2401db0f 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,6 +1,7 @@ +name: samtools_idxstats channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index b22d0843..00d916bb 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test new file mode 100644 index 00000000..f6c92150 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process SAMTOOLS_IDXSTATS" + script "../main.nf" + process "SAMTOOLS_IDXSTATS" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/idxstats" + + test("BAM") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.idxstats).match() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap new file mode 100644 index 00000000..4c6c12bd --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "BAM": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "timestamp": "2023-11-14T15:52:19.875194" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/tests/tags.yml b/modules/nf-core/samtools/idxstats/tests/tags.yml new file mode 100644 index 00000000..d3057c61 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/idxstats: + - modules/nf-core/samtools/idxstats/** diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 04c82f14..296ed99e 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,7 @@ +name: samtools_index channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 256bd7c4..8ad18fdc 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 00000000..0ed260ef --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 00000000..c76a9169 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("sarscov2 [BAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.bai).match("bai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CRAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.crai).match("crai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CSI]") { + + config "./csi.nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 00000000..b3baee7f --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "crai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ] + ], + "timestamp": "2023-11-15T15:17:37.30801" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ] + ], + "timestamp": "2023-11-15T15:17:30.869234" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 00000000..e0f58a7a --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 04c82f14..1f7fe49f 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,6 +1,7 @@ +name: samtools_merge channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 21f785cf..e104b90a 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input_files, stageAs: "?/*") @@ -44,10 +44,14 @@ process SAMTOOLS_MERGE { """ stub: + def args = task.ext.args ?: '' prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" def file_type = input_files instanceof List ? input_files[0].getExtension() : input_files.getExtension() + def index_type = file_type == "bam" ? "csi" : "crai" + def index = args.contains("--write-index") ? "touch ${prefix}.${index_type}" : "" """ touch ${prefix}.${file_type} + ${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/merge/tests/index.config b/modules/nf-core/samtools/merge/tests/index.config new file mode 100644 index 00000000..8c5668cf --- /dev/null +++ b/modules/nf-core/samtools/merge/tests/index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--write-index" +} \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test new file mode 100644 index 00000000..024f9f70 --- /dev/null +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -0,0 +1,156 @@ +nextflow_process { + + name "Test Process SAMTOOLS_MERGE" + script "../main.nf" + process "SAMTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/merge" + + test("sarscov2 - [bam1, bam2, bam3], [], []") { + + config "./index.config" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + file(process.out.csi[0][1]).name, + process.out.crai, + process.out.versions + ).match() } + ) + } + + } + + test("homo_sapiens - [cram1, cram2], fasta, fai") { + + config "./index.config" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + ] + ] + input[1] = [ + [id:'genome'], + file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + ] + input[2] = [ + [id:'genome'], + file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.cram[0][1]).name, + process.out.bam, + file(process.out.crai[0][1]).name, + process.out.csi, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - bam, [], []") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), + ] + input[1] = [[],[]] + input[2] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + process.out.crai, + process.out.csi, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [bam1, bam2, bam3], [], [] - stub") { + + config "./index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.cram, + file(process.out.csi[0][1]).name, + process.out.crai, + process.out.versions + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..3ab57d81 --- /dev/null +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 - bam, [], []": { + "content": [ + "test.bam", + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" + ] + ], + "timestamp": "2023-12-04T17:13:30.244841621" + }, + "sarscov2 - [bam1, bam2, bam3], [], [] - stub": { + "content": [ + "test.bam", + [ + + ], + "test.csi", + [ + + ], + [ + "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" + ] + ], + "timestamp": "2023-12-04T17:10:14.861445721" + }, + "homo_sapiens - [cram1, cram2], fasta, fai": { + "content": [ + "test.cram", + [ + + ], + "test.cram.crai", + [ + + ], + [ + "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" + ] + ], + "timestamp": "2023-12-04T17:09:29.716002618" + }, + "sarscov2 - [bam1, bam2, bam3], [], []": { + "content": [ + "test.bam", + [ + + ], + "test.bam.csi", + [ + + ], + [ + "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" + ] + ], + "timestamp": "2023-12-04T17:08:42.329973045" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/tests/tags.yml b/modules/nf-core/samtools/merge/tests/tags.yml new file mode 100644 index 00000000..b869abcb --- /dev/null +++ b/modules/nf-core/samtools/merge/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/merge: + - "modules/nf-core/samtools/merge/**" diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 04c82f14..cd50868c 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,6 +1,7 @@ +name: samtools_sort channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 60f0c634..4a666d42 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 1f72f3b9..abb80978 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -61,7 +61,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() } ) } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index a43566da..ff722259 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" ] ], "1": [ ], "2": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" ], "bam": [ [ @@ -23,17 +23,26 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" ] ], "csi": [ ], "versions": [ - "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" ] } ], - "timestamp": "2023-10-17T17:21:46.5427968" + "timestamp": "2023-12-04T11:11:22.005628301" + }, + "test_samtools_sort_stub": { + "content": [ + "test.sorted.bam", + [ + "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + ] + ], + "timestamp": "2023-12-04T17:47:22.314445935" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 04c82f14..b89ce647 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,6 +1,7 @@ +name: samtools_stats channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::samtools=1.17 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 07286ef4..7539140a 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e037132c..20c3efe1 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -4,7 +4,7 @@ nextflow_process { script "../main.nf" process "SAMTOOLS_STATS" tag "modules" - tag "modules/nf-core" + tag "modules_nfcore" tag "samtools" tag "samtools/stats" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 516b2b01..025c83a5 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" ] ], "1": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ], "stats": [ [ @@ -20,15 +20,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,6e768486d5df0257351c5419a79f9c9b" + "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" ] ], "versions": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ] } ], - "timestamp": "2023-10-18T12:12:42.998746" + "timestamp": "2023-12-04T11:07:28.26821485" }, "SAMTOOLS CRAM Should run without failures": { "content": [ @@ -39,11 +39,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" ] ], "1": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ], "stats": [ [ @@ -51,14 +51,14 @@ "id": "test", "single_end": false }, - "test.stats:md5,7c9ee5747793cceb9d6f4d733345641a" + "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" ] ], "versions": [ - "versions.yml:md5,08035f3409d934d47a416150884bb0df" + "versions.yml:md5,650a365c6635001436008350ae83337c" ] } ], - "timestamp": "2023-10-18T12:13:30.747222" + "timestamp": "2023-12-04T11:07:50.356233402" } } \ No newline at end of file diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml index 7d54aa5b..62f3d5aa 100644 --- a/modules/nf-core/snpeff/download/environment.yml +++ b/modules/nf-core/snpeff/download/environment.yml @@ -1,3 +1,4 @@ +name: snpeff_download channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index 26e728f7..f367c696 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -1,4 +1,4 @@ -name: SNPEFF_DOWNLOAD +name: snpeff_download description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml index 7d54aa5b..b492e6a8 100644 --- a/modules/nf-core/snpeff/snpeff/environment.yml +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -1,3 +1,4 @@ +name: snpeff_snpeff channels: - conda-forge - bioconda diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 0b771447..7559c3de 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -1,4 +1,4 @@ -name: SNPEFF_SNPEFF +name: snpeff_snpeff description: Genetic variant annotation and functional effect prediction toolbox keywords: - annotation diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index a61d2f6d..36fcd022 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,9 @@ +name: star_align channels: - conda-forge - bioconda - defaults dependencies: - bioconda::star=2.7.10a - - bioconda::samtools=1.16.1 + - bioconda::samtools=1.18 - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index fa645a6d..8e9c48b1 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,8 +4,8 @@ process STAR_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test new file mode 100644 index 00000000..4c878474 --- /dev/null +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -0,0 +1,339 @@ +nextflow_process { + + name "Test Process STAR_ALIGN" + script "../main.nf" + process "STAR_ALIGN" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/align" + + test("homo_sapiens - single_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end - arriba") { + config "./nextflow.arriba.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") } + ) + } + } + + test("homo_sapiens - paired_end - starfusion") { + config "./nextflow.starfusion.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") } + ) + } + } + + test("homo_sapiens - paired_end - multiple") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap new file mode 100644 index 00000000..08edb914 --- /dev/null +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -0,0 +1,769 @@ +{ + "homo_sapiens - paired_end - multiple - bam_sorted": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" + ] + ] + ], + "timestamp": "2023-12-04T18:01:19.968225733" + }, + "homo_sapiens - 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single_end - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.SJ.out.tab:md5,75a516ab950fb958f40b29996474949c" + ] + ] + ], + "timestamp": "2023-12-04T17:53:26.50932751" + }, + "homo_sapiens - paired_end - starfusion - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a" + ] + ] + ], + "timestamp": "2023-12-04T17:59:58.731699486" + }, + "homo_sapiens - single_end - log_out": { + "content": [ + "test.Log.out" + ], + "timestamp": "2023-11-23T13:22:55.126286" + }, + "homo_sapiens - paired_end - log_final": { + "content": [ + "test.Log.final.out" + ], + "timestamp": "2023-11-23T13:23:33.253884" + }, + "homo_sapiens - single_end - log_final": { + "content": [ + "test.Log.final.out" + ], + "timestamp": "2023-11-23T13:22:55.11799" + }, + "homo_sapiens - paired_end - bam_transcript": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.287684" + }, + "homo_sapiens - paired_end - starfusion - log_progress": { + "content": [ + "test.Log.progress.out" + ], + "timestamp": "2023-11-23T13:27:55.971484" + }, + "homo_sapiens - paired_end - multiple - bam_transcript": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:29:01.264176" + }, + "homo_sapiens - paired_end - multiple - read_per_gene_tab": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:29:01.596406" + }, + "homo_sapiens - single_end - read_per_gene_tab": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:22:55.205936" + }, + "homo_sapiens - paired_end - junction": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.340653" + }, + "homo_sapiens - paired_end - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" + ] + ] + ], + "timestamp": "2023-12-04T17:54:12.185730856" + }, + "homo_sapiens - paired_end - starfusion - sam": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:27:56.300637" + }, + "homo_sapiens - paired_end - arriba - bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5" + ] + ] + ], + "timestamp": "2023-12-04T17:56:12.190560178" + }, + "homo_sapiens - single_end - log_progress": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8" + ] + ] + ], + "timestamp": "2023-12-04T17:53:26.450352138" + }, + "homo_sapiens - paired_end - starfusion - wig": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:27:56.422018" + }, + "homo_sapiens - paired_end - wig": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.429457" + }, + "homo_sapiens - paired_end - starfusion - log_out": { + "content": [ + "test.Log.out" + ], + "timestamp": "2023-11-23T13:27:55.93945" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config new file mode 100644 index 00000000..2324b9e5 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config new file mode 100644 index 00000000..c4ac5808 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config new file mode 100644 index 00000000..467b6497 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/tags.yml b/modules/nf-core/star/align/tests/tags.yml new file mode 100644 index 00000000..8beace16 --- /dev/null +++ b/modules/nf-core/star/align/tests/tags.yml @@ -0,0 +1,2 @@ +star/align: + - modules/nf-core/star/align/** diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index a61d2f6d..93e4476a 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,11 @@ +name: star_genomegenerate + channels: - conda-forge - bioconda - defaults + dependencies: + - bioconda::samtools=1.18 - bioconda::star=2.7.10a - - bioconda::samtools=1.16.1 - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 473e62a6..b8855715 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -4,8 +4,8 @@ process STAR_GENOMEGENERATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" input: tuple val(meta), path(fasta) @@ -19,9 +19,10 @@ process STAR_GENOMEGENERATE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def args_list = args.tokenize() - def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + def args = task.ext.args ?: '' + def args_list = args.tokenize() + def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + def include_gtf = gtf ? "--sjdbGTFfile $gtf" : '' if (args_list.contains('--genomeSAindexNbases')) { """ mkdir star @@ -29,7 +30,7 @@ process STAR_GENOMEGENERATE { --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ - --sjdbGTFfile $gtf \\ + $include_gtf \\ --runThreadN $task.cpus \\ $memory \\ $args @@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE { --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ - --sjdbGTFfile $gtf \\ + $include_gtf \\ --runThreadN $task.cpus \\ --genomeSAindexNbases \$NUM_BASES \\ $memory \\ @@ -67,30 +68,52 @@ process STAR_GENOMEGENERATE { } stub: - """ - mkdir star - touch star/Genome - touch star/Log.out - touch star/SA - touch star/SAindex - touch star/chrLength.txt - touch star/chrName.txt - touch star/chrNameLength.txt - touch star/chrStart.txt - touch star/exonGeTrInfo.tab - touch star/exonInfo.tab - touch star/geneInfo.tab - touch star/genomeParameters.txt - touch star/sjdbInfo.txt - touch star/sjdbList.fromGTF.out.tab - touch star/sjdbList.out.tab - touch star/transcriptInfo.tab + if (gtf) { + """ + mkdir star + touch star/Genome + touch star/Log.out + touch star/SA + touch star/SAindex + touch star/chrLength.txt + touch star/chrName.txt + touch star/chrNameLength.txt + touch star/chrStart.txt + touch star/exonGeTrInfo.tab + touch star/exonInfo.tab + touch star/geneInfo.tab + touch star/genomeParameters.txt + touch star/sjdbInfo.txt + touch star/sjdbList.fromGTF.out.tab + touch star/sjdbList.out.tab + touch star/transcriptInfo.tab - cat <<-END_VERSIONS > versions.yml - "${task.process}": - star: \$(STAR --version | sed -e "s/STAR_//g") - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') - END_VERSIONS - """ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + } else { + """ + mkdir star + touch star/Genome + touch star/Log.out + touch star/SA + touch star/SAindex + touch star/chrLength.txt + touch star/chrName.txt + touch star/chrNameLength.txt + touch star/chrStart.txt + touch star/genomeParameters.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + } } diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test new file mode 100644 index 00000000..af0c9421 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_process { + + name "Test Process STAR_GENOMEGENERATE" + script "../main.nf" + process "STAR_GENOMEGENERATE" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/genomegenerate" + + test("homo_sapiens") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-without_gtf") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ [], [] ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-without_gtf-stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ [], [] ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap new file mode 100644 index 00000000..9de08c74 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "timestamp": "2023-12-19T11:05:51.741109" + }, + "index_with_gtf": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "timestamp": "2023-12-19T11:38:14.551548" + }, + "index_without_gtf": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + ], + "timestamp": "2023-12-19T11:38:22.382905" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml new file mode 100644 index 00000000..79f619bf --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/tags.yml @@ -0,0 +1,2 @@ +star/genomegenerate: + - modules/nf-core/star/genomegenerate/** diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index fdd84057..028461c9 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,3 +1,4 @@ +name: tabix_bgziptabix channels: - conda-forge - bioconda diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index fdd84057..7167fb87 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,3 +1,4 @@ +name: tabix_tabix channels: - conda-forge - bioconda diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 2d52ce64..d6917da3 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,3 +1,4 @@ +name: untar channels: - conda-forge - bioconda diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test new file mode 100644 index 00000000..d40db13d --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test @@ -0,0 +1,77 @@ +nextflow_process { + + name "Test Process UNTAR" + script "../main.nf" + process "UNTAR" + + tag "modules" + tag "modules_nfcore" + tag "untar" + + test("test_untar") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar") }, + ) + } + + } + + test("test_untar_different_output_path") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_different_output_path") }, + ) + } + + } + + test("test_untar_onlyfiles") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + ) + } + + } + +} diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap new file mode 100644 index 00000000..146c8678 --- /dev/null +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -0,0 +1,513 @@ +{ + "test_untar_different_output_path": { + "content": [ + [ + [ + [ + + ], + [ + [ + [ + [ + [ + [ + "s_1_1101.bcl:md5,ad01889e2ff43e2f194224e20bdb600c", + "s_1_1101.stats:md5,4bbbf103454b37fbc3138fadf1b4446b" + ], + [ + "s_1_1101.bcl:md5,565384bbe67a694dfd690bae6d1d30c2", + "s_1_1101.stats:md5,55e5abd8f129ff38ef169873547abdb8" + ], + [ + "s_1_1101.bcl:md5,650fa58a630a9148835ba79e323d4237", + "s_1_1101.stats:md5,77403669ca1b05340c390dff64425c1e" + ], + [ + "s_1_1101.bcl:md5,54471c9e97299cd141e202e204637702", + 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"TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c" + ], + "RunInfo.xml:md5,03038959f4dd181c86bc97ae71fe270a" + ] + ] + ] + ], + "timestamp": "2023-10-18T11:56:39.562418" + }, + "test_untar_onlyfiles": { + "content": [ + [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ] + ], + "timestamp": "2023-10-18T11:56:46.878844" + }, + "test_untar": { + "content": [ + [ + [ + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ] + ], + "timestamp": "2023-10-18T11:56:08.16574" + } +} \ No newline at end of file diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml new file mode 100644 index 00000000..feb6f15c --- /dev/null +++ b/modules/nf-core/untar/tests/tags.yml @@ -0,0 +1,2 @@ +untar: + - modules/nf-core/untar/** From c10810f2daeef125504080e0d41019ca1b8bf908 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 29 Dec 2023 10:55:07 +0100 Subject: [PATCH 073/275] docker.runOptions --- conf/modules.config | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b1890a84..34c689ae 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -120,7 +120,7 @@ process { // ALIGN_STAR withName: STAR_ALIGN { - ext.args = [ + ext.args = { [ '--outSAMtype BAM SortedByCoordinate', '--readFilesCommand zcat', params.save_unaligned ? '--outReadsUnmapped Fastx' : '', @@ -129,7 +129,7 @@ process { params.star_max_memory_bamsort > 0 ? "--limitBAMsortRAM ${params.star_max_memory_bamsort}" : "", params.star_bins_bamsort > 0 ? "--outBAMsortingBinsN ${params.star_bins_bamsort}" : "", params.star_max_collapsed_junc > 0 ? "--limitOutSJcollapsed ${params.star_max_collapsed_junc}" : "" - ].join(' ').trim() + ].flatten().unique(false).join(' ').trim() } publishDir = [ [ path: { "${params.outdir}/reports/stats/${meta.id}/STAR_log" }, diff --git a/nextflow.config b/nextflow.config index 8f82d0b4..8c841b8a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -188,7 +188,7 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' From 50ab7d1c23a3b30cc43cab10b937dae477d4934b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 29 Dec 2023 11:22:27 +0100 Subject: [PATCH 074/275] fix channels for GATK4_HAPLOTYPECALLER --- workflows/rnavar.nf | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 6674386a..743d5da8 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -422,11 +422,11 @@ workflow RNAVAR { GATK4_HAPLOTYPECALLER( ch_haplotypecaller_interval_bam, - ch_fasta.map{ meta, fasta -> [fasta] }, - ch_fasta_fai, - ch_dict.map{ meta, dict -> [dict] }, - ch_dbsnp, - ch_dbsnp_tbi + ch_fasta, + ch_fasta_fai.map{ it -> [[id:it.baseName], it] }, + ch_dict, + ch_dbsnp.map{ it -> [[id:it.baseName], it] }, + ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } ) From 54cfaf473fcf4966563f3c2bc8463f86800a0f3c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 29 Dec 2023 11:28:04 +0100 Subject: [PATCH 075/275] update CHANGELOG --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 084197e7..f538a071 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#95](https://github.com/nf-core/rnavar/pull/95) - Template update from nf-core/tools 2.5 -> 2.9 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules +- [#111](https://github.com/nf-core/rnavar/pull/111) - Template update from nf-core/tools 2.11 ### Fixed @@ -21,8 +22,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ---------- | ----------- | ----------- | +| bcftools | 1.17 | 1.18 | +| bedtools | 2.31.0 | 2.31.1 | | fastqc | 0.11.9 | 0.12.1 | -| multiqc | 1.15 | 1.17 | +| mosdepth | 0.3.3 | 0.3.6 | +| multiqc | 1.15 | 1.18 | +| samtools | 1.17 | 1.18 | ## [1.0.0] nfcore/rnavar - 2022/06/20 From 9a3748ff805855c5a30d4ce1620752ab0d726f6b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 29 Dec 2023 11:42:59 +0100 Subject: [PATCH 076/275] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f538a071..675c25d1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules - [#111](https://github.com/nf-core/rnavar/pull/111) - Template update from nf-core/tools 2.11 +- [#117](https://github.com/nf-core/rnavar/pull/117) - Template update from nf-core/tools 2.11.1 ### Fixed From 9902e812552a170fe43fc2f4d157202b49f62a70 Mon Sep 17 00:00:00 2001 From: bioloni Date: Fri, 29 Dec 2023 13:30:55 +0000 Subject: [PATCH 077/275] Fixed prettier issues --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bb6adee7..23d26ba0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,9 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [1.1.0dev] nfcore/rnavar ### Added + - Added`unzip` from nf-core modules for working with unzipped fasta and gtf files ### Changed + - [#95](https://github.com/nf-core/rnavar/pull/95) - Template update from nf-core/tools 2.5 -> 2.9 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules From 99eb9355917dcc962366da5bd4f509b97ee62cf8 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 24 Jan 2024 21:40:32 +0000 Subject: [PATCH 078/275] [automated] Fix linting with Prettier --- .devcontainer/devcontainer.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..4a9bc5c7 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.linting.pylintPath": "/opt/conda/bin/pylint", }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } - } + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], + }, + }, } From 1f25a71475f41afd6f434f85e87b08ba65368617 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 29 Jan 2024 15:13:18 +0000 Subject: [PATCH 079/275] Template update for nf-core/tools version 2.12 --- .editorconfig | 8 + .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 67 +++++ .github/workflows/fix-linting.yml | 72 +++-- .github/workflows/linting.yml | 61 +--- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 4 +- .gitpod.yml | 1 + .pre-commit-config.yaml | 7 +- README.md | 8 +- assets/email_template.html | 2 +- assets/email_template.txt | 2 +- assets/nf-core-rnavar_logo_light.png | Bin 65097 -> 68146 bytes docs/images/nf-core-rnavar_logo_dark.png | Bin 65175 -> 25354 bytes docs/images/nf-core-rnavar_logo_light.png | Bin 65097 -> 21970 bytes lib/WorkflowMain.groovy | 16 +- lib/nfcore_external_java_deps.jar | Bin 2291171 -> 0 bytes main.nf | 2 +- modules.json | 6 +- .../dumpsoftwareversions/environment.yml | 2 +- .../custom/dumpsoftwareversions/main.nf | 4 +- .../dumpsoftwareversions/tests/main.nf.test | 7 +- .../tests/main.nf.test.snap | 50 ++-- modules/nf-core/fastqc/tests/main.nf.test | 265 ++++++++++++------ .../nf-core/fastqc/tests/main.nf.test.snap | 12 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 1 - modules/nf-core/multiqc/tests/main.nf.test | 48 +++- .../nf-core/multiqc/tests/main.nf.test.snap | 21 ++ nextflow.config | 3 +- pyproject.toml | 17 +- workflows/rnavar.nf | 7 + 36 files changed, 490 insertions(+), 221 deletions(-) create mode 100644 .github/workflows/download_pipeline.yml delete mode 100644 lib/nfcore_external_java_deps.jar create mode 100644 modules/nf-core/multiqc/tests/main.nf.test.snap diff --git a/.editorconfig b/.editorconfig index b6b31907..9b990088 100644 --- a/.editorconfig +++ b/.editorconfig @@ -22,3 +22,11 @@ indent_size = unset [/assets/email*] indent_size = unset + +# ignore Readme +[README.md] +indent_style = unset + +# ignore python +[*.{py}] +indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 3e2b977a..4858f99f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index ea0bd288..030354e1 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 40e9c617..acba0c5f 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v1 + uses: mshick/add-pr-comment@v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index 694e90ec..e37cfda5 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v7 + - uses: actions/stale@v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml new file mode 100644 index 00000000..8611458a --- /dev/null +++ b/.github/workflows/download_pipeline.yml @@ -0,0 +1,67 @@ +name: Test successful pipeline download with 'nf-core download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to master branch +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. +on: + workflow_dispatch: + pull_request: + types: + - opened + branches: + - master + pull_request_target: + branches: + - master + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + architecture: "x64" + - uses: eWaterCycle/setup-singularity@v7 + with: + singularity-version: 3.8.3 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install git+https://github.com/nf-core/tools.git@dev + + - name: Get the repository name and current branch set as environment variable + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + run: | + nf-core download ${{ env.REPO_LOWERCASE }} \ + --revision ${{ env.REPO_BRANCH }} \ + --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Run the downloaded pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index f79652ab..aba5c3ba 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -4,7 +4,7 @@ on: types: [created] jobs: - deploy: + fix-linting: # Only run if comment is on a PR with the main repo, and if it contains the magic keywords if: > contains(github.event.comment.html_url, '/pull/') && @@ -13,10 +13,17 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} + # indication that the linting is being fixed + - name: React on comment + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: eyes + # Action runs on the issue comment, so we don't get the PR by default # Use the gh cli to check out the PR - name: Checkout Pull Request @@ -24,32 +31,59 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v4 + # Install and run pre-commit + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + with: + python-version: 3.11 - - name: Install Prettier - run: npm install -g prettier @prettier/plugin-php + - name: Install pre-commit + run: pip install pre-commit - # Check that we actually need to fix something - - name: Run 'prettier --check' - id: prettier_status - run: | - if prettier --check ${GITHUB_WORKSPACE}; then - echo "result=pass" >> $GITHUB_OUTPUT - else - echo "result=fail" >> $GITHUB_OUTPUT - fi + - name: Run pre-commit + id: pre-commit + run: pre-commit run --all-files + continue-on-error: true - - name: Run 'prettier --write' - if: steps.prettier_status.outputs.result == 'fail' - run: prettier --write ${GITHUB_WORKSPACE} + # indication that the linting has finished + - name: react if linting finished succesfully + if: steps.pre-commit.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: "+1" - name: Commit & push changes - if: steps.prettier_status.outputs.result == 'fail' + id: commit-and-push + if: steps.pre-commit.outcome == 'failure' run: | git config user.email "core@nf-co.re" git config user.name "nf-core-bot" git config push.default upstream git add . git status - git commit -m "[automated] Fix linting with Prettier" + git commit -m "[automated] Fix code linting" git push + + - name: react if linting errors were fixed + id: react-if-fixed + if: steps.commit-and-push.outcome == 'success' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: hooray + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + comment-id: ${{ github.event.comment.id }} + reactions: confused + + - name: react if linting errors were not fixed + if: steps.commit-and-push.outcome == 'failure' + uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 + with: + issue-number: ${{ github.event.issue.number }} + body: | + @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. + See [CI log](https://github.com/nf-core/rnavar/actions/runs/${{ github.run_id }}) for more details. diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 905c58e4..81cd098e 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -11,61 +11,22 @@ on: types: [published] jobs: - EditorConfig: + pre-commit: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-node@v4 - - - name: Install editorconfig-checker - run: npm install -g editorconfig-checker - - - name: Run ECLint check - run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') - - Prettier: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - uses: actions/setup-node@v4 - - - name: Install Prettier - run: npm install -g prettier - - - name: Run Prettier --check - run: prettier --check ${GITHUB_WORKSPACE} - - PythonBlack: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Check code lints with Black - uses: psf/black@stable - - # If the above check failed, post a comment on the PR explaining the failure - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v1 + - name: Set up Python 3.11 + uses: actions/setup-python@v5 with: - message: | - ## Python linting (`black`) is failing - - To keep the code consistent with lots of contributors, we run automated code consistency checks. - To fix this CI test, please run: - - * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` - * Fix formatting errors in your pipeline: `black .` - - Once you push these changes the test should pass, and you can hide this comment :+1: + python-version: 3.11 + cache: "pip" - We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + - name: Install pre-commit + run: pip install pre-commit - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false + - name: Run pre-commit + run: pre-commit run --all-files nf-core: runs-on: ubuntu-latest @@ -76,7 +37,7 @@ jobs: - name: Install Nextflow uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.11" architecture: "x64" @@ -99,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bbcd30f..147bcd10 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v2 + uses: dawidd6/action-download-artifact@v3 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 6ad33927..21ac3f06 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +56,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.0.2 + - uses: zentered/bluesky-post-action@v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/.gitpod.yml b/.gitpod.yml index acf72695..363d5b1d 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -7,6 +7,7 @@ tasks: - name: unset JAVA_TOOL_OPTIONS command: | unset JAVA_TOOL_OPTIONS + vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c31cdb9..af57081f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,10 @@ repos: - repo: https://github.com/pre-commit/mirrors-prettier - rev: "v2.7.1" + rev: "v3.1.0" hooks: - id: prettier + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python + rev: "2.7.3" + hooks: + - id: editorconfig-checker + alias: ec diff --git a/README.md b/README.md index a6457ef9..8ac1f59d 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ -# ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_light.png#gh-light-mode-only) ![nf-core/rnavar](docs/images/nf-core-rnavar_logo_dark.png#gh-dark-mode-only) - +

    + + + nf-core/rnavar + +

    [![GitHub Actions CI Status](https://github.com/nf-core/rnavar/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+CI%22) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) diff --git a/assets/email_template.html b/assets/email_template.html index e8bda58a..f1564699 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -12,7 +12,7 @@ -

    nf-core/rnavar v${version}

    +

    nf-core/rnavar ${version}

    Run Name: $runName

    <% if (!success){ diff --git a/assets/email_template.txt b/assets/email_template.txt index cbc1a918..023008b7 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -4,7 +4,7 @@ |\\ | |__ __ / ` / \\ |__) |__ } { | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, `._,._,' - nf-core/rnavar v${version} + nf-core/rnavar ${version} ---------------------------------------------------- Run Name: $runName diff --git a/assets/nf-core-rnavar_logo_light.png b/assets/nf-core-rnavar_logo_light.png index 509f923f092c056161198ce9745d0fe4fc83e867..c1488845e55d16d01c0a671a4f4698b3b83b9645 100644 GIT binary patch literal 68146 zcmeEui93|*|NktQ%2p{POG2_GTh>fbF$vKkWvL`7S+eglWvLVyq^!vx5wgoR)sd*| zWoJr4wy}@>_kPs*ocb4j*Y~ijuVhOY*KysvQ|q$y*J-S zk72oMpYe0q?VAbaq#*9EMu$IdcoXp^so>_-$xz2=@*S~&`he~jv*V1qmOg7gB~|ku z4iN>q9{kdyZ|YpwtFN7@xuSZ(Q#H%X?NoYKwa=aXj}v2~+N64J89ds7jyopzTE&lL zTX=gIP6(U()S#j$694J$cS-q-%;cBHV%V6wo@O1Lq5Km$NZ4lj<2c zwqe?icigw3j2(aYEkjNIUZPcw=4bC$%q+7b?p1P^!$01``3%CuY^87 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zR(SliZInVGdFiX-+?ulq^Pr062u)ng5j(}CTiGLQkv6?rkcPd!;?fH5U^+iRKzvfu zV~;6qm0a{ko%Q&bhwCxwcNjHtrRuX~uPJ4SI{~}WvHI=pn{11L;PnA=|26zUHCTRb zgzHKw^0*vqpCo`j;lJKoyKx8d7!8AI%m}wVX-c@2B_KnHw}>4U#aDXTOq7<|Wd4Tsc3c@~MlU!Do- z;44!I44#TL{egGhbo--w?_)Cnawj*O*6B(*W)rTAlB^EKDv_8PPE_4zdul@}vk=<2 zWM<}+1wca(EgDR~^?BHoZ|m^g5Plb!5RP%HK2`I`LZtE_&_TmfZv$SS=39Ykn@g)h zK2xOBBV8(O>$B1^yv5v)z{*v8xsq2EHw6IY)|ObEUM$)D;2ldBzXL^o2#D*TR7q2+ zDkW3pWRJ7P86=mB!#~|iPx<77n)$##FJ%f5Y(taKVql$zJJ-sa2Lq?0v^>t=^){tS z15cnLfeqNGIDqY|K4E1|Nz)c>_jNb-`iKXYX>tUy3D1%=D4xIVLh5@N-8J$JWP1}C zk1ce0UGgFBPREZ`^YsLWgRZcTtn1;*uP{d&`VCLk^-43Sr>Q}8Ke)}JYvPzo( diff --git a/main.nf b/main.nf index 8c727ca8..6d848d3a 100644 --- a/main.nf +++ b/main.nf @@ -44,7 +44,7 @@ if (params.validate_params) { validateParameters() } -WorkflowMain.initialise(workflow, params, log) +WorkflowMain.initialise(workflow, params, log, args) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/modules.json b/modules.json index f3fdaddd..74d7541e 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", + "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "4ab13872435962dadc239979554d13709e20bf29", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index f0c63f69..9b3272bc 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.17 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 7685b33c..f2187611 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test index eec1db10..b1e1630b 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -31,7 +31,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } ) } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 4274ed57..5f59a936 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -1,27 +1,33 @@ { "Should run without failures": { "content": [ - { - "0": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ], - "1": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "2": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "mqc_yml": [ - "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" - ], - "versions": [ - "versions.yml:md5,3843ac526e762117eedf8825b40683df" - ], - "yml": [ - "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" - ] - } + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] ], - "timestamp": "2023-11-03T14:43:22.157011" + "timestamp": "2024-01-09T23:01:18.710682" } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index b9e8f926..1f21c664 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -3,24 +3,20 @@ nextflow_process { name "Test Process FASTQC" script "../main.nf" process "FASTQC" + tag "modules" tag "modules_nfcore" tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) """ } } @@ -28,82 +24,189 @@ nextflow_process { then { assertAll ( { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. // looks like this:
    Mon 2 Oct 2023
    test.gz
    // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, - { assert path(process.out.html.get(0).get(1)).getText().contains("") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 paired-end [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 interleaved [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } ) } } -// TODO -// // -// // Test with paired-end data -// // -// workflow test_fastqc_paired_end { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with interleaved data -// // -// workflow test_fastqc_interleaved { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with bam data -// // -// workflow test_fastqc_bam { -// input = [ -// [id: 'test', single_end: false], // meta map -// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with multiple samples -// // -// workflow test_fastqc_multiple { -// input = [ -// [id: 'test', single_end: false], // meta map -// [ -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), -// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) -// ] -// ] - -// FASTQC ( input ) -// } - -// // -// // Test with custom prefix -// // -// workflow test_fastqc_custom_prefix { -// input = [ -// [ id:'mysample', single_end:true ], // meta map -// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) -// ] - -// FASTQC ( input ) -// } + + test("sarscov2 paired-end [bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 multiple [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 custom_prefix") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastq] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match() } + ) + } + } + } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 636a32ce..5d624bb8 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,10 +1,20 @@ { + "sarscov2 single-end [fastq] - stub": { + "content": [ + [ + "test.html", + "test.zip", + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2024-01-17T18:40:57.254299" + }, "versions": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2023-10-09T23:40:54+0000" + "timestamp": "2024-01-17T18:36:50.033627" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index bc0bdb5b..7625b752 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.18 + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 00cc48d2..1b9f7c43 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : - 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -43,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f1aa660e..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index c2dad217..d0438eda 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -7,12 +7,9 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" - test("MULTIQC: FASTQC") { + test("sarscov2 single-end [fastqc]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -26,20 +23,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } ) } } - test("MULTIQC: FASTQC and a config file") { + test("sarscov2 single-end [fastqc] [config]") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) @@ -53,9 +47,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.report.get(0)).exists() }, - { assert path(process.out.data.get(0)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match() } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 00000000..d37e7304 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:02:49.911994" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:03:14.524346" + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 2fd2a3fc..aabc8be5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -71,7 +71,7 @@ try { } // Load nf-core/rnavar custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! +// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! // try { // includeConfig "${params.custom_config_base}/pipeline/rnavar.config" // } catch (Exception e) { @@ -91,6 +91,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + channels = ['conda-forge', 'bioconda', 'defaults'] apptainer.enabled = false } mamba { diff --git a/pyproject.toml b/pyproject.toml index 0d62beb6..7d08e1c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,10 +1,13 @@ -# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. +# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.black] +[tool.ruff] line-length = 120 -target_version = ["py37", "py38", "py39", "py310"] +target-version = "py38" +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] +cache-dir = "~/.cache/ruff" -[tool.isort] -profile = "black" -known_first_party = ["nf_core"] -multi_line_output = 3 +[tool.ruff.isort] +known-first-party = ["nf_core"] + +[tool.ruff.per-file-ignores] +"__init__.py" = ["E402", "F401"] diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 6b44734f..6c976f6a 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -127,6 +127,13 @@ workflow.onComplete { } } +workflow.onError { + if (workflow.errorReport.contains("Process requirement exceeds available memory")) { + println("🛑 Default resources exceed availability 🛑 ") + println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") + } +} + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END From ce95d673be149e3a774a85594eb5e2b9b5eec7cb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Feb 2024 16:51:46 +0100 Subject: [PATCH 080/275] fix schema --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 45eb0ce1..e628e568 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -97,7 +97,7 @@ }, "read_length": { "type": "number", - "default": 151, + "default": 150, "description": "Read length", "help_text": "Specify the read length for the STAR aligner." }, @@ -167,7 +167,7 @@ "type": "string", "format": "directory-path", "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes", + "default": "s3://ngi-igenomes/igenomes/", "fa_icon": "fas fa-cloud-download-alt", "hidden": true }, From c226ebe526ce9a3b626a170ef7236536f201ee07 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Feb 2024 16:59:42 +0100 Subject: [PATCH 081/275] template logo --- assets/nf-core-rnavar_logo_light.png | Bin 68146 -> 68088 bytes docs/images/nf-core-rnavar_logo_dark.png | Bin 25354 -> 25458 bytes docs/images/nf-core-rnavar_logo_light.png | Bin 21970 -> 22076 bytes 3 files changed, 0 insertions(+), 0 deletions(-) diff --git a/assets/nf-core-rnavar_logo_light.png b/assets/nf-core-rnavar_logo_light.png index c1488845e55d16d01c0a671a4f4698b3b83b9645..7eec13602f27933d91014e784eb4177b89c8c453 100644 GIT binary patch delta 34947 zcmc$Gc{o)4-~TKag^?1%P|-q3D*IL`6S|Y3R6=QyeabMhote6$6iV7;DNCX(CHr=| zCEXQ5vc#A+yD^fCkl*`I-~0Rgp5Gt8f1c-iUAODL;+)TUudnxd&f{1i!BwGL*hRPHrvKiU6UYVmfP zd1uIPjvjrXz326RmruReU})m`w4|jnglpj!$o65!(uRT&Y{GzH=E^k1x91S~bDkk&I|9jtbNa29QBt2ZE)LR+dPY)kFBC$i4iF@HSj^xxO3xmJ$~N2tm8*qxhondAqHv&n`6Q}rK3mB ze2g06HAuxgQ8Q`3qH1AgKRCEia5yR7@T)XZJ7lKk!K^6`k#QZmT-)v#{2Y0wgyeg- zx=ue$a*@5mA#V|T95H(Gz@tzqFE^mo*+%5j;A?5S_HwxYRb&K-6?}U$q zdU|>etuwCX*R>ycj(fLuAAQo>EU&P#?#z2q-0>E&;+PZiLGJasZ|}FT_U37smn-S% z^HaP&kWJ&P$x}PVx?BEyQs;;y6DXs{qB;$D*eLYGT+H;{fCny zk2qQf2PE31kxqq}B@W}`wOf5|P`s68XOy{s+AWHWsk7k4RH5L@urg)Q~^>=#g+alKrt~?E#Sk}sH)!l zNnGSPyJ5YYtI0%FHS|6Y;S*DgU#n((ENf7;h!Hv7Es%5)Iq080^C_T0cS_zZum4GD z{Q*O~?l$WE81IW@x#Z)F%@THfoj*qJDo~bQyF@f?G$2oTcAP}n4N@UR;y0tBE~nyB zjQF3(rZJYUHY&ogse$CF!G)ANFEg7^>&`Hn<%4pR^+)}F{J7GM{KZywODGvKFtA^R zIe|2jcFoQfsHNdZp|iJ|c(&^sY`(T9oh?iX70K}?n)3K6UiYKA&RX35=sm@J1h@gp>JfaG&|7>U&xEuRAm?(!QY4aD>pB6e2;7pOOVfBvF!y?svS+_RK!~FUR#r zs-KKGDRy_W|G0j6XJ4S_bQ+v-#A@+rA<>+rQI-k+#Cs9OGg+TpggYUza{L_QBF#c2(*1y@{ zRAba=MRU{VtAHfiJ(wjAGP>SG6HVI>_{j_K(PQ#YN+hP<4h>M-V+?qYS9`r&ZMu5M z>OtE+@iK#w6zf&nNjqqFY)tCJ;L)@Tv&X0|?*ESd%~tlxLP{jo>hU-3^HUI<3|DqD z1KDPMLhB8zi98ufL%0~*$DE4Yt}JNtXlq zy`4=lWSBc-R-=wXyO@7qtjLeClZNhhB{{Cx^Ct#r7PPzGL0rMd~YlkuoF_dZ5;v;{D>pPmO4@+~bm=%^N*Iwi)ja%yAXwZp92JnJSoau%aWA_hhFsST;AYWN+pT6?PP?${L!{v(LK9B=43#F!+wee49sr)rha;?pzmk=Y3Z@nVCmKeZF0n2mw3HRe}ndQ z;Kbz`4kbs$fjhO>U%HQyjPDoZB98BQ2M%5TVRZQv*OlJ?cx>`OOQB)s;sz<&-)~Qb zCy94F=luW9dcuajernt zpVmc?MY*7mI*+)?^}JDbTkm-sdFq4*;F?#yWUdwC z*<}F!rPtn009#7$+;!wZf=>XHROnk7)TCWe`Nkha^oGisE;1dRJq*2}`p3)si_(~h7?@Q;Y$& z%uwZtc`8%1jsjiklsVh=3zelTIAqFYftf@ZPMvUQ9@5jKbE)mIKt0aLz+iL4TX!89 zT+T&a@6}Rdaz~?qB=Ajt@i@&YxL{p|-P9kTLW=`Eg$?*EQQ+5K-g==11VSWT7%8%8CGm>gt3i9Du|0rNKr}MJd0PD&G^Cn*LF~t7`(>VZJ3k# zz*|3V&oa>Q9pLQcIgqo_JC8)L3!#oRB}ZOldxE+keK_`($7sRHZet4V!znJNEZYtM z7LKn0FFmZ!e+mIg{o*mJ8-u&1f9@>24)_;iS^bMpE4Dvl+vOf}(tU&W1l}L$7f_V{ zOfO67>xny3AmpBH;IT|6#^%d6z<0Me$x_~=M}MoBxu&}K=W>Ikvyo=*tc>(=@~Cf$ z;TfZxX3tC8srPC91uE~ZrV!0vFy@DoiD83xK@`~yQhQq5bqa_plMUyNJ?O|3EFn56QYbmI&m%g?B8Z;Vb)Z!c>zW-5#4OhuyE58;xyKFLHoH2}#a#Hi>fIeZPykV+L2 z`~esEE@2~zswoKag(<}yjxDJ@# zZa}0cy9wbS?#2Uix>qpJHCXyaj?Zk6%Dg1T-qRpu=FfnDV8z(B2SeeEo^=+LkUx4P ztE6ri2#Gwnpi`<>yIe&w&4%g1*qpS>n^}@Kd$gZPokvy`WM6I?m=KVd)G>%l3hY-Y zhJ^Avpe-u({uFrRy--P4S$xfQs$J_RHYG)6R=RthfzsIDMG_T2ytD^x0XY77fSV4{ z;I$ZPzhEZ?D!Z-BI0{$+i4X5#9b}J$pMbyDY-)~_C(2WH9|lc`adjbzY>!_|Sulv? 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tXMtMs$4&76y`?2NX8|5wS4znHxBLTZ|0aUa`7;oB5%9LSs?$D{{{fIJUWWhx From 06d30fe242f3218f7774f1f989ae86e43f0cd033 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Feb 2024 17:02:28 +0100 Subject: [PATCH 082/275] update .editorconfig --- .editorconfig | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.editorconfig b/.editorconfig index 9b990088..866cde4d 100644 --- a/.editorconfig +++ b/.editorconfig @@ -27,6 +27,6 @@ indent_size = unset [README.md] indent_style = unset -# ignore python -[*.{py}] +# ignore python and markdown (is taken care off by prettier) +[*.{py,md}] indent_style = unset From ccce756a2385f36a02c9772b67ef96b8d0845419 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Feb 2024 17:04:29 +0100 Subject: [PATCH 083/275] prettier --- .devcontainer/devcontainer.json | 8 ++++---- .github/workflows/download_pipeline.yml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4a9bc5c7..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint", + "python.linting.pylintPath": "/opt/conda/bin/pylint" }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], - }, - }, + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + } + } } diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8611458a..8a330045 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -64,4 +64,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results From 9f457439800fd35d643625ae53261a6980780622 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Feb 2024 17:11:38 +0100 Subject: [PATCH 084/275] editor config --- tests/config/nextflow.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 1241d7d8..a28463fd 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -9,9 +9,9 @@ params { } process { - cpus = 2 - memory = 6.GB - time = 48.h + cpus = 2 + memory = 6.GB + time = 48.h } if ("$PROFILE" == "singularity") { @@ -31,5 +31,5 @@ if ("$PROFILE" == "singularity") { includeConfig '../../conf/modules.config' manifest { - nextflowVersion = '!>=21.10.3' + nextflowVersion = '!>=21.10.3' } From ca46c28f25236d6b79f5e69c66a0e49213f15a92 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 1 Feb 2024 17:35:49 +0100 Subject: [PATCH 085/275] logo from template --- assets/nf-core-rnavar_logo_light.png | Bin 68088 -> 68146 bytes docs/images/nf-core-rnavar_logo_dark.png | Bin 25458 -> 25354 bytes docs/images/nf-core-rnavar_logo_light.png | Bin 22076 -> 21970 bytes 3 files changed, 0 insertions(+), 0 deletions(-) diff --git a/assets/nf-core-rnavar_logo_light.png b/assets/nf-core-rnavar_logo_light.png index 7eec13602f27933d91014e784eb4177b89c8c453..c1488845e55d16d01c0a671a4f4698b3b83b9645 100644 GIT binary patch delta 34981 zcmc$Gc{r5&-~WukWE&|V3>7VuO4${a>_tu5>`_Vf3?th;bLvFO+M^-fU_H$<2% zrP9|a802O;HC&vV^>Mqk^42?b=HcF;q3WdmGRsddsa5EB!o8pxzbNsu6ZIvNmqLz^ z#{JqxE^ha)VB8Twf|wdaAamiak#hO;x-r=G9ZBvh9NwVP( z|7D4Zr~&K3x$v!Y!$whusiiCx8_*YE7o%CPvM-QiQ%`NiAOUP+W 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z#FhmH<`bg<^g}!uu?)4n)O!>@N*(518BZ-5weVHlHp#JB*A^y-+d*vfjE8W&zGsM%37-QEheMCGo+U)*F<|9es4RTo4`$r@%tqj)fTTgU8{DmuZ!;2kG;pG!kSm&J}< zO`60m1gjLKTlBy;b{mttZNIi}rS!cN0Yo!HxupmWqjD@IH~uMTw3JKCF|D5BMbh54-ES?*IS* From e5493bbd114eee3dd0681c4e5e8cbc82880ee173 Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 8 Feb 2024 15:56:37 +0000 Subject: [PATCH 086/275] Fixed S3 bucket path in conditional statements --- workflows/rnavar.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 0a4d8fc2..977e38af 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -129,7 +129,7 @@ vep_species = params.vep_species ?: Channel.empty() // Initialize files channels based on params, not defined within the params.genomes[params.genome] scope if (params.snpeff_cache && params.annotate_tools && (params.annotate_tools.split(',').contains("snpeff") || params.annotate_tools.split(',').contains("merge"))) { def snpeff_annotation_cache_key = '' - if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache") { + if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache/") { snpeff_annotation_cache_key = "${params.snpeff_genome}.${params.snpeff_db}/" } else { snpeff_annotation_cache_key = params.use_annotation_cache_keys ? "${params.snpeff_genome}.${params.snpeff_db}/" : "" @@ -137,7 +137,7 @@ if (params.snpeff_cache && params.annotate_tools && (params.annotate_tools.split def snpeff_cache_dir = "${snpeff_annotation_cache_key}${params.snpeff_genome}.${params.snpeff_db}" def snpeff_cache_path_full = file("$params.snpeff_cache/$snpeff_cache_dir", type: 'dir') if ( !snpeff_cache_path_full.exists() || !snpeff_cache_path_full.isDirectory() ) { - if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache") { + if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache/") { error("This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request for it.") } else { error("Files within --snpeff_cache invalid. Make sure there is a directory named ${snpeff_cache_dir} in ${params.snpeff_cache}.\nhttps://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation") @@ -145,9 +145,9 @@ if (params.snpeff_cache && params.annotate_tools && (params.annotate_tools.split } snpeff_cache = Channel.fromPath(file("${params.snpeff_cache}/${snpeff_annotation_cache_key}"), checkIfExists: true).collect() .map{ cache -> [ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], cache ] } - } else if (params.annotate_tools && (params.annotate_tools.split(',').contains("snpeff") || params.annotate_tools.split(',').contains("merge")) && !params.download_cache) { +} else if (params.annotate_tools && (params.annotate_tools.split(',').contains("snpeff") || params.annotate_tools.split(',').contains("merge")) && !params.download_cache) { error("No cache for SnpEff or automatic download of said cache has been detected.\nPlease refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.") - } else snpeff_cache = [] +} else snpeff_cache = [] if (params.vep_cache && params.annotate_tools && (params.annotate_tools.split(',').contains("vep") || params.annotate_tools.split(',').contains("merge"))) { def vep_annotation_cache_key = '' From 557d23f673ae91b0f265b70759eb7ee26298dddb Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 8 Feb 2024 16:00:57 +0000 Subject: [PATCH 087/275] Updated Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 23d26ba0..496e19c3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added`unzip` from nf-core modules for working with unzipped fasta and gtf files ### Changed - - [#95](https://github.com/nf-core/rnavar/pull/95) - Template update from nf-core/tools 2.5 -> 2.9 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules @@ -20,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - [#97](https://github.com/nf-core/rnavar/pull/97) - Update all gatk4 modules to disable JVM hotspot +- [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache ### Dependencies From a42bb7e9754f7a1b55dcfa2d4275a5893ed7d498 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 12 Feb 2024 09:31:39 +0000 Subject: [PATCH 088/275] [automated] Fix linting with Prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 496e19c3..0070c6c4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added`unzip` from nf-core modules for working with unzipped fasta and gtf files ### Changed + - [#95](https://github.com/nf-core/rnavar/pull/95) - Template update from nf-core/tools 2.5 -> 2.9 - [#97](https://github.com/nf-core/rnavar/pull/97) - Template update from nf-core/tools 2.10 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules From 111e322ffb1fe7402fb89aa520dcd029a9a86973 Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 15 Feb 2024 13:59:55 +0000 Subject: [PATCH 089/275] Fixed VEP s3 bucket path --- CHANGELOG.md | 1 + workflows/rnavar.nf | 10 +++++----- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0070c6c4..1386be58 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#97](https://github.com/nf-core/rnavar/pull/97) - Update all gatk4 modules to disable JVM hotspot - [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache +- []() - Fixed s3 bucket path in conditional statement for VEP cache ### Dependencies diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index e16037dd..65365c5d 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -151,24 +151,24 @@ if (params.snpeff_cache && params.annotate_tools && (params.annotate_tools.split if (params.vep_cache && params.annotate_tools && (params.annotate_tools.split(',').contains("vep") || params.annotate_tools.split(',').contains("merge"))) { def vep_annotation_cache_key = '' - if (params.vep_cache == "s3://annotation-cache/vep_cache") { + if (params.vep_cache == "s3://annotation-cache/vep_cache/") { vep_annotation_cache_key = "${params.vep_cache_version}_${params.vep_genome}/" } else { vep_annotation_cache_key = params.use_annotation_cache_keys ? "${params.vep_cache_version}_${params.vep_genome}/" : "" } - def vep_cache_dir = "${vep_annotation_cache_key}${params.vep_cache_version}_${params.vep_genome}/${params.vep_species}" + def vep_cache_dir = "${vep_annotation_cache_key}/${params.vep_species}" def vep_cache_path_full = file("$params.vep_cache/$vep_cache_dir", type: 'dir') if ( !vep_cache_path_full.exists() || !vep_cache_path_full.isDirectory() ) { - if (params.vep_cache == "s3://annotation-cache/vep_cache") { + if (params.vep_cache == "s3://annotation-cache/vep_cache/") { error("This path is not available within annotation-cache. Please check https://annotation-cache.github.io/ to create a request for it.") } else { error("Files within --vep_cache invalid. Make sure there is a directory named ${vep_cache_dir} in ${params.vep_cache}.\nhttps://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation") } } vep_cache = Channel.fromPath(file("${params.vep_cache}/${vep_annotation_cache_key}"), checkIfExists: true).collect() - } else if (params.annotate_tools && (params.annotate_tools.split(',').contains("vep") || params.annotate_tools.split(',').contains("merge")) && !params.download_cache) { +} else if (params.annotate_tools && (params.annotate_tools.split(',').contains("vep") || params.annotate_tools.split(',').contains("merge")) && !params.download_cache) { error("No cache for VEP or automatic download of said cache has been detected.\nPlease refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.") - } else vep_cache = [] +} else vep_cache = [] vep_extra_files = [] From 3de9b74412f013305adce7a29abc27057394cdfa Mon Sep 17 00:00:00 2001 From: bioloni Date: Thu, 15 Feb 2024 14:03:31 +0000 Subject: [PATCH 090/275] Updated changelog with PR --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1386be58..927bcde7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#97](https://github.com/nf-core/rnavar/pull/97) - Update all gatk4 modules to disable JVM hotspot - [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache -- []() - Fixed s3 bucket path in conditional statement for VEP cache +- [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache ### Dependencies From 36755fe11b43bb04b30fde0fbeae88ed9dc7451a Mon Sep 17 00:00:00 2001 From: bioloni Date: Tue, 20 Feb 2024 14:48:12 +0000 Subject: [PATCH 091/275] Added missing defs --- CHANGELOG.md | 2 +- subworkflows/local/splitncigar/main.nf | 4 ++-- workflows/rnavar.nf | 10 ++++++---- 3 files changed, 9 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 927bcde7..5957d3df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#117](https://github.com/nf-core/rnavar/pull/117) - Template update from nf-core/tools 2.11.1 ### Fixed - +- []() - Added missing "def" in local variables - [#97](https://github.com/nf-core/rnavar/pull/97) - Update all gatk4 modules to disable JVM hotspot - [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache - [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index cbc30618..e479d34b 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -18,7 +18,7 @@ workflow SPLITNCIGAR { ch_versions = Channel.empty() bam_interval = bam.combine(intervals).map{ meta, bam, bai, intervals -> - new_meta = meta.clone() + def new_meta = meta.clone() new_meta.id = meta.id + "_" + intervals.baseName new_meta.sample = meta.id [new_meta, bam, bai, intervals] @@ -35,7 +35,7 @@ workflow SPLITNCIGAR { bam_splitncigar_interval = bam_splitncigar .map{ meta, bam -> - new_meta = meta.clone() + def new_meta = meta.clone() new_meta.id = meta.sample [new_meta, bam] }.groupTuple() diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 65365c5d..5958e1f2 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -465,8 +465,9 @@ workflow RNAVAR { ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf .map{ meta, vcf -> - meta.id = meta.sample - [meta, vcf] + def new_meta = meta.clone() + new_meta.id = meta.sample + [new_meta, vcf] }.groupTuple() ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) @@ -478,8 +479,9 @@ workflow RNAVAR { ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index .map{ meta, idx -> - meta.id = meta.sample - [meta, idx] + def new_meta = meta.clone() + new_meta.id = meta.sample + [new_meta, idx] }.groupTuple() ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) From 146282304cec897167ee9c99f62a4cf3493bd7a2 Mon Sep 17 00:00:00 2001 From: bioloni Date: Tue, 20 Feb 2024 15:05:54 +0000 Subject: [PATCH 092/275] Modified Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5957d3df..0ff64833 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#117](https://github.com/nf-core/rnavar/pull/117) - Template update from nf-core/tools 2.11.1 ### Fixed -- []() - Added missing "def" in local variables +- [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables - [#97](https://github.com/nf-core/rnavar/pull/97) - Update all gatk4 modules to disable JVM hotspot - [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache - [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache From 7a3bef9f2dc1864f79ffaa64c36213bb126bb300 Mon Sep 17 00:00:00 2001 From: bioloni Date: Tue, 20 Feb 2024 15:07:33 +0000 Subject: [PATCH 093/275] Updated readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 8dbc1fbf..327a633b 100644 --- a/README.md +++ b/README.md @@ -100,7 +100,8 @@ The pipeline is primarily maintained by Praveen Raj ([@praveenraj2018](https://g Many thanks to other who have helped out along the way too, including (but not limited to): [@ewels](https://github.com/ewels), -[@drpatelh](https://github.com/drpatelh). +[@drpatelh](https://github.com/drpatelh), +[@nschcolnicov](https://github.com/nschcolnicov). ## Contributions and Support From 80f755cfe63d09733477ab73f880747d31ca4ca6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?= <90359308+nschcolnicov@users.noreply.github.com> Date: Tue, 20 Feb 2024 12:26:01 -0300 Subject: [PATCH 094/275] Update CHANGELOG.md Co-authored-by: Maxime U Garcia --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0ff64833..dcbaaeed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,10 +18,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#117](https://github.com/nf-core/rnavar/pull/117) - Template update from nf-core/tools 2.11.1 ### Fixed -- [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables + - [#97](https://github.com/nf-core/rnavar/pull/97) - Update all gatk4 modules to disable JVM hotspot - [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache - [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache +- [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables ### Dependencies From 37282c429aa5f7b756f3e9fce3bed48781f62626 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 20 Feb 2024 15:30:21 +0000 Subject: [PATCH 095/275] Template update for nf-core/tools version 2.13 --- .editorconfig | 9 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/branch.yml | 2 +- .github/workflows/ci.yml | 7 +- .github/workflows/clean-up.yml | 2 +- .github/workflows/download_pipeline.yml | 17 +- .github/workflows/linting.yml | 12 +- .github/workflows/linting_comment.yml | 4 +- .github/workflows/release-announcements.yml | 11 +- README.md | 5 +- assets/multiqc_config.yml | 2 + assets/schema_input.json | 21 +- bin/check_samplesheet.py | 259 ----------- conf/modules.config | 8 - lib/NfcoreTemplate.groovy | 356 -------------- lib/Utils.groovy | 47 -- lib/WorkflowMain.groovy | 77 --- lib/WorkflowRnavar.groovy | 122 ----- main.nf | 100 ++-- modules.json | 28 +- modules/local/samplesheet_check.nf | 31 -- .../dumpsoftwareversions/environment.yml | 7 - .../custom/dumpsoftwareversions/main.nf | 24 - .../custom/dumpsoftwareversions/meta.yml | 37 -- .../templates/dumpsoftwareversions.py | 102 ---- .../dumpsoftwareversions/tests/main.nf.test | 43 -- .../tests/main.nf.test.snap | 33 -- .../dumpsoftwareversions/tests/tags.yml | 2 - modules/nf-core/fastqc/tests/main.nf.test | 14 +- .../nf-core/fastqc/tests/main.nf.test.snap | 76 ++- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/tests/main.nf.test | 13 +- .../nf-core/multiqc/tests/main.nf.test.snap | 32 +- nextflow.config | 5 +- nextflow_schema.json | 1 + pyproject.toml | 8 +- subworkflows/local/input_check.nf | 44 -- .../utils_nfcore_rnavar_pipeline/main.nf | 247 ++++++++++ .../nf-core/utils_nextflow_pipeline/main.nf | 126 +++++ .../nf-core/utils_nextflow_pipeline/meta.yml | 38 ++ .../tests/main.function.nf.test | 54 +++ .../tests/main.function.nf.test.snap | 12 + .../tests/main.workflow.nf.test | 123 +++++ .../tests/nextflow.config | 9 + .../utils_nextflow_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfcore_pipeline/main.nf | 440 ++++++++++++++++++ .../nf-core/utils_nfcore_pipeline/meta.yml | 24 + .../tests/main.function.nf.test | 134 ++++++ .../tests/main.function.nf.test.snap | 138 ++++++ .../tests/main.workflow.nf.test | 29 ++ .../tests/main.workflow.nf.test.snap | 15 + .../tests/nextflow.config | 9 + .../utils_nfcore_pipeline/tests/tags.yml | 2 + .../nf-core/utils_nfvalidation_plugin/main.nf | 62 +++ .../utils_nfvalidation_plugin/meta.yml | 44 ++ .../tests/main.nf.test | 200 ++++++++ .../tests/nextflow_schema.json | 96 ++++ .../utils_nfvalidation_plugin/tests/tags.yml | 2 + workflows/rnavar.nf | 133 ++---- 61 files changed, 2108 insertions(+), 1406 deletions(-) delete mode 100755 bin/check_samplesheet.py delete mode 100755 lib/NfcoreTemplate.groovy delete mode 100644 lib/Utils.groovy delete mode 100755 lib/WorkflowMain.groovy delete mode 100755 lib/WorkflowRnavar.groovy delete mode 100644 modules/local/samplesheet_check.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml delete mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap delete mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml delete mode 100644 subworkflows/local/input_check.nf create mode 100644 subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json create mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 9b990088..dd9ffa53 100644 --- a/.editorconfig +++ b/.editorconfig @@ -18,7 +18,12 @@ end_of_line = unset insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset -indent_size = unset +[/subworkflows/nf-core/**] +charset = unset +end_of_line = unset +insert_final_newline = unset +trim_trailing_whitespace = unset +indent_style = unset [/assets/email*] indent_size = unset @@ -28,5 +33,5 @@ indent_size = unset indent_style = unset # ignore python -[*.{py}] +[*.{py,md}] indent_style = unset diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 4858f99f..e95c7a82 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 030354e1..8daec84b 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v2 + uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index acba0c5f..0d32dfd4 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -19,7 +19,7 @@ jobs: # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - name: Post PR comment if: failure() - uses: mshick/add-pr-comment@v2 + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | ## This PR is against the `master` branch :x: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 95243592..6cc0e744 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,13 +28,16 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 with: version: "${{ matrix.NXF_VER }}" + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Run pipeline with test data # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml index e37cfda5..0b6b1f27 100644 --- a/.github/workflows/clean-up.yml +++ b/.github/workflows/clean-up.yml @@ -10,7 +10,7 @@ jobs: issues: write pull-requests: write steps: - - uses: actions/stale@v9 + - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9 with: stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 8611458a..f823210d 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download' # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: + inputs: + testbranch: + description: "The specific branch you wish to utilize for the test execution of nf-core download." + required: true + default: "dev" pull_request: types: - opened @@ -23,13 +28,13 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" - - uses: eWaterCycle/setup-singularity@v7 + - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: singularity-version: 3.8.3 @@ -42,13 +47,13 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./ run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ @@ -64,4 +69,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 81cd098e..748b4311 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Set up Python 3.11 - uses: actions/setup-python@v5 + uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: 3.11 cache: "pip" @@ -32,12 +32,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v4 + uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.11" architecture: "x64" @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 147bcd10..b706875f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@v3 + uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 with: workflow: linting.yml workflow_conclusion: completed @@ -21,7 +21,7 @@ jobs: run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 + uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2 with: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 21ac3f06..c3674af2 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -9,6 +9,11 @@ jobs: toot: runs-on: ubuntu-latest steps: + - name: get topics and convert to hashtags + id: get_topics + run: | + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + - uses: rzr/fediverse-action@master with: access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} @@ -20,11 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} + ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@v5 + - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: python-version: "3.10" - name: Install dependencies @@ -56,7 +63,7 @@ jobs: bsky-post: runs-on: ubuntu-latest steps: - - uses: zentered/bluesky-post-action@v0.1.0 + - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0 with: post: | Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! diff --git a/README.md b/README.md index 8ac1f59d..61c2579e 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,9 @@ nf-core/rnavar -[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnavar/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) + +[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 15689f51..e838f017 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -11,3 +11,5 @@ report_section_order: order: -1002 export_plots: true + +disable_version_detection: true diff --git a/assets/schema_input.json b/assets/schema_input.json index 32bc7f93..11fb8e80 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,25 +10,22 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] }, "fastq_1": { "type": "string", + "format": "file-path", + "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { - "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", - "anyOf": [ - { - "type": "string", - "pattern": "^\\S+\\.f(ast)?q\\.gz$" - }, - { - "type": "string", - "maxLength": 0 - } - ] + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.f(ast)?q\\.gz$", + "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } }, "required": ["sample", "fastq_1"] diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py deleted file mode 100755 index 4a758fe0..00000000 --- a/bin/check_samplesheet.py +++ /dev/null @@ -1,259 +0,0 @@ -#!/usr/bin/env python - - -"""Provide a command line tool to validate and transform tabular samplesheets.""" - - -import argparse -import csv -import logging -import sys -from collections import Counter -from pathlib import Path - -logger = logging.getLogger() - - -class RowChecker: - """ - Define a service that can validate and transform each given row. - - Attributes: - modified (list): A list of dicts, where each dict corresponds to a previously - validated and transformed row. The order of rows is maintained. - - """ - - VALID_FORMATS = ( - ".fq.gz", - ".fastq.gz", - ) - - def __init__( - self, - sample_col="sample", - first_col="fastq_1", - second_col="fastq_2", - single_col="single_end", - **kwargs, - ): - """ - Initialize the row checker with the expected column names. - - Args: - sample_col (str): The name of the column that contains the sample name - (default "sample"). - first_col (str): The name of the column that contains the first (or only) - FASTQ file path (default "fastq_1"). - second_col (str): The name of the column that contains the second (if any) - FASTQ file path (default "fastq_2"). - single_col (str): The name of the new column that will be inserted and - records whether the sample contains single- or paired-end sequencing - reads (default "single_end"). - - """ - super().__init__(**kwargs) - self._sample_col = sample_col - self._first_col = first_col - self._second_col = second_col - self._single_col = single_col - self._seen = set() - self.modified = [] - - def validate_and_transform(self, row): - """ - Perform all validations on the given row and insert the read pairing status. - - Args: - row (dict): A mapping from column headers (keys) to elements of that row - (values). - - """ - self._validate_sample(row) - self._validate_first(row) - self._validate_second(row) - self._validate_pair(row) - self._seen.add((row[self._sample_col], row[self._first_col])) - self.modified.append(row) - - def _validate_sample(self, row): - """Assert that the sample name exists and convert spaces to underscores.""" - if len(row[self._sample_col]) <= 0: - raise AssertionError("Sample input is required.") - # Sanitize samples slightly. - row[self._sample_col] = row[self._sample_col].replace(" ", "_") - - def _validate_first(self, row): - """Assert that the first FASTQ entry is non-empty and has the right format.""" - if len(row[self._first_col]) <= 0: - raise AssertionError("At least the first FASTQ file is required.") - self._validate_fastq_format(row[self._first_col]) - - def _validate_second(self, row): - """Assert that the second FASTQ entry has the right format if it exists.""" - if len(row[self._second_col]) > 0: - self._validate_fastq_format(row[self._second_col]) - - def _validate_pair(self, row): - """Assert that read pairs have the same file extension. Report pair status.""" - if row[self._first_col] and row[self._second_col]: - row[self._single_col] = False - first_col_suffix = Path(row[self._first_col]).suffixes[-2:] - second_col_suffix = Path(row[self._second_col]).suffixes[-2:] - if first_col_suffix != second_col_suffix: - raise AssertionError("FASTQ pairs must have the same file extensions.") - else: - row[self._single_col] = True - - def _validate_fastq_format(self, filename): - """Assert that a given filename has one of the expected FASTQ extensions.""" - if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): - raise AssertionError( - f"The FASTQ file has an unrecognized extension: {filename}\n" - f"It should be one of: {', '.join(self.VALID_FORMATS)}" - ) - - def validate_unique_samples(self): - """ - Assert that the combination of sample name and FASTQ filename is unique. - - In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the - number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. - - """ - if len(self._seen) != len(self.modified): - raise AssertionError("The pair of sample name and FASTQ must be unique.") - seen = Counter() - for row in self.modified: - sample = row[self._sample_col] - seen[sample] += 1 - row[self._sample_col] = f"{sample}_T{seen[sample]}" - - -def read_head(handle, num_lines=10): - """Read the specified number of lines from the current position in the file.""" - lines = [] - for idx, line in enumerate(handle): - if idx == num_lines: - break - lines.append(line) - return "".join(lines) - - -def sniff_format(handle): - """ - Detect the tabular format. - - Args: - handle (text file): A handle to a `text file`_ object. The read position is - expected to be at the beginning (index 0). - - Returns: - csv.Dialect: The detected tabular format. - - .. _text file: - https://docs.python.org/3/glossary.html#term-text-file - - """ - peek = read_head(handle) - handle.seek(0) - sniffer = csv.Sniffer() - dialect = sniffer.sniff(peek) - return dialect - - -def check_samplesheet(file_in, file_out): - """ - Check that the tabular samplesheet has the structure expected by nf-core pipelines. - - Validate the general shape of the table, expected columns, and each row. Also add - an additional column which records whether one or two FASTQ reads were found. - - Args: - file_in (pathlib.Path): The given tabular samplesheet. The format can be either - CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. - file_out (pathlib.Path): Where the validated and transformed samplesheet should - be created; always in CSV format. - - Example: - This function checks that the samplesheet follows the following structure, - see also the `viral recon samplesheet`_:: - - sample,fastq_1,fastq_2 - SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz - SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz - SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, - - .. _viral recon samplesheet: - https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv - - """ - required_columns = {"sample", "fastq_1", "fastq_2"} - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_in.open(newline="") as in_handle: - reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) - # Validate the existence of the expected header columns. - if not required_columns.issubset(reader.fieldnames): - req_cols = ", ".join(required_columns) - logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") - sys.exit(1) - # Validate each row. - checker = RowChecker() - for i, row in enumerate(reader): - try: - checker.validate_and_transform(row) - except AssertionError as error: - logger.critical(f"{str(error)} On line {i + 2}.") - sys.exit(1) - checker.validate_unique_samples() - header = list(reader.fieldnames) - header.insert(1, "single_end") - # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. - with file_out.open(mode="w", newline="") as out_handle: - writer = csv.DictWriter(out_handle, header, delimiter=",") - writer.writeheader() - for row in checker.modified: - writer.writerow(row) - - -def parse_args(argv=None): - """Define and immediately parse command line arguments.""" - parser = argparse.ArgumentParser( - description="Validate and transform a tabular samplesheet.", - epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", - ) - parser.add_argument( - "file_in", - metavar="FILE_IN", - type=Path, - help="Tabular input samplesheet in CSV or TSV format.", - ) - parser.add_argument( - "file_out", - metavar="FILE_OUT", - type=Path, - help="Transformed output samplesheet in CSV format.", - ) - parser.add_argument( - "-l", - "--log-level", - help="The desired log level (default WARNING).", - choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), - default="WARNING", - ) - return parser.parse_args(argv) - - -def main(argv=None): - """Coordinate argument parsing and program execution.""" - args = parse_args(argv) - logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") - if not args.file_in.is_file(): - logger.error(f"The given input file {args.file_in} was not found!") - sys.exit(2) - args.file_out.parent.mkdir(parents=True, exist_ok=True) - check_samplesheet(args.file_in, args.file_out) - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/conf/modules.config b/conf/modules.config index d91c6aba..e3ea8fa6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -18,14 +18,6 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: SAMPLESHEET_CHECK { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: FASTQC { ext.args = '--quiet' } diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy deleted file mode 100755 index e248e4c3..00000000 --- a/lib/NfcoreTemplate.groovy +++ /dev/null @@ -1,356 +0,0 @@ -// -// This file holds several functions used within the nf-core pipeline template. -// - -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - -class NfcoreTemplate { - - // - // Check AWS Batch related parameters have been specified correctly - // - public static void awsBatch(workflow, params) { - if (workflow.profile.contains('awsbatch')) { - // Check params.awsqueue and params.awsregion have been set if running on AWSBatch - assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" - // Check outdir paths to be S3 buckets if running on AWSBatch - assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" - } - } - - // - // Warn if a -profile or Nextflow config has not been provided to run the pipeline - // - public static void checkConfigProvided(workflow, log) { - if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " - } - } - - // - // Generate version string - // - public static String version(workflow) { - String version_string = "" - - if (workflow.manifest.version) { - def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' - version_string += "${prefix_v}${workflow.manifest.version}" - } - - if (workflow.commitId) { - def git_shortsha = workflow.commitId.substring(0, 7) - version_string += "-g${git_shortsha}" - } - - return version_string - } - - // - // Construct and send completion email - // - public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { - - // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" - if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" - } - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['Date Started'] = workflow.start - misc_fields['Date Completed'] = workflow.complete - misc_fields['Pipeline script file path'] = workflow.scriptFile - misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build - misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - - def email_fields = [:] - email_fields['version'] = NfcoreTemplate.version(workflow) - email_fields['runName'] = workflow.runName - email_fields['success'] = workflow.success - email_fields['dateComplete'] = workflow.complete - email_fields['duration'] = workflow.duration - email_fields['exitStatus'] = workflow.exitStatus - email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - email_fields['errorReport'] = (workflow.errorReport ?: 'None') - email_fields['commandLine'] = workflow.commandLine - email_fields['projectDir'] = workflow.projectDir - email_fields['summary'] = summary << misc_fields - - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" - } - mqc_report = mqc_report[0] - } - } - } catch (all) { - if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" - } - } - - // Check if we are only sending emails on failure - def email_address = params.email - if (!params.email && params.email_on_fail && !workflow.success) { - email_address = params.email_on_fail - } - - // Render the TXT template - def engine = new groovy.text.GStringTemplateEngine() - def tf = new File("$projectDir/assets/email_template.txt") - def txt_template = engine.createTemplate(tf).make(email_fields) - def email_txt = txt_template.toString() - - // Render the HTML template - def hf = new File("$projectDir/assets/email_template.html") - def html_template = engine.createTemplate(hf).make(email_fields) - def email_html = html_template.toString() - - // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] - def sf = new File("$projectDir/assets/sendmail_template.txt") - def sendmail_template = engine.createTemplate(sf).make(smail_fields) - def sendmail_html = sendmail_template.toString() - - // Send the HTML e-mail - Map colors = logColours(params.monochrome_logs) - if (email_address) { - try { - if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } - // Try to send HTML e-mail using sendmail - def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") - sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { - // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] - } - mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" - } - } - - // Write summary e-mail HTML to a file - def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") - output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); - output_hf.delete() - - // Write summary e-mail TXT to a file - def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") - output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); - output_tf.delete() - } - - // - // Construct and send a notification to a web server as JSON - // e.g. Microsoft Teams and Slack - // - public static void IM_notification(workflow, params, summary_params, projectDir, log) { - def hook_url = params.hook_url - - def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } - - def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp - - def msg_fields = [:] - msg_fields['version'] = NfcoreTemplate.version(workflow) - msg_fields['runName'] = workflow.runName - msg_fields['success'] = workflow.success - msg_fields['dateComplete'] = workflow.complete - msg_fields['duration'] = workflow.duration - msg_fields['exitStatus'] = workflow.exitStatus - msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') - msg_fields['errorReport'] = (workflow.errorReport ?: 'None') - msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") - msg_fields['projectDir'] = workflow.projectDir - msg_fields['summary'] = summary << misc_fields - - // Render the JSON template - def engine = new groovy.text.GStringTemplateEngine() - // Different JSON depending on the service provider - // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format - def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" - def hf = new File("$projectDir/assets/${json_path}") - def json_template = engine.createTemplate(hf).make(msg_fields) - def json_message = json_template.toString() - - // POST - def post = new URL(hook_url).openConnection(); - post.setRequestMethod("POST") - post.setDoOutput(true) - post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); - } - } - - // - // Dump pipeline parameters in a json file - // - public static void dump_parameters(workflow, params) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) - - FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") - temp_pf.delete() - } - - // - // Print pipeline summary on completion - // - public static void summary(workflow, params, log) { - Map colors = logColours(params.monochrome_logs) - if (workflow.success) { - if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" - } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" - } - } - - // - // ANSII Colours used for terminal logging - // - public static Map logColours(Boolean monochrome_logs) { - Map colorcodes = [:] - - // Reset / Meta - colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" - colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" - colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" - colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" - colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" - colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" - colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" - - // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" - - // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" - - // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" - - // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" - - // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" - - return colorcodes - } - - // - // Does what is says on the tin - // - public static String dashedLine(monochrome_logs) { - Map colors = logColours(monochrome_logs) - return "-${colors.dim}----------------------------------------------------${colors.reset}-" - } - - // - // nf-core logo - // - public static String logo(workflow, monochrome_logs) { - Map colors = logColours(monochrome_logs) - String workflow_version = NfcoreTemplate.version(workflow) - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) - } -} diff --git a/lib/Utils.groovy b/lib/Utils.groovy deleted file mode 100644 index 8d030f4e..00000000 --- a/lib/Utils.groovy +++ /dev/null @@ -1,47 +0,0 @@ -// -// This file holds several Groovy functions that could be useful for any Nextflow pipeline -// - -import org.yaml.snakeyaml.Yaml - -class Utils { - - // - // When running with -profile conda, warn if channels have not been set-up appropriately - // - public static void checkCondaChannels(log) { - Yaml parser = new Yaml() - def channels = [] - try { - def config = parser.load("conda config --show channels".execute().text) - channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return - } - - // Check that all channels are present - // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] - def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean - - // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } - - if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - } - } -} diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy deleted file mode 100755 index 28b15df4..00000000 --- a/lib/WorkflowMain.groovy +++ /dev/null @@ -1,77 +0,0 @@ -// -// This file holds several functions specific to the main.nf workflow in the nf-core/rnavar pipeline -// - -import nextflow.Nextflow - -class WorkflowMain { - - // - // Citation string for pipeline - // - public static String citation(workflow) { - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - // TODO nf-core: Add Zenodo DOI for pipeline after first release - //"* The pipeline\n" + - //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" - } - - - // - // Validate parameters and print summary to screen - // - public static void initialise(workflow, params, log, args) { - - // Print workflow version and exit on --version - if (params.version) { - String workflow_version = NfcoreTemplate.version(workflow) - log.info "${workflow.manifest.name} ${workflow_version}" - System.exit(0) - } - - // Check that a -profile or Nextflow config has been provided to run the pipeline - NfcoreTemplate.checkConfigProvided(workflow, log) - // Check that the profile doesn't contain spaces and doesn't end with a trailing comma - checkProfile(workflow.profile, args, log) - - // Check that conda channels are set-up correctly - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - Utils.checkCondaChannels(log) - } - - // Check AWS batch settings - NfcoreTemplate.awsBatch(workflow, params) - - // Check input has been provided - if (!params.input) { - Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") - } - } - // - // Get attribute from genome config file e.g. fasta - // - public static Object getGenomeAttribute(params, attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } - } - return null - } - - // - // Exit pipeline if --profile contains spaces - // - private static void checkProfile(profile, args, log) { - if (profile.endsWith(',')) { - Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - if (args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." - } - } -} diff --git a/lib/WorkflowRnavar.groovy b/lib/WorkflowRnavar.groovy deleted file mode 100755 index 08a4d64e..00000000 --- a/lib/WorkflowRnavar.groovy +++ /dev/null @@ -1,122 +0,0 @@ -// -// This file holds several functions specific to the workflow/rnavar.nf in the nf-core/rnavar pipeline -// - -import nextflow.Nextflow -import groovy.text.SimpleTemplateEngine - -class WorkflowRnavar { - - // - // Check and validate parameters - // - public static void initialise(params, log) { - - genomeExistsError(params, log) - - - if (!params.fasta) { - Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - } - } - - // - // Get workflow summary for MultiQC - // - public static String paramsSummaryMultiqc(workflow, summary) { - String summary_section = '' - for (group in summary.keySet()) { - def group_params = summary.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" - } - summary_section += "
    \n" - } - } - - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" - return yaml_file_text - } - - // - // Generate methods description for MultiQC - // - - public static String toolCitationText(params) { - - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def citation_text = [ - "Tools used in the workflow included:", - "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", - "." - ].join(' ').trim() - - return citation_text - } - - public static String toolBibliographyText(params) { - - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report - def reference_text = [ - "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " - ].join(' ').trim() - - return reference_text - } - - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file - def meta = [:] - meta.workflow = run_workflow.toMap() - meta["manifest_map"] = run_workflow.manifest.toMap() - - // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " - - // Tool references - meta["tool_citations"] = "" - meta["tool_bibliography"] = "" - - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) - - - def methods_text = mqc_methods_yaml.text - - def engine = new SimpleTemplateEngine() - def description_html = engine.createTemplate(methods_text).make(meta) - - return description_html - } - - // - // Exit pipeline if incorrect --genome key provided - // - private static void genomeExistsError(params, log) { - if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + - " Currently, the available genome keys are:\n" + - " ${params.genomes.keySet().join(", ")}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - Nextflow.error(error_string) - } - } -} diff --git a/main.nf b/main.nf index 6d848d3a..5ca33427 100644 --- a/main.nf +++ b/main.nf @@ -13,66 +13,96 @@ nextflow.enable.dsl = 2 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') +include { RNAVAR } from './workflows/rnavar' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnavar_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rnavar_pipeline' + +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_rnavar_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE & PRINT PARAMETER SUMMARY + GENOME PARAMETER VALUES ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { validateParameters; paramsHelp } from 'plugin/nf-validation' - -// Print help message if needed -if (params.help) { - def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) - def citation = '\n' + WorkflowMain.citation(workflow) + '\n' - def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) - System.exit(0) -} - -// Validate input parameters -if (params.validate_params) { - validateParameters() -} - -WorkflowMain.initialise(workflow, params, log, args) +// TODO nf-core: Remove this line if you don't need a FASTA file +// This is an example of how to use getGenomeAttribute() to fetch parameters +// from igenomes.config using `--genome` +params.fasta = getGenomeAttribute('fasta') /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - NAMED WORKFLOW FOR PIPELINE + NAMED WORKFLOWS FOR PIPELINE ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { RNAVAR } from './workflows/rnavar' - // -// WORKFLOW: Run main nf-core/rnavar analysis pipeline +// WORKFLOW: Run main analysis pipeline depending on type of input // workflow NFCORE_RNAVAR { - RNAVAR () -} + take: + samplesheet // channel: samplesheet read in from --input + + main: + + // + // WORKFLOW: Run pipeline + // + RNAVAR ( + samplesheet + ) + + emit: + multiqc_report = RNAVAR.out.multiqc_report // channel: /path/to/multiqc_report.html + +} /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN ALL WORKFLOWS + RUN MAIN WORKFLOW ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// -// WORKFLOW: Execute a single named workflow for the pipeline -// See: https://github.com/nf-core/rnaseq/issues/619 -// workflow { - NFCORE_RNAVAR () + + main: + + // + // SUBWORKFLOW: Run initialisation tasks + // + PIPELINE_INITIALISATION ( + params.version, + params.help, + params.validate_params, + params.monochrome_logs, + args, + params.outdir, + params.input + ) + + // + // WORKFLOW: Run main workflow + // + NFCORE_RNAVAR ( + PIPELINE_INITIALISATION.out.samplesheet + ) + + // + // SUBWORKFLOW: Run completion tasks + // + PIPELINE_COMPLETION ( + params.email, + params.email_on_fail, + params.plaintext_email, + params.outdir, + params.monochrome_logs, + params.hook_url, + NFCORE_RNAVAR.out.multiqc_report + ) } /* diff --git a/modules.json b/modules.json index 74d7541e..907db614 100644 --- a/modules.json +++ b/modules.json @@ -5,22 +5,36 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] - }, "fastqc": { "branch": "master", - "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", + "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", + "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", "installed_by": ["modules"] } } + }, + "subworkflows": { + "nf-core": { + "utils_nextflow_pipeline": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + }, + "utils_nfcore_pipeline": { + "branch": "master", + "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "installed_by": ["subworkflows"] + }, + "utils_nfvalidation_plugin": { + "branch": "master", + "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "installed_by": ["subworkflows"] + } + } } } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 852dcbf9..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,31 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/rnavar/bin/ - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml deleted file mode 100644 index 9b3272bc..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: custom_dumpsoftwareversions -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf deleted file mode 100644 index f2187611..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_single' - - // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" - - input: - path versions - - output: - path "software_versions.yml" , emit: yml - path "software_versions_mqc.yml", emit: mqc_yml - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - template 'dumpsoftwareversions.py' -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml deleted file mode 100644 index 5f15a5fd..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ /dev/null @@ -1,37 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json -name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template -keywords: - - custom - - dump - - version -tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] -input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" -output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" -maintainers: - - "@drpatelh" - - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100755 index e55b8d43..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,102 +0,0 @@ -#!/usr/bin/env python - - -"""Provide functions to merge multiple versions.yml files.""" - - -import platform -from textwrap import dedent - -import yaml - - -def _make_versions_html(versions): - """Generate a tabular HTML output of all versions for MultiQC.""" - html = [ - dedent( - """\\ - -
    Process Name \\", + " \\ Software Version
    CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    File typeConventional base calls
    - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -def main(): - """Load all version files and generate merged output.""" - versions_this_module = {} - versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, - } - - with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - - # aggregate versions by the module name (derived from fully-qualified process name) - versions_by_module = {} - for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - if versions_by_module[module] != process_versions: - raise AssertionError( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - - versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", - } - - versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), - } - - with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) - with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - - with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) - - -if __name__ == "__main__": - main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test deleted file mode 100644 index b1e1630b..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test +++ /dev/null @@ -1,43 +0,0 @@ -nextflow_process { - - name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" - script "../main.nf" - process "CUSTOM_DUMPSOFTWAREVERSIONS" - tag "modules" - tag "modules_nfcore" - tag "custom" - tag "dumpsoftwareversions" - tag "custom/dumpsoftwareversions" - - test("Should run without failures") { - when { - process { - """ - def tool1_version = ''' - TOOL1: - tool1: 0.11.9 - '''.stripIndent() - - def tool2_version = ''' - TOOL2: - tool2: 1.9 - '''.stripIndent() - - input[0] = Channel.of(tool1_version, tool2_version).collectFile() - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot( - process.out.versions, - file(process.out.mqc_yml[0]).readLines()[0..10], - file(process.out.yml[0]).readLines()[0..7] - ).match() - } - ) - } - } -} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap deleted file mode 100644 index 5f59a936..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ /dev/null @@ -1,33 +0,0 @@ -{ - "Should run without failures": { - "content": [ - [ - "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" - ], - [ - "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", - " \\n\\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n \\n \\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\", - " \\ \\n\\n\\n\\n\\n\\n \\n\\", - " \\ \\n \\n\\n\\n\\n\\", - " \\n\\n \\n \\n\\" - ], - [ - "CUSTOM_DUMPSOFTWAREVERSIONS:", - " python: 3.11.7", - " yaml: 5.4.1", - "TOOL1:", - " tool1: 0.11.9", - "TOOL2:", - " tool2: '1.9'", - "Workflow:" - ] - ], - "timestamp": "2024-01-09T23:01:18.710682" - } -} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml deleted file mode 100644 index 405aa24a..00000000 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 1f21c664..70edae4d 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -33,7 +33,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -63,7 +63,7 @@ nextflow_process { { assert path(process.out.html[0][1][0]).text.contains("") }, { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -89,7 +89,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -115,7 +115,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -153,7 +153,7 @@ nextflow_process { { assert path(process.out.html[0][1][2]).text.contains("") }, { assert path(process.out.html[0][1][3]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -179,7 +179,7 @@ nextflow_process { { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, { assert path(process.out.html[0][1]).text.contains("") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } @@ -204,7 +204,7 @@ nextflow_process { { assert process.success }, { assert snapshot(process.out.html.collect { file(it[1]).getName() } + process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match() } + process.out.versions ).match("fastqc_stub") } ) } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 5d624bb8..86f7c311 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "sarscov2 single-end [fastq] - stub": { + "fastqc_versions_interleaved": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:07.293713" + }, + "fastqc_stub": { "content": [ [ "test.html", @@ -7,14 +19,70 @@ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:40:57.254299" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:31:01.425198" + }, + "fastqc_versions_multiple": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:55.797907" + }, + "fastqc_versions_bam": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:40:26.795862" + }, + "fastqc_versions_single": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:27.043675" + }, + "fastqc_versions_paired": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:39:47.584191" }, - "versions": { + "fastqc_versions_custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], - "timestamp": "2024-01-17T18:36:50.033627" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 7625b752..2212096a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.19 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1b9f7c43..354f4430 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : - 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index d0438eda..f1c4242e 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process MULTIQC" script "../main.nf" process "MULTIQC" + tag "modules" tag "modules_nfcore" tag "multiqc" @@ -12,7 +13,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -25,7 +26,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_single") } ) } @@ -36,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] @@ -49,7 +50,7 @@ nextflow_process { { assert process.success }, { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out.versions).match("multiqc_versions_config") } ) } } @@ -61,7 +62,7 @@ nextflow_process { when { process { """ - input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) input[1] = [] input[2] = [] input[3] = [] @@ -75,7 +76,7 @@ nextflow_process { { assert snapshot(process.out.report.collect { file(it).getName() } + process.out.data.collect { file(it).getName() } + process.out.plots.collect { file(it).getName() } + - process.out.versions ).match() } + process.out.versions ).match("multiqc_stub") } ) } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index d37e7304..c204b488 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,21 +1,41 @@ { - "versions": { + "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:02:49.911994" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:28:51.744211298" }, - "sarscov2 single-end [fastqc] - stub": { + "multiqc_stub": { "content": [ [ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" ] ], - "timestamp": "2024-01-09T23:03:14.524346" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:28.847433492" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T09:29:13.223621555" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index aabc8be5..dda1b90f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,9 +16,7 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - - - // MultiQC options + fasta = null// MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -43,7 +41,6 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options // Defaults only, expecting to be overwritten diff --git a/nextflow_schema.json b/nextflow_schema.json index c22a7db9..d8e53bf7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,6 +16,7 @@ "type": "string", "format": "file-path", "exists": true, + "schema": "assets/schema_input.json", "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", "description": "Path to comma-separated file containing information about the samples in the experiment.", diff --git a/pyproject.toml b/pyproject.toml index 7d08e1c8..56110621 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,11 +3,13 @@ [tool.ruff] line-length = 120 target-version = "py38" -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] cache-dir = "~/.cache/ruff" -[tool.ruff.isort] +[tool.ruff.lint] +select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] + +[tool.ruff.lint.isort] known-first-party = ["nf_core"] -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] "__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 0aecf87f..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,44 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf new file mode 100644 index 00000000..dc90ad90 --- /dev/null +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -0,0 +1,247 @@ +// +// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { fromSamplesheet } from 'plugin/nf-validation' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' +include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' +include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' +include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' +include { imNotification } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' +include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' + +/* +======================================================================================== + SUBWORKFLOW TO INITIALISE PIPELINE +======================================================================================== +*/ + +workflow PIPELINE_INITIALISATION { + + take: + version // boolean: Display version and exit + help // boolean: Display help text + validate_params // boolean: Boolean whether to validate parameters against the schema at runtime + monochrome_logs // boolean: Do not use coloured log outputs + nextflow_cli_args // array: List of positional nextflow CLI args + outdir // string: The output directory where the results will be saved + input // string: Path to input samplesheet + + main: + + ch_versions = Channel.empty() + + // + // Print version and exit if required and dump pipeline parameters to JSON file + // + UTILS_NEXTFLOW_PIPELINE ( + version, + true, + outdir, + workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 + ) + + // + // Validate parameters and generate parameter summary to stdout + // + pre_help_text = nfCoreLogo(monochrome_logs) + post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) + def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " + UTILS_NFVALIDATION_PLUGIN ( + help, + workflow_command, + pre_help_text, + post_help_text, + validate_params, + "nextflow_schema.json" + ) + + // + // Check config provided to the pipeline + // + UTILS_NFCORE_PIPELINE ( + nextflow_cli_args + ) + // + // Custom validation for pipeline parameters + // + validateInputParameters() + + // + // Create channel from input file provided through params.input + // + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + validateInputSamplesheet(it) + } + .map { + meta, fastqs -> + return [ meta, fastqs.flatten() ] + } + .set { ch_samplesheet } + + emit: + samplesheet = ch_samplesheet + versions = ch_versions +} + +/* +======================================================================================== + SUBWORKFLOW FOR PIPELINE COMPLETION +======================================================================================== +*/ + +workflow PIPELINE_COMPLETION { + + take: + email // string: email address + email_on_fail // string: email address sent on pipeline failure + plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published + monochrome_logs // boolean: Disable ANSI colour codes in log output + hook_url // string: hook URL for notifications + multiqc_report // string: Path to MultiQC report + + main: + + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + + // + // Completion email and summary + // + workflow.onComplete { + if (email || email_on_fail) { + completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + } + + completionSummary(monochrome_logs) + + if (hook_url) { + imNotification(summary_params, hook_url) + } + } +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ +// +// Check and validate pipeline parameters +// +def validateInputParameters() { + genomeExistsError() +}// +// Validate channels from input samplesheet +// +def validateInputSamplesheet(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] +} +// +// Get attribute from genome config file e.g. fasta +// +def getGenomeAttribute(attribute) { + if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { + if (params.genomes[ params.genome ].containsKey(attribute)) { + return params.genomes[ params.genome ][ attribute ] + } + } + return null +} + +// +// Exit pipeline if incorrect --genome key provided +// +def genomeExistsError() { + if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + + " Currently, the available genome keys are:\n" + + " ${params.genomes.keySet().join(", ")}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + error(error_string) + } +}// +// Generate methods description for MultiQC +// +def toolCitationText() { + // TODO nf-core: Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text +} + +def toolBibliographyText() { + // TODO nf-core: Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text +} + +def methodsDescriptionText(mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = workflow.toMap() + meta["manifest_map"] = workflow.manifest.toMap() + + // Pipeline DOI + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + // meta["tool_bibliography"] = toolBibliographyText() + + + def methods_text = mqc_methods_yaml.text + + def engine = new groovy.text.SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html.toString() +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf new file mode 100644 index 00000000..ac31f28f --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -0,0 +1,126 @@ +// +// Subworkflow with functionality that may be useful for any Nextflow pipeline +// + +import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NEXTFLOW_PIPELINE { + + take: + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results + check_conda_channels // boolean: check conda channels + + main: + + // + // Print workflow version and exit on --version + // + if (print_version) { + log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + System.exit(0) + } + + // + // Dump pipeline parameters to a JSON file + // + if (dump_parameters && outdir) { + dumpParametersToJSON(outdir) + } + + // + // When running with Conda, warn if channels have not been set-up appropriately + // + if (check_conda_channels) { + checkCondaChannels() + } + + emit: + dummy_emit = true +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Generate version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Dump pipeline parameters to a JSON file +// +def dumpParametersToJSON(outdir) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() +} + +// +// When running with -profile conda, warn if channels have not been set-up appropriately +// +def checkCondaChannels() { + Yaml parser = new Yaml() + def channels = [] + try { + def config = parser.load("conda config --show channels".execute().text) + channels = config.channels + } catch(NullPointerException | IOException e) { + log.warn "Could not verify conda channel configuration." + return + } + + // Check that all channels are present + // This channel list is ordered by required channel priority. + def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean + + // Check that they are in the right order + def channel_priority_violation = false + def n = required_channels_in_order.size() + for (int i = 0; i < n - 1; i++) { + channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + } + + if (channels_missing | channel_priority_violation) { + log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + " There is a problem with your Conda configuration!\n\n" + + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + + " Please refer to https://bioconda.github.io/\n" + + " The observed channel order is \n" + + " ${channels}\n" + + " but the following channel order is required:\n" + + " ${required_channels_in_order}\n" + + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml new file mode 100644 index 00000000..e5c3a0a8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml @@ -0,0 +1,38 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NEXTFLOW_PIPELINE" +description: Subworkflow with functionality that may be useful for any Nextflow pipeline +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - print_version: + type: boolean + description: | + Print the version of the pipeline and exit + - dump_parameters: + type: boolean + description: | + Dump the parameters of the pipeline to a JSON file + - output_directory: + type: directory + description: Path to output dir to write JSON file to. + pattern: "results/" + - check_conda_channel: + type: boolean + description: | + Check if the conda channel priority is correct. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" + - "@drpatelh" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..8ed4310c --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -0,0 +1,54 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/nf-core/utils_nextflow_pipeline/main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Test Function getWorkflowVersion") { + + function "getWorkflowVersion" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dumpParametersToJSON") { + + function "dumpParametersToJSON" + + when { + function { + """ + // define inputs of the function here. Example: + input[0] = "$outputDir" + """.stripIndent() + } + } + + then { + assertAll( + { assert function.success } + ) + } + } + + test("Test Function checkCondaChannels") { + + function "checkCondaChannels" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..db2030f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,12 @@ +{ + "Test Function getWorkflowVersion": { + "content": [ + "v9.9.9" + ], + "timestamp": "2024-01-19T11:32:36.031083" + }, + "Test Function checkCondaChannels": { + "content": null, + "timestamp": "2024-01-19T11:32:50.456" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..f7c54bc6 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,123 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NEXTFLOW_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config" + workflow "UTILS_NEXTFLOW_PIPELINE" + tag 'subworkflows' + tag 'utils_nextflow_pipeline' + tag 'subworkflows/utils_nextflow_pipeline' + + test("Should run no inputs") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = false + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should print version") { + + when { + params { + outdir = "tests/results" + } + workflow { + """ + print_version = true + dump_parameters = false + outdir = null + check_conda_channels = false + + input[0] = print_version + input[1] = dump_parameters + input[2] = outdir + input[3] = check_conda_channels + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } + ) + } + } + + test("Should dump params") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = params.outdir + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should not create params JSON if no output directory") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + print_version = false + dump_parameters = true + outdir = params.outdir + check_conda_channels = false + + input[0] = false + input[1] = true + input[2] = null + input[3] = false + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config new file mode 100644 index 00000000..53574ffe --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml new file mode 100644 index 00000000..f8476112 --- /dev/null +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nextflow_pipeline: + - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf new file mode 100644 index 00000000..a8b55d6f --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -0,0 +1,440 @@ +// +// Subworkflow with utility functions specific to the nf-core pipeline template +// + +import org.yaml.snakeyaml.Yaml +import nextflow.extension.FilesEx + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFCORE_PIPELINE { + + take: + nextflow_cli_args + + main: + valid_config = checkConfigProvided() + checkProfileProvided(nextflow_cli_args) + + emit: + valid_config +} + +/* +======================================================================================== + FUNCTIONS +======================================================================================== +*/ + +// +// Warn if a -profile or Nextflow config has not been provided to run the pipeline +// +def checkConfigProvided() { + valid_config = true + if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { + log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + + "Please refer to the quick start section and usage docs for the pipeline.\n " + valid_config = false + } + return valid_config +} + +// +// Exit pipeline if --profile contains spaces +// +def checkProfileProvided(nextflow_cli_args) { + if (workflow.profile.endsWith(',')) { + error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } + if (nextflow_cli_args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + } +} + +// +// Citation string for pipeline +// +def workflowCitation() { + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + + "* The pipeline\n" + + " ${workflow.manifest.doi}\n\n" + + "* The nf-core framework\n" + + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + + "* Software dependencies\n" + + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" +} + +// +// Generate workflow version string +// +def getWorkflowVersion() { + String version_string = "" + if (workflow.manifest.version) { + def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' + version_string += "${prefix_v}${workflow.manifest.version}" + } + + if (workflow.commitId) { + def git_shortsha = workflow.commitId.substring(0, 7) + version_string += "-g${git_shortsha}" + } + + return version_string +} + +// +// Get software versions for pipeline +// +def processVersionsFromYAML(yaml_file) { + Yaml yaml = new Yaml() + versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + return yaml.dumpAsMap(versions).trim() +} + +// +// Get workflow version for pipeline +// +def workflowVersionToYAML() { + return """ + Workflow: + $workflow.manifest.name: ${getWorkflowVersion()} + Nextflow: $workflow.nextflow.version + """.stripIndent().trim() +} + +// +// Get channel of software versions used in pipeline in YAML format +// +def softwareVersionsToYAML(ch_versions) { + return ch_versions + .unique() + .map { processVersionsFromYAML(it) } + .unique() + .mix(Channel.of(workflowVersionToYAML())) +} + +// +// Get workflow summary for MultiQC +// +def paramsSummaryMultiqc(summary_params) { + def summary_section = '' + for (group in summary_params.keySet()) { + def group_params = summary_params.get(group) // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    $group

    \n" + summary_section += "
    \n" + for (param in group_params.keySet()) { + summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" + } + } + + String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" + + return yaml_file_text +} + +// +// nf-core logo +// +def nfCoreLogo(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + String.format( + """\n + ${dashedLine(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} + ${dashedLine(monochrome_logs)} + """.stripIndent() + ) +} + +// +// Return dashed line +// +def dashedLine(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" +} + +// +// ANSII colours used for terminal logging +// +def logColours(monochrome_logs=true) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes +} + +// +// Attach the multiqc report to email +// +def attachMultiqcReport(multiqc_report) { + def mqc_report = null + try { + if (workflow.success) { + mqc_report = multiqc_report.getVal() + if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { + if (mqc_report.size() > 1) { + log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + } + mqc_report = mqc_report[0] + } + } + } catch (all) { + if (multiqc_report) { + log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + } + } + return mqc_report +} + +// +// Construct and send completion email +// +def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { + + // Set up the e-mail variables + def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + if (!workflow.success) { + subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + } + + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['Date Started'] = workflow.start + misc_fields['Date Completed'] = workflow.complete + misc_fields['Pipeline script file path'] = workflow.scriptFile + misc_fields['Pipeline script hash ID'] = workflow.scriptId + if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository + if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId + if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build + misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp + + def email_fields = [:] + email_fields['version'] = getWorkflowVersion() + email_fields['runName'] = workflow.runName + email_fields['success'] = workflow.success + email_fields['dateComplete'] = workflow.complete + email_fields['duration'] = workflow.duration + email_fields['exitStatus'] = workflow.exitStatus + email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + email_fields['errorReport'] = (workflow.errorReport ?: 'None') + email_fields['commandLine'] = workflow.commandLine + email_fields['projectDir'] = workflow.projectDir + email_fields['summary'] = summary << misc_fields + + // On success try attach the multiqc report + def mqc_report = attachMultiqcReport(multiqc_report) + + // Check if we are only sending emails on failure + def email_address = email + if (!email && email_on_fail && !workflow.success) { + email_address = email_on_fail + } + + // Render the TXT template + def engine = new groovy.text.GStringTemplateEngine() + def tf = new File("${workflow.projectDir}/assets/email_template.txt") + def txt_template = engine.createTemplate(tf).make(email_fields) + def email_txt = txt_template.toString() + + // Render the HTML template + def hf = new File("${workflow.projectDir}/assets/email_template.html") + def html_template = engine.createTemplate(hf).make(email_fields) + def email_html = html_template.toString() + + // Render the sendmail template + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") + def sendmail_template = engine.createTemplate(sf).make(smail_fields) + def sendmail_html = sendmail_template.toString() + + // Send the HTML e-mail + Map colors = logColours(monochrome_logs) + if (email_address) { + try { + if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } + [ 'sendmail', '-t' ].execute() << sendmail_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" + } catch (all) { + // Catch failures and try with plaintext + def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + mail_cmd.execute() << email_html + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + } + } + + // Write summary e-mail HTML to a file + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") + output_hf.withWriter { w -> w << email_html } + FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") + output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() +} + +// +// Print pipeline summary on completion +// +def completionSummary(monochrome_logs=true) { + Map colors = logColours(monochrome_logs) + if (workflow.success) { + if (workflow.stats.ignoredCount == 0) { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + } + } else { + log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } +} + +// +// Construct and send a notification to a web server as JSON e.g. Microsoft Teams and Slack +// +def imNotification(summary_params, hook_url) { + def summary = [:] + for (group in summary_params.keySet()) { + summary << summary_params[group] + } + + def misc_fields = [:] + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) misc_fields['repository'] = workflow.repository + if (workflow.commitId) misc_fields['commitid'] = workflow.commitId + if (workflow.revision) misc_fields['revision'] = workflow.revision + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + + def msg_fields = [:] + msg_fields['version'] = getWorkflowVersion() + msg_fields['runName'] = workflow.runName + msg_fields['success'] = workflow.success + msg_fields['dateComplete'] = workflow.complete + msg_fields['duration'] = workflow.duration + msg_fields['exitStatus'] = workflow.exitStatus + msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') + msg_fields['errorReport'] = (workflow.errorReport ?: 'None') + msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") + msg_fields['projectDir'] = workflow.projectDir + msg_fields['summary'] = summary << misc_fields + + // Render the JSON template + def engine = new groovy.text.GStringTemplateEngine() + // Different JSON depending on the service provider + // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format + def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" + def hf = new File("${workflow.projectDir}/assets/${json_path}") + def json_template = engine.createTemplate(hf).make(msg_fields) + def json_message = json_template.toString() + + // POST + def post = new URL(hook_url).openConnection(); + post.setRequestMethod("POST") + post.setDoOutput(true) + post.setRequestProperty("Content-Type", "application/json") + post.getOutputStream().write(json_message.getBytes("UTF-8")); + def postRC = post.getResponseCode(); + if (! postRC.equals(200)) { + log.warn(post.getErrorStream().getText()); + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml new file mode 100644 index 00000000..d08d2434 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml @@ -0,0 +1,24 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFCORE_PIPELINE" +description: Subworkflow with utility functions specific to the nf-core pipeline template +keywords: + - utility + - pipeline + - initialise + - version +components: [] +input: + - nextflow_cli_args: + type: list + description: | + Nextflow CLI positional arguments +output: + - success: + type: boolean + description: | + Dummy output to indicate success +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test new file mode 100644 index 00000000..1dc317f8 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -0,0 +1,134 @@ + +nextflow_function { + + name "Test Functions" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Test Function checkConfigProvided") { + + function "checkConfigProvided" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function checkProfileProvided") { + + function "checkProfileProvided" + + when { + function { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function workflowCitation") { + + function "workflowCitation" + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function nfCoreLogo") { + + function "nfCoreLogo" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function dashedLine") { + + function "dashedLine" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function without logColours") { + + function "logColours" + + when { + function { + """ + input[0] = true + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } + + test("Test Function with logColours") { + function "logColours" + + when { + function { + """ + input[0] = false + """ + } + } + + then { + assertAll( + { assert function.success }, + { assert snapshot(function.result).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap new file mode 100644 index 00000000..10f948e6 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -0,0 +1,138 @@ +{ + "Test Function checkProfileProvided": { + "content": null, + "timestamp": "2024-02-09T15:43:55.145717" + }, + "Test Function checkConfigProvided": { + "content": [ + true + ], + "timestamp": "2024-01-19T11:34:13.548431224" + }, + "Test Function nfCoreLogo": { + "content": [ + "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" + ], + "timestamp": "2024-01-19T11:34:38.840454873" + }, + "Test Function workflowCitation": { + "content": [ + "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" + ], + "timestamp": "2024-01-19T11:34:22.24352016" + }, + "Test Function without logColours": { + "content": [ + { + "reset": "", + "bold": "", + "dim": "", + "underlined": "", + "blink": "", + "reverse": "", + "hidden": "", + "black": "", + "red": "", + "green": "", + "yellow": "", + "blue": "", + "purple": "", + "cyan": "", + "white": "", + "bblack": "", + "bred": "", + "bgreen": "", + "byellow": "", + "bblue": "", + "bpurple": "", + "bcyan": "", + "bwhite": "", + "ublack": "", + "ured": "", + "ugreen": "", + "uyellow": "", + "ublue": "", + "upurple": "", + "ucyan": "", + "uwhite": "", + "iblack": "", + "ired": "", + "igreen": "", + "iyellow": "", + "iblue": "", + "ipurple": "", + "icyan": "", + "iwhite": "", + "biblack": "", + "bired": "", + "bigreen": "", + "biyellow": "", + "biblue": "", + "bipurple": "", + "bicyan": "", + "biwhite": "" + } + ], + "timestamp": "2024-01-19T11:35:04.418416984" + }, + "Test Function dashedLine": { + "content": [ + "-\u001b[2m----------------------------------------------------\u001b[0m-" + ], + "timestamp": "2024-01-19T11:34:55.420000755" + }, + "Test Function with logColours": { + "content": [ + { + "reset": "\u001b[0m", + "bold": "\u001b[1m", + "dim": "\u001b[2m", + "underlined": "\u001b[4m", + "blink": "\u001b[5m", + "reverse": "\u001b[7m", + "hidden": "\u001b[8m", + "black": "\u001b[0;30m", + "red": "\u001b[0;31m", + "green": "\u001b[0;32m", + "yellow": "\u001b[0;33m", + "blue": "\u001b[0;34m", + "purple": "\u001b[0;35m", + "cyan": "\u001b[0;36m", + "white": "\u001b[0;37m", + "bblack": "\u001b[1;30m", + "bred": "\u001b[1;31m", + "bgreen": "\u001b[1;32m", + "byellow": "\u001b[1;33m", + "bblue": "\u001b[1;34m", + "bpurple": "\u001b[1;35m", + "bcyan": "\u001b[1;36m", + "bwhite": "\u001b[1;37m", + "ublack": "\u001b[4;30m", + "ured": "\u001b[4;31m", + "ugreen": "\u001b[4;32m", + "uyellow": "\u001b[4;33m", + "ublue": "\u001b[4;34m", + "upurple": "\u001b[4;35m", + "ucyan": "\u001b[4;36m", + "uwhite": "\u001b[4;37m", + "iblack": "\u001b[0;90m", + "ired": "\u001b[0;91m", + "igreen": "\u001b[0;92m", + "iyellow": "\u001b[0;93m", + "iblue": "\u001b[0;94m", + "ipurple": "\u001b[0;95m", + "icyan": "\u001b[0;96m", + "iwhite": "\u001b[0;97m", + "biblack": "\u001b[1;90m", + "bired": "\u001b[1;91m", + "bigreen": "\u001b[1;92m", + "biyellow": "\u001b[1;93m", + "biblue": "\u001b[1;94m", + "bipurple": "\u001b[1;95m", + "bicyan": "\u001b[1;96m", + "biwhite": "\u001b[1;97m" + } + ], + "timestamp": "2024-01-19T11:35:13.436366565" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test new file mode 100644 index 00000000..8940d32d --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test @@ -0,0 +1,29 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFCORE_PIPELINE" + script "../main.nf" + config "subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config" + workflow "UTILS_NFCORE_PIPELINE" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "utils_nfcore_pipeline" + tag "subworkflows/utils_nfcore_pipeline" + + test("Should run without failures") { + + when { + workflow { + """ + input[0] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap new file mode 100644 index 00000000..d07ce54c --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -0,0 +1,15 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + true + ], + "valid_config": [ + true + ] + } + ], + "timestamp": "2024-01-19T11:35:22.538940073" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config new file mode 100644 index 00000000..d0a926bf --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config @@ -0,0 +1,9 @@ +manifest { + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml new file mode 100644 index 00000000..ac8523c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfcore_pipeline: + - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf new file mode 100644 index 00000000..2585b65d --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -0,0 +1,62 @@ +// +// Subworkflow that uses the nf-validation plugin to render help text and parameter summary +// + +/* +======================================================================================== + IMPORT NF-VALIDATION PLUGIN +======================================================================================== +*/ + +include { paramsHelp } from 'plugin/nf-validation' +include { paramsSummaryLog } from 'plugin/nf-validation' +include { validateParameters } from 'plugin/nf-validation' + +/* +======================================================================================== + SUBWORKFLOW DEFINITION +======================================================================================== +*/ + +workflow UTILS_NFVALIDATION_PLUGIN { + + take: + print_help // boolean: print help + workflow_command // string: default commmand used to run pipeline + pre_help_text // string: string to be printed before help text and summary log + post_help_text // string: string to be printed after help text and summary log + validate_params // boolean: validate parameters + schema_filename // path: JSON schema file, null to use default value + + main: + + log.debug "Using schema file: ${schema_filename}" + + // Default values for strings + pre_help_text = pre_help_text ?: '' + post_help_text = post_help_text ?: '' + workflow_command = workflow_command ?: '' + + // + // Print help message if needed + // + if (print_help) { + log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + System.exit(0) + } + + // + // Print parameter summary to stdout + // + log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + + // + // Validate parameters relative to the parameter JSON schema + // + if (validate_params){ + validateParameters(parameters_schema: schema_filename) + } + + emit: + dummy_emit = true +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml new file mode 100644 index 00000000..3d4a6b04 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "UTILS_NFVALIDATION_PLUGIN" +description: Use nf-validation to initiate and validate a pipeline +keywords: + - utility + - pipeline + - initialise + - validation +components: [] +input: + - print_help: + type: boolean + description: | + Print help message and exit + - workflow_command: + type: string + description: | + The command to run the workflow e.g. "nextflow run main.nf" + - pre_help_text: + type: string + description: | + Text to print before the help message + - post_help_text: + type: string + description: | + Text to print after the help message + - validate_params: + type: boolean + description: | + Validate the parameters and error if invalid. + - schema_filename: + type: string + description: | + The filename of the schema to validate against. +output: + - dummy_emit: + type: boolean + description: | + Dummy emit to make nf-core subworkflows lint happy +authors: + - "@adamrtalbot" +maintainers: + - "@adamrtalbot" + - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test new file mode 100644 index 00000000..517ee54e --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -0,0 +1,200 @@ +nextflow_workflow { + + name "Test Workflow UTILS_NFVALIDATION_PLUGIN" + script "../main.nf" + workflow "UTILS_NFVALIDATION_PLUGIN" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "plugin/nf-validation" + tag "'plugin/nf-validation'" + tag "utils_nfvalidation_plugin" + tag "subworkflows/utils_nfvalidation_plugin" + + test("Should run nothing") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should run help") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with command") { + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = null + post_help_text = null + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } } + ) + } + } + + test("Should run help with extra text") { + + + when { + + params { + monochrome_logs = true + test_data = '' + } + workflow { + """ + help = true + workflow_command = "nextflow run noorg/doesntexist" + pre_help_text = "pre-help-text" + post_help_text = "post-help-text" + validate_params = false + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert workflow.exitStatus == 0 }, + { assert workflow.stdout.any { it.contains('pre-help-text') } }, + { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, + { assert workflow.stdout.any { it.contains('Input/output options') } }, + { assert workflow.stdout.any { it.contains('--outdir') } }, + { assert workflow.stdout.any { it.contains('post-help-text') } } + ) + } + } + + test("Should validate params") { + + when { + + params { + monochrome_logs = true + test_data = '' + outdir = 1 + } + workflow { + """ + help = false + workflow_command = null + pre_help_text = null + post_help_text = null + validate_params = true + schema_filename = "$moduleTestDir/nextflow_schema.json" + + input[0] = help + input[1] = workflow_command + input[2] = pre_help_text + input[3] = post_help_text + input[4] = validate_params + input[5] = schema_filename + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } + ) + } + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json new file mode 100644 index 00000000..7626c1c9 --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -0,0 +1,96 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", + "title": ". pipeline parameters", + "description": "", + "type": "object", + "definitions": { + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": ["outdir"], + "properties": { + "validate_params": { + "type": "boolean", + "description": "Validate parameters?", + "default": true, + "hidden": true + }, + "outdir": { + "type": "string", + "format": "directory-path", + "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", + "fa_icon": "fas fa-folder-open" + }, + "test_data_base": { + "type": "string", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules", + "description": "Base for test data directory", + "hidden": true + }, + "test_data": { + "type": "string", + "description": "Fake test data param", + "hidden": true + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "help": { + "type": "boolean", + "description": "Display help text.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "version": { + "type": "boolean", + "description": "Display version and exit.", + "fa_icon": "fas fa-question-circle", + "hidden": true + }, + "logo": { + "type": "boolean", + "default": true, + "description": "Display nf-core logo in console output.", + "fa_icon": "fas fa-image", + "hidden": true + }, + "singularity_pull_docker_container": { + "type": "boolean", + "description": "Pull Singularity container from Docker?", + "hidden": true + }, + "publish_dir_mode": { + "type": "string", + "default": "copy", + "description": "Method used to save pipeline results to output directory.", + "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", + "fa_icon": "fas fa-copy", + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "hidden": true + }, + "monochrome_logs": { + "type": "boolean", + "description": "Use monochrome_logs", + "hidden": true + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" + }, + { + "$ref": "#/definitions/generic_options" + } + ] +} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml new file mode 100644 index 00000000..60b1cfff --- /dev/null +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/utils_nfvalidation_plugin: + - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 6c976f6a..5719e94c 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -1,54 +1,15 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - PRINT PARAMS SUMMARY + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' - -def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) -def citation = '\n' + WorkflowMain.citation(workflow) + '\n' -def summary_params = paramsSummaryMap(workflow) - -// Print parameter summary log to screen -log.info logo + paramsSummaryLog(workflow) + citation - -WorkflowRnavar.initialise(params, log) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CONFIG FILES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() -ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() -ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT LOCAL MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules -// -include { INPUT_CHECK } from '../subworkflows/local/input_check' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - IMPORT NF-CORE MODULES/SUBWORKFLOWS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// -// MODULE: Installed directly from nf-core/modules -// -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnavar_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -56,50 +17,45 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoft ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -// Info required for completion email and summary -def multiqc_report = [] - workflow RNAVAR { - ch_versions = Channel.empty() + take: + ch_samplesheet // channel: samplesheet read in from --input - // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files - // - INPUT_CHECK ( - file(params.input) - ) - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + main: + + ch_versions = Channel.empty() + ch_multiqc_files = Channel.empty() // // MODULE: Run FastQC // FASTQC ( - INPUT_CHECK.out.reads + ch_samplesheet ) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) ch_versions = ch_versions.mix(FASTQC.out.versions.first()) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.unique().collectFile(name: 'collated_versions.yml') - ) + // + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + .set { ch_collated_versions } // // MODULE: MultiQC // - workflow_summary = WorkflowRnavar.paramsSummaryMultiqc(workflow, summary_params) - ch_workflow_summary = Channel.value(workflow_summary) - - methods_description = WorkflowRnavar.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) - ch_methods_description = Channel.value(methods_description) - - ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) MULTIQC ( ch_multiqc_files.collect(), @@ -107,31 +63,10 @@ workflow RNAVAR { ch_multiqc_custom_config.toList(), ch_multiqc_logo.toList() ) - multiqc_report = MULTIQC.out.report.toList() -} - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - COMPLETION EMAIL AND SUMMARY -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -workflow.onComplete { - if (params.email || params.email_on_fail) { - NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) - } - NfcoreTemplate.dump_parameters(workflow, params) - NfcoreTemplate.summary(workflow, params, log) - if (params.hook_url) { - NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) - } -} -workflow.onError { - if (workflow.errorReport.contains("Process requirement exceeds available memory")) { - println("🛑 Default resources exceed availability 🛑 ") - println("💡 See here on how to configure pipeline: https://nf-co.re/docs/usage/configuration#tuning-workflow-resources 💡") - } + emit: + multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From f22ec03a17717acd887bed84fb1ce6863e3618b9 Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 21 Feb 2024 15:13:26 +0000 Subject: [PATCH 096/275] Fixed null value in publish dir --- CHANGELOG.md | 1 + workflows/rnavar.nf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dcbaaeed..e45babae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#124](https://github.com/nf-core/rnavar/pull/124) - Fixed s3 bucket path in conditional statement for SnpEff cache - [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache - [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables +- [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir ### Dependencies diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 5958e1f2..08a297a0 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -419,7 +419,7 @@ workflow RNAVAR { ch_haplotypecaller_vcf = Channel.empty() ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) .map{ meta, bam, bai, interval_list -> - [meta + [id:meta.id + "_" + interval_list.baseName], bam, bai, interval_list, []] + [meta + [id:meta.id + "_" + interval_list.baseName, variantcaller:'haplotypecaller'], bam, bai, interval_list, []] } // From a31daa66fdd29d723a6101d23b29e7f2a6d3ab1b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 29 Feb 2024 16:12:09 +0000 Subject: [PATCH 097/275] Template update for nf-core/tools version 2.13.1 --- .devcontainer/devcontainer.json | 10 +---- .github/CONTRIBUTING.md | 14 ++++--- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 4 +- .github/workflows/awstest.yml | 4 +- .github/workflows/ci.yml | 2 +- .github/workflows/download_pipeline.yml | 2 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .gitpod.yml | 6 +-- README.md | 3 +- modules.json | 8 ++-- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 12 +++--- .../utils_nfcore_rnavar_pipeline/main.nf | 10 +++-- .../tests/main.function.nf.test | 2 +- .../tests/main.function.nf.test.snap | 12 +++++- .../tests/main.workflow.nf.test | 20 ++------- .../tests/nextflow.config | 2 +- .../tests/main.function.nf.test.snap | 42 +++++++++++++++---- .../tests/main.workflow.nf.test.snap | 6 ++- .../tests/main.nf.test | 2 +- 23 files changed, 99 insertions(+), 74 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..b290e090 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 04afaff2..0f558d4a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -:::info -If you need help using or modifying nf-core/rnavar then the best place to ask is on the nf-core Slack [#rnavar](https://nfcore.slack.com/channels/rnavar) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/rnavar then the best place to ask is on the nf-core Slack [#rnavar](https://nfcore.slack.com/channels/rnavar) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`. Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. ### Naming schemes diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 866f5cb1..a4a88ed6 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnav - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e95c7a82..4858f99f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -31,7 +31,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 8daec84b..030354e1 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6cc0e744..cbfa6e34 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -31,7 +31,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index f823210d..08622fd5 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b4311..073e1876 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af2..d468aeaa 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.gitpod.yml b/.gitpod.yml index 363d5b1d..105a1821 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -10,13 +10,11 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code + - charliermarsh.ruff # Code linter Ruff diff --git a/README.md b/README.md index 61c2579e..8403d4f5 100644 --- a/README.md +++ b/README.md @@ -7,12 +7,13 @@ [![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnavar) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnavar) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/modules.json b/modules.json index 907db614..d3234e1c 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096a..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f4430..47ac352f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c204b488..bfebd802 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:28:51.744211298" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:28.847433492" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:13.223621555" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index dc90ad90..e00b8ccd 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/rnavar pipeline // /* @@ -152,7 +152,9 @@ workflow PIPELINE_COMPLETION { // def validateInputParameters() { genomeExistsError() -}// +} + +// // Validate channels from input samplesheet // def validateInputSamplesheet(input) { @@ -190,7 +192,9 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +// // Generate methods description for MultiQC // def toolCitationText() { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310c..68718e4f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f8..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc6..ca964ce8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ffe..d0a926bf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e6..1037232c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function nfCoreLogo": { "content": [ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" }, "Test Function workflowCitation": { "content": [ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54c..859d1030 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54e..5784a33f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +} From 83fef7b5daac39468803e043d4439461bef88b70 Mon Sep 17 00:00:00 2001 From: bioloni Date: Tue, 19 Mar 2024 16:07:59 +0000 Subject: [PATCH 098/275] Replaced UNZIP with GUNZIP --- CHANGELOG.md | 1 + modules.json | 186 ++++++++++++++++------ modules/nf-core/unzip/environment.yml | 7 - modules/nf-core/unzip/main.nf | 37 ----- modules/nf-core/unzip/meta.yml | 42 ----- subworkflows/local/prepare_genome/main.nf | 26 +-- 6 files changed, 145 insertions(+), 154 deletions(-) delete mode 100644 modules/nf-core/unzip/environment.yml delete mode 100644 modules/nf-core/unzip/main.nf delete mode 100644 modules/nf-core/unzip/meta.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index e45babae..e1ff34da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache - [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables - [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir +- [#134](https://github.com/nf-core/rnavar/pull/134) - Replaced unzip module with gunzip, removed unzip module ### Dependencies diff --git a/modules.json b/modules.json index a6d8182c..2e9f7ab2 100755 --- a/modules.json +++ b/modules.json @@ -8,207 +8,289 @@ "bcftools/concat": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep", + "vcf_annotate_ensemblvep_snpeff" + ] }, "fastqc": { "branch": "master", "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/applybqsr": { "branch": "master", "git_sha": "f1b92874e0de01dd82fe1bf7c6a7409673578065", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/baserecalibrator": { "branch": "master", "git_sha": "85561f483acc3bc6a885667ea431b3bb3fccdecb", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/combinegvcfs": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "eab2bd29e589bd05da2b47c9bf95ef10b9508699", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/indexfeaturefile": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/markduplicates": { "branch": "master", "git_sha": "bc93a4b8904472ce64c6bb50b1fb0a1659b9cf78", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/splitncigarreads": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gffread": { "branch": "master", "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/idxstats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/stats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/snpeff": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep_snpeff", + "vcf_annotate_snpeff" + ] }, "star/align": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "star/genomegenerate": { "branch": "master", "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_snpeff" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep", + "vcf_annotate_ensemblvep_snpeff" + ] }, "untar": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] - }, - "unzip": { - "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -217,20 +299,26 @@ "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_ensemblvep_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/unzip/environment.yml b/modules/nf-core/unzip/environment.yml deleted file mode 100644 index d3a535f1..00000000 --- a/modules/nf-core/unzip/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: unzip -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - conda-forge::p7zip=16.02 diff --git a/modules/nf-core/unzip/main.nf b/modules/nf-core/unzip/main.nf deleted file mode 100644 index 08cfc3c4..00000000 --- a/modules/nf-core/unzip/main.nf +++ /dev/null @@ -1,37 +0,0 @@ -process UNZIP { - tag "$archive" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/p7zip:16.02' : - 'biocontainers/p7zip:16.02' }" - - input: - tuple val(meta), path(archive) - - output: - tuple val(meta), path("${prefix}/"), emit: unzipped_archive - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - if ( archive instanceof List && archive.name.size > 1 ) { error "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } - - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName) - """ - 7za \\ - x \\ - -o"${prefix}"/ \\ - $args \\ - $archive - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - 7za: \$(echo \$(7za --help) | sed 's/.*p7zip Version //; s/(.*//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml deleted file mode 100644 index e8e377e2..00000000 --- a/modules/nf-core/unzip/meta.yml +++ /dev/null @@ -1,42 +0,0 @@ -name: unzip -description: Unzip ZIP archive files -keywords: - - unzip - - decompression - - zip - - archiving -tools: - - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. - homepage: https://sourceforge.net/projects/p7zip/ - documentation: https://sourceforge.net/projects/p7zip/ - tool_dev_url: https://sourceforge.net/projects/p7zip" - licence: ["LGPL-2.1-or-later"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: ZIP file - pattern: "*.zip" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - unzipped_archive: - type: directory - description: Directory contents of the unzipped archive - pattern: "${archive.baseName}/" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@jfy133" -maintainers: - - "@jfy133" diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 130c96cc..aebce673 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -9,9 +9,9 @@ include { GFFREAD } from '../../../modules/nf-core/gffrea include { GTF2BED } from '../../../modules/local/gtf2bed' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' -include { UNZIP as UNZIP_FASTA } from '../../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_GTF } from '../../../modules/nf-core/unzip/main' -include { UNZIP as UNZIP_GFF } from '../../../modules/nf-core/unzip/main' +include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip/main' workflow PREPARE_GENOME { take: @@ -26,31 +26,19 @@ workflow PREPARE_GENOME { //Unzip reference genome files if needed if (params.fasta.endsWith('.gz')) { - UNZIP_FASTA(ch_fasta_raw) + GUNZIP_FASTA(ch_fasta_raw) - ch_fasta = - UNZIP_FASTA.out.unzipped_archive - .map{ meta,file -> //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder - def file_name = file.baseName - def full_file_path = file.toString() + '/' + file_name + '.fa' + ch_fasta = GUNZIP_FASTA.out.gunzip - [meta,full_file_path] - } } else { ch_fasta = ch_fasta_raw } if (params.gtf.endsWith('.gz')) { - UNZIP_GTF(ch_gtf_raw) + GUNZIP_GTF(ch_gtf_raw) - ch_gtf = - UNZIP_GTF.out.unzipped_archive - .map{ meta,file -> //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder - def file_name = file.baseName - def full_file_path = file.toString() + '/' + file_name + '.gtf' + ch_gtf = GUNZIP_GTF.out.gunzip - [meta,full_file_path] - } } else { ch_gtf = ch_gtf_raw } From 4438535995b7b290c26ac0ba62e833375b818416 Mon Sep 17 00:00:00 2001 From: bioloni Date: Tue, 19 Mar 2024 20:44:04 +0000 Subject: [PATCH 099/275] Updated changelog, removed unnecesary module, not in use --- CHANGELOG.md | 2 +- subworkflows/local/prepare_genome/main.nf | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1ff34da..aa82163a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,7 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache - [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables - [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir -- [#134](https://github.com/nf-core/rnavar/pull/134) - Replaced unzip module with gunzip, removed unzip module +- [#136](https://github.com/nf-core/rnavar/pull/136) - Replaced unzip module with gunzip, removed unzip module ### Dependencies diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index aebce673..0ad0ef53 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -11,7 +11,6 @@ include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtoo include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip/main' workflow PREPARE_GENOME { take: From 02d48254b547c02bbc433bb0b54ff9941a3d04ed Mon Sep 17 00:00:00 2001 From: mathieucharlesINRAE Date: Thu, 21 Mar 2024 15:51:33 +0100 Subject: [PATCH 100/275] Modification for indexation on gvcf --- conf/modules.config | 5 +++-- modules/nf-core/modules/samtools/merge/main.nf | 1 + workflows/rnavar.nf | 12 ++++++------ 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index f05b3322..630d0dcb 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -313,15 +313,16 @@ process { ext.args = [ '--dont-use-soft-clipped-bases', params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '', - params.bam_csi_index ? "--create-output-variant-index false" : "" + params.bam_csi_index ? "--create-output-variant-index true" : "" ].join(' ').trim() publishDir = [ enabled: false ] } withName: GATK4_HAPLOTYPECALLERGVCF { ext.args = [ '--dont-use-soft-clipped-bases', + '-ERC GVCF', params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '', - params.bam_csi_index ? "--create-output-variant-index false" : "", "-ERC GVCF" + params.bam_csi_index ? "--create-output-variant-index true" : "" ].join(' ').trim() ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ enabled: false ] diff --git a/modules/nf-core/modules/samtools/merge/main.nf b/modules/nf-core/modules/samtools/merge/main.nf index bbf7e8fb..4f6ffc1d 100644 --- a/modules/nf-core/modules/samtools/merge/main.nf +++ b/modules/nf-core/modules/samtools/merge/main.nf @@ -28,6 +28,7 @@ process SAMTOOLS_MERGE { samtools \\ merge \\ --threads ${task.cpus-1} \\ + -f \\ $args \\ ${reference} \\ ${prefix}.${file_type} \\ diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index d0871a60..c5db4bbb 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -65,7 +65,7 @@ include { GATK4_BASERECALIBRATOR } from '../modules/ include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/modules/gatk4/bedtointervallist/main' include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/modules/gatk4/intervallisttools/main' include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' -include { GATK4_HAPLOTYPECALLER as GATK4_HAPLOTYPECALLERGVCF } from '../modules/nf-core/modules/gatk4/haplotypecaller/main' +include { GATK4_HAPLOTYPECALLERGVCF } from '../modules/nf-core/modules/gatk4/haplotypecallergvcf/main' include { GATK4_MERGEVCFS } from '../modules/nf-core/modules/gatk4/mergevcfs/main' include { GATK4_COMBINEGVCFS } from '../modules/nf-core/modules/gatk4/combinegvcfs/main' include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/modules/gatk4/indexfeaturefile/main' @@ -404,17 +404,17 @@ workflow RNAVAR { // MODULE: IndexFeatureFile from GATK4 // Index the gVCF files // - GATK4_INDEXFEATUREFILE( - GATK4_HAPLOTYPECALLERGVCF.out.vcf - ) + ////GATK4_INDEXFEATUREFILE( + //// GATK4_HAPLOTYPECALLERGVCF.out.vcf + ////) - ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index + ch_haplotypecallergvcf_raw_index = GATK4_HAPLOTYPECALLERGVCF.out.tbi .map{ meta, idx -> meta.id = meta.sample [meta, idx]} .groupTuple() - ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) + ////ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) // // MODULE: CombineGVCFS from GATK4 From eb25240d38dc158f659632214805bfd4aad10b9e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 4 Apr 2024 14:24:41 +0200 Subject: [PATCH 101/275] restore old version of subworkflow --- subworkflows/local/prepare_genome/main.nf | 29 +++++++++++++++-------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index bf98bbf9..ac39901a 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -9,8 +9,9 @@ include { GFFREAD } from '../../../modules/nf-core/gffrea include { GTF2BED } from '../../../modules/local/gtf2bed' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' -include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' +include { UNZIP as UNZIP_FASTA } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_GTF } from '../../../modules/nf-core/unzip/main' +include { UNZIP as UNZIP_GFF } from '../../../modules/nf-core/unzip/main' workflow PREPARE_GENOME { take: @@ -25,20 +26,28 @@ workflow PREPARE_GENOME { //Unzip reference genome files if needed if (params.fasta.endsWith('.gz')) { - GUNZIP_FASTA(ch_fasta_raw) + UNZIP_FASTA(ch_fasta_raw) - ch_fasta = GUNZIP_FASTA.out.gunzip - ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions) - } else { + //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder + ch_fasta = UNZIP_FASTA.out.unzipped_archive.map{ meta, file -> + def file_name = file.baseName + def full_file_path = file.toString() + '/' + file_name + '.fa' + + [meta, full_file_path] } + } else { ch_fasta = ch_fasta_raw } if (params.gtf.endsWith('.gz')) { - GUNZIP_GTF(ch_gtf_raw) + UNZIP_GTF(ch_gtf_raw) + + //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder + ch_gtf = UNZIP_GTF.out.unzipped_archive.map{ meta, file -> + def file_name = file.baseName + def full_file_path = file.toString() + '/' + file_name + '.gtf' - ch_gtf = GUNZIP_GTF.out.gunzip - ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) - } else { + [meta,full_file_path] } + } else { ch_gtf = ch_gtf_raw } From 2d3ef4de6631bbfcc6c33d09d733cce41d7ae4d0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 4 Apr 2024 14:25:22 +0200 Subject: [PATCH 102/275] code polish --- subworkflows/local/prepare_genome/main.nf | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index ac39901a..beddb94a 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -33,8 +33,9 @@ workflow PREPARE_GENOME { def file_name = file.baseName def full_file_path = file.toString() + '/' + file_name + '.fa' - [meta, full_file_path] } - } else { + [meta, full_file_path] + } + } else { ch_fasta = ch_fasta_raw } @@ -46,8 +47,9 @@ workflow PREPARE_GENOME { def file_name = file.baseName def full_file_path = file.toString() + '/' + file_name + '.gtf' - [meta,full_file_path] } - } else { + [meta,full_file_path] + } + } else { ch_gtf = ch_gtf_raw } From 0b1a7a4d6f847d91186002ea369d598bed1c21fc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 4 Apr 2024 14:25:38 +0200 Subject: [PATCH 103/275] code polish --- subworkflows/local/prepare_genome/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index beddb94a..f44d8a2a 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -28,7 +28,7 @@ workflow PREPARE_GENOME { if (params.fasta.endsWith('.gz')) { UNZIP_FASTA(ch_fasta_raw) - //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder + // File gets saved into a folder with the same name as the file, need to add the missing depth to the folder ch_fasta = UNZIP_FASTA.out.unzipped_archive.map{ meta, file -> def file_name = file.baseName def full_file_path = file.toString() + '/' + file_name + '.fa' @@ -42,7 +42,7 @@ workflow PREPARE_GENOME { if (params.gtf.endsWith('.gz')) { UNZIP_GTF(ch_gtf_raw) - //file gets saved into a folder with the same name as the file, need to add the missing depth to the folder + // File gets saved into a folder with the same name as the file, need to add the missing depth to the folder ch_gtf = UNZIP_GTF.out.unzipped_archive.map{ meta, file -> def file_name = file.baseName def full_file_path = file.toString() + '/' + file_name + '.gtf' From 36050636b8d56b36861acfad629808fc4522143e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 4 Apr 2024 14:25:54 +0200 Subject: [PATCH 104/275] code polish --- subworkflows/local/prepare_genome/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index f44d8a2a..d378bd69 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -47,7 +47,7 @@ workflow PREPARE_GENOME { def file_name = file.baseName def full_file_path = file.toString() + '/' + file_name + '.gtf' - [meta,full_file_path] + [meta, full_file_path] } } else { ch_gtf = ch_gtf_raw From b0fac8f5b00522fc652cf367681a668831f922f0 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 8 May 2024 14:01:03 +0000 Subject: [PATCH 105/275] Template update for nf-core/tools version 2.14.0 --- .editorconfig | 6 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 10 +- .github/workflows/awstest.yml | 12 +- .github/workflows/ci.yml | 4 +- .github/workflows/download_pipeline.yml | 22 ++- .github/workflows/fix-linting.yml | 6 +- .github/workflows/linting.yml | 18 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 6 +- .nf-core.yml | 1 + .pre-commit-config.yaml | 3 + README.md | 2 +- conf/base.config | 3 - conf/modules.config | 8 - conf/test.config | 2 +- conf/test_full.config | 2 +- docs/usage.md | 2 + modules.json | 4 +- modules/nf-core/fastqc/main.nf | 6 + nextflow.config | 176 +++++++++--------- nextflow_schema.json | 7 + pyproject.toml | 15 -- .../utils_nfcore_rnavar_pipeline/main.nf | 16 +- .../nf-core/utils_nfcore_pipeline/main.nf | 8 +- workflows/rnavar.nf | 46 +++-- 26 files changed, 220 insertions(+), 169 deletions(-) delete mode 100644 pyproject.toml diff --git a/.editorconfig b/.editorconfig index dd9ffa53..72dda289 100644 --- a/.editorconfig +++ b/.editorconfig @@ -28,10 +28,6 @@ indent_style = unset [/assets/email*] indent_size = unset -# ignore Readme -[README.md] -indent_style = unset - -# ignore python +# ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index a4a88ed6..866f5cb1 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnav - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 4858f99f..46a3767e 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -8,12 +8,12 @@ on: types: [published] workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS full tests if: github.repository == 'nf-core/rnavar' runs-on: ubuntu-latest steps: - - name: Launch workflow via tower + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) @@ -33,7 +33,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 030354e1..1b6b4206 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -5,13 +5,13 @@ name: nf-core AWS test on: workflow_dispatch: jobs: - run-tower: + run-platform: name: Run AWS tests if: github.repository == 'nf-core/rnavar' runs-on: ubuntu-latest steps: - # Launch workflow using Tower CLI tool action - - name: Launch workflow via tower + # Launch workflow using Seqera Platform CLI tool action + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -27,7 +27,7 @@ jobs: - uses: actions/upload-artifact@v4 with: - name: Tower debug log file + name: Seqera Platform debug log file path: | - tower_action_*.log - tower_action_*.json + seqera_platform_action_*.log + seqera_platform_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cbfa6e34..9993584f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,10 +28,10 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 08622fd5..2d20d644 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -14,6 +14,8 @@ on: pull_request: types: - opened + - edited + - synchronize branches: - master pull_request_target: @@ -28,11 +30,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: @@ -65,8 +70,17 @@ jobs: - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} - - name: Run the downloaded pipeline + - name: Run the downloaded pipeline (stub) + id: stub_run_pipeline + continue-on-error: true env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + - name: Run the downloaded pipeline (stub run not supported) + id: run_pipeline + if: ${{ job.steps.stub_run_pipeline.status == failure() }} + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index aba5c3ba..7ca33128 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,9 +32,9 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 + python-version: "3.12" - name: Install pre-commit run: pip install pre-commit diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 073e1876..a3fb2541 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,12 +14,12 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Set up Python 3.11 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - name: Set up Python 3.12 + uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: 3.11 + python-version: "3.12" cache: "pip" - name: Install pre-commit @@ -32,14 +32,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: - python-version: "3.11" + python-version: "3.12" architecture: "x64" - name: Install dependencies @@ -60,7 +60,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index b706875f..40acc23f 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3 + uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index d468aeaa..03ecfcf7 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: @@ -25,13 +25,13 @@ jobs: Please see the changelog: ${{ github.event.release.html_url }} - ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics + ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics send-tweet: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 + - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..d6daa403 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,2 @@ repository_type: pipeline +nf_core_version: "2.14.0" diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index af57081f..4dc0f1dc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,6 +3,9 @@ repos: rev: "v3.1.0" hooks: - id: prettier + additional_dependencies: + - prettier@3.2.5 + - repo: https://github.com/editorconfig-checker/editorconfig-checker.python rev: "2.7.3" hooks: diff --git a/README.md b/README.md index 8403d4f5..167ef66b 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnavar) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/conf/base.config b/conf/base.config index 89b498e5..969a3162 100644 --- a/conf/base.config +++ b/conf/base.config @@ -59,7 +59,4 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules.config b/conf/modules.config index e3ea8fa6..d203d2b6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -22,14 +22,6 @@ process { ext.args = '--quiet' } - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - publishDir = [ - path: { "${params.outdir}/pipeline_info" }, - mode: params.publish_dir_mode, - pattern: '*_versions.yml' - ] - } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 768a188f..bd95ea07 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,7 +22,7 @@ params { // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/conf/test_full.config b/conf/test_full.config index 979f49f7..82f01879 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,7 +17,7 @@ params { // Input data for full size test // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' // Genome references genome = 'R64-1-1' diff --git a/docs/usage.md b/docs/usage.md index fc3321a7..d31e7c03 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -156,6 +156,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) +- `wave` + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. diff --git a/modules.json b/modules.json index d3234e1c..aabfbc51 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] }, "multiqc": { @@ -26,7 +26,7 @@ }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9e19a74c..d79f1c86 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -25,6 +25,11 @@ process FASTQC { def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // FastQC memory value allowed range (100 - 10000) + def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -33,6 +38,7 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ + --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/nextflow.config b/nextflow.config index dda1b90f..81386593 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,8 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - fasta = null// MultiQC options + + // MultiQC options multiqc_config = null multiqc_title = null multiqc_logo = null @@ -24,15 +25,16 @@ params { multiqc_methods_description = null // Boilerplate options - outdir = null - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - version = false + outdir = null + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + version = false + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' // Config options config_profile_name = null @@ -68,103 +70,109 @@ try { } // Load nf-core/rnavar custom profiles from different institutions. -// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/rnavar.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/rnavar profiles: ${params.custom_config_base}/pipeline/rnavar.config") -// } +try { + includeConfig "${params.custom_config_base}/pipeline/rnavar.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/rnavar profiles: ${params.custom_config_base}/pipeline/rnavar.config") +} profiles { debug { - dumpHashes = true - process.beforeScript = 'echo $HOSTNAME' - cleanup = false + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false nextflow.enable.configProcessNamesValidation = true } conda { - conda.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - channels = ['conda-forge', 'bioconda', 'defaults'] - apptainer.enabled = false + conda.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + conda.channels = ['conda-forge', 'bioconda', 'defaults'] + apptainer.enabled = false } mamba { - conda.enabled = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + conda.enabled = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } shifter { - shifter.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + shifter.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false + apptainer.enabled = false } charliecloud { - charliecloud.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - apptainer.enabled = false + charliecloud.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + } + wave { + apptainer.ociAutoPull = true + singularity.ociAutoPull = true + wave.enabled = true + wave.freeze = true + wave.strategy = 'conda,container' } gitpod { - executor.name = 'local' - executor.cpus = 4 - executor.memory = 8.GB + executor.name = 'local' + executor.cpus = 4 + executor.memory = 8.GB } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } diff --git a/nextflow_schema.json b/nextflow_schema.json index d8e53bf7..43ca4b36 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -265,6 +265,13 @@ "description": "Validation of parameters in lenient more.", "hidden": true, "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." + }, + "pipelines_testdata_base_path": { + "type": "string", + "fa_icon": "far fa-check-circle", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "hidden": true } } } diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 56110621..00000000 --- a/pyproject.toml +++ /dev/null @@ -1,15 +0,0 @@ -# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff. -# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. -[tool.ruff] -line-length = 120 -target-version = "py38" -cache-dir = "~/.cache/ruff" - -[tool.ruff.lint] -select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"] - -[tool.ruff.lint.isort] -known-first-party = ["nf_core"] - -[tool.ruff.lint.per-file-ignores] -"__init__.py" = ["E402", "F401"] diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index e00b8ccd..009baaff 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -140,6 +140,10 @@ workflow PIPELINE_COMPLETION { imNotification(summary_params, hook_url) } } + + workflow.onError { + log.error "Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting" + } } /* @@ -230,8 +234,16 @@ def methodsDescriptionText(mqc_methods_yaml) { meta["manifest_map"] = workflow.manifest.toMap() // Pipeline DOI - meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" - meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + if (meta.manifest_map.doi) { + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + def temp_doi_ref = "" + String[] manifest_doi = meta.manifest_map.doi.tokenize(",") + for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) + } else meta["doi_text"] = "" + meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " // Tool references meta["tool_citations"] = "" diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index a8b55d6f..14558c39 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -65,9 +65,15 @@ def checkProfileProvided(nextflow_cli_args) { // Citation string for pipeline // def workflowCitation() { + def temp_doi_ref = "" + String[] manifest_doi = workflow.manifest.doi.tokenize(",") + // Using a loop to handle multiple DOIs + // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers + // Removing ` ` since the manifest.doi is a string and not a proper list + for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + - " ${workflow.manifest.doi}\n\n" + + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 5719e94c..2de63080 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -40,22 +40,44 @@ workflow RNAVAR { // Collate and save software versions // softwareVersionsToYAML(ch_versions) - .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) - .set { ch_collated_versions } + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_pipeline_software_mqc_versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } // // MODULE: MultiQC // - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false)) + ch_multiqc_config = Channel.fromPath( + "$projectDir/assets/multiqc_config.yml", checkIfExists: true) + ch_multiqc_custom_config = params.multiqc_config ? + Channel.fromPath(params.multiqc_config, checkIfExists: true) : + Channel.empty() + ch_multiqc_logo = params.multiqc_logo ? + Channel.fromPath(params.multiqc_logo, checkIfExists: true) : + Channel.empty() + + summary_params = paramsSummaryMap( + workflow, parameters_schema: "nextflow_schema.json") + ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? + file(params.multiqc_methods_description, checkIfExists: true) : + file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + ch_methods_description = Channel.value( + methodsDescriptionText(ch_multiqc_custom_methods_description)) + + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) + ch_multiqc_files = ch_multiqc_files.mix( + ch_methods_description.collectFile( + name: 'methods_description_mqc.yaml', + sort: true + ) + ) MULTIQC ( ch_multiqc_files.collect(), From 11b5cfc19dac4f9088c1709b5d5a3f26f14ddb8a Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 9 May 2024 11:44:21 +0000 Subject: [PATCH 106/275] Template update for nf-core/tools version 2.14.1 --- .github/workflows/linting.yml | 1 - .nf-core.yml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a3fb2541..1fcafe88 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -20,7 +20,6 @@ jobs: uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" - cache: "pip" - name: Install pre-commit run: pip install pre-commit diff --git a/.nf-core.yml b/.nf-core.yml index d6daa403..e0b85a77 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,2 @@ repository_type: pipeline -nf_core_version: "2.14.0" +nf_core_version: "2.14.1" From c0981be72cd2e04b457d4f746739333ec5c3bfc4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 15:46:30 +0200 Subject: [PATCH 107/275] merge 137 --- conf/modules.config | 18 +--- workflows/rnavar.nf | 221 ++++++++++++++++++++------------------------ 2 files changed, 100 insertions(+), 139 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 3a19ed25..98e7d992 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -291,26 +291,12 @@ process { withName: GATK4_HAPLOTYPECALLER { ext.args = [ '--dont-use-soft-clipped-bases', + '--create-output-variant-index true', params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '', - params.bam_csi_index ? "--create-output-variant-index true" : "" + params.generate_gvcf ? "-ERC GVCF" : "" ].join(' ').trim() publishDir = [ enabled: false ] } - withName: GATK4_HAPLOTYPECALLERGVCF { - ext.args = [ - '--dont-use-soft-clipped-bases', - '-ERC GVCF', - params.gatk_hc_call_conf ? "--standard-min-confidence-threshold-for-calling $params.gatk_hc_call_conf" : '', - params.bam_csi_index ? "--create-output-variant-index true" : "" - ].join(' ').trim() - ext.prefix = {"${meta.id}.haplotypecaller"} - publishDir = [ enabled: false ] - } - withName: GATK4_INDEXFEATUREFILE { - publishDir = [ - enabled: false - ] - } withName: GATK4_MERGEVCFS { ext.prefix = {"${meta.id}.haplotypecaller"} diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 3041d164..934e2615 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -70,9 +70,9 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { GTF2BED } from '../modules/local/gtf2bed/main' include { ALIGN_STAR } from '../subworkflows/local/align_star/main' // Align reads to genome and sort and index the alignment file include { BAM_MARKDUPLICATES } from '../subworkflows/local/bam_markduplicates/main' // Mark duplicates in the BAM file +include { GTF2BED } from '../modules/local/gtf2bed/main' include { PREPARE_CACHE } from '../subworkflows/local/prepare_cache/main' // Download annotation cache if needed include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome/main' // Build the genome index and other reference files include { RECALIBRATE } from '../subworkflows/local/recalibrate/main' // Estimate and correct systematic bias @@ -85,22 +85,21 @@ include { VCF_ANNOTATE_ALL } from '../subworkflows/local/vcf_annotate_all/main ======================================================================================== */ -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' -include { GATK4_BASERECALIBRATOR } from '../modules/nf-core/gatk4/baserecalibrator/main' -include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/gatk4/bedtointervallist/main' -include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/gatk4/intervallisttools/main' -include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/gatk4/haplotypecaller/main' -include { GATK4_HAPLOTYPECALLER as GATK4_HAPLOTYPECALLERGVCF } from '../modules/nf-core/gatk4/haplotypecaller/main' -include { GATK4_MERGEVCFS } from '../modules/nf-core/gatk4/mergevcfs/main' -include { GATK4_COMBINEGVCFS } from '../modules/nf-core/gatk4/combinegvcfs/main' -include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/gatk4/indexfeaturefile/main' -include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/gatk4/variantfiltration/main' -include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main' -include { TABIX_TABIX as TABIX } from '../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/tabix/tabix/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { GATK4_BASERECALIBRATOR } from '../modules/nf-core/gatk4/baserecalibrator/main' +include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/gatk4/bedtointervallist/main' +include { GATK4_COMBINEGVCFS } from '../modules/nf-core/gatk4/combinegvcfs/main' +include { GATK4_HAPLOTYPECALLER } from '../modules/nf-core/gatk4/haplotypecaller/main' +include { GATK4_INDEXFEATUREFILE } from '../modules/nf-core/gatk4/indexfeaturefile/main' +include { GATK4_INTERVALLISTTOOLS } from '../modules/nf-core/gatk4/intervallisttools/main' +include { GATK4_MERGEVCFS } from '../modules/nf-core/gatk4/mergevcfs/main' +include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/gatk4/variantfiltration/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/main' +include { TABIX_TABIX as TABIX } from '../modules/nf-core/tabix/tabix/main' +include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/tabix/tabix/main' /* ======================================================================================== @@ -110,8 +109,8 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/ include { ALIGN_STAR } from '../subworkflows/nf-core/align_star' // Align reads to genome and sort and index the alignment file include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' // Mark duplicates in the BAM file -include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' // Estimate and correct systematic bias +include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string /* ======================================================================================== @@ -447,7 +446,6 @@ workflow RNAVAR { ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } ) - ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf .map{ meta, vcf -> meta.id = meta.sample @@ -456,55 +454,91 @@ workflow RNAVAR { ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) - // - // MODULE: MergeVCFS from GATK4 - // Merge multiple VCF files into one VCF - // - GATK4_MERGEVCFS(ch_haplotypecaller_raw, ch_dict) - ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf - ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) - - if (params.generate_gvcf){ - GATK4_HAPLOTYPECALLERGVCF( - ch_haplotypecaller_interval_bam, - ch_fasta.map{ meta, fasta -> [fasta] }, - ch_fasta_fai, - ch_dict.map{ meta, dict -> [dict] }, - ch_dbsnp, - ch_dbsnp_tbi - ) + if (!params.generate_gvcf){ + // + // MODULE: MergeVCFS from GATK4 + // Merge multiple VCF files into one VCF + // + GATK4_MERGEVCFS( + ch_haplotypecaller_raw, + PREPARE_GENOME.out.dict + ) + ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf + ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) + + // + // MODULE: Index the VCF using TABIX + // + TABIX( + ch_haplotypecaller_vcf + ) + + ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf + .join(TABIX.out.tbi, by: [0], remainder: true) + .join(TABIX.out.csi, by: [0], remainder: true) + .map{meta, vcf, tbi, csi -> + if (tbi) [meta, vcf, tbi] + else [meta, vcf, csi] + } + + ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) + ch_final_vcf = ch_haplotypecaller_vcf + + // + // MODULE: VariantFiltration from GATK4 + // Filter variant calls based on certain criteria + // + if (!params.skip_variantfiltration && !params.bam_csi_index ) { + + GATK4_VARIANTFILTRATION( + ch_haplotypecaller_vcf_tbi, + PREPARE_GENOME.out.fasta, + PREPARE_GENOME.out.fai, + PREPARE_GENOME.out.dict + ) + + ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf + ch_final_vcf = ch_filtered_vcf + ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) + } + + // + // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. + // + if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { + ANNOTATE( + ch_final_vcf, + params.annotate_tools, + ch_snpeff_db, + ch_snpeff_cache, + ch_vep_genome, + ch_vep_species, + ch_vep_cache_version, + ch_vep_cache) + + // Gather QC reports + ch_reports = ch_reports.mix(ANNOTATE.out.reports) + ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) + } - ch_haplotypecallergvcf_raw = GATK4_HAPLOTYPECALLERGVCF.out.vcf - .map{ meta, vcf -> - def new_meta = meta.clone() - new_meta.id = meta.sample - [new_meta, vcf] - }.groupTuple() + } + else{ + ch_haplotypecaller_raw_index = GATK4_HAPLOTYPECALLER.out.tbi + .map{ meta, idx -> + meta.id = meta.sample + [meta, idx]} + .groupTuple() - ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLERGVCF.out.versions.first().ifEmpty(null)) - // - // MODULE: IndexFeatureFile from GATK4 - // Index the gVCF files // - GATK4_INDEXFEATUREFILE(GATK4_HAPLOTYPECALLERGVCF.out.vcf) - - ch_haplotypecallergvcf_raw_index = GATK4_INDEXFEATUREFILE.out.index - .map{ meta, idx -> [meta + [id:meta.sample], idx]} - .groupTuple() - - ch_versions = ch_versions.mix(GATK4_INDEXFEATUREFILE.out.versions.first().ifEmpty(null)) - // MODULE: CombineGVCFS from GATK4 // Merge multiple GVCF files into one GVCF - - ch_haplotypecallergvcf_raw_tbi = ch_haplotypecallergvcf_raw - .join(ch_haplotypecallergvcf_raw_index, remainder: true) - + // GATK4_COMBINEGVCFS( - ch_haplotypecallergvcf_raw_tbi, - ch_fasta.map{ meta, fasta -> [fasta] }, - ch_fasta_fai, - ch_dict.map{ meta, dict -> [dict] } + ch_haplotypecaller_raw, + ch_haplotypecaller_raw_index, + PREPARE_GENOME.out.fasta, + PREPARE_GENOME.out.fai, + PREPARE_GENOME.out.dict ) ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) @@ -515,8 +549,8 @@ workflow RNAVAR { TABIXGVCF(ch_haplotypecaller_gvcf) ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf - .join(TABIXGVCF.out.tbi, remainder: true) - .join(TABIXGVCF.out.csi, remainder: true) + .join(TABIXGVCF.out.tbi, by: [0], remainder: true) + .join(TABIXGVCF.out.csi, by: [0], remainder: true) .map{meta, vcf, tbi, csi -> if (tbi) [meta, vcf, tbi] else [meta, vcf, csi] @@ -525,65 +559,6 @@ workflow RNAVAR { ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) } - - // - // MODULE: Index the VCF using TABIX - // - TABIX(ch_haplotypecaller_vcf) - - ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf - .join(TABIX.out.tbi, remainder: true) - .join(TABIX.out.csi, remainder: true) - .map{meta, vcf, tbi, csi -> - if (tbi) [meta, vcf, tbi] - else [meta, vcf, csi] - } - - ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) - ch_final_vcf = ch_haplotypecaller_vcf - - // - // MODULE: VariantFiltration from GATK4 - // Filter variant calls based on certain criteria - // - if (!params.skip_variantfiltration && !params.bam_csi_index ) { - - GATK4_VARIANTFILTRATION( - ch_haplotypecaller_vcf_tbi, - ch_fasta, - ch_fasta_fai.map{ it -> [ [id:'fai'], it ] }, - ch_dict - ) - - ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf - ch_final_vcf = ch_filtered_vcf - ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) - } - - // - // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. - // - if ((!params.skip_variantannotation) &&(params.annotate_tools) && (params.annotate_tools.split(',').contains('merge') || params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('vep'))) { - - vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []] - - VCF_ANNOTATE_ALL( - ch_final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, - vep_fasta, - params.annotate_tools, - params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}", - snpeff_cache, - vep_genome, - vep_species, - vep_cache_version, - vep_cache, - vep_extra_files) - - // Gather QC reports - ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports) - ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions.first().ifEmpty(null)) - } - } ch_version_yaml = Channel.empty() From 175730917e33f166b7cb08e6d6105fad6b8d4bea Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 27 May 2024 15:48:00 +0200 Subject: [PATCH 108/275] Apply suggestions from code review --- workflows/rnavar.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 934e2615..15702f4a 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -415,8 +415,8 @@ workflow RNAVAR { // Gather QC reports ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) - //} else { - // ch_bam_variant_calling = ch_splitncigar_bam_bai + } else { + ch_bam_variant_calling = ch_splitncigar_bam_bai } interval_flag = params.no_intervals From 50bdeadc8608b00bbba046f13e4a072f1ea53585 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 15:51:52 +0200 Subject: [PATCH 109/275] prettier --- modules.json | 181 +++++++++++++-------------------------------------- 1 file changed, 44 insertions(+), 137 deletions(-) diff --git a/modules.json b/modules.json index 2e9f7ab2..b6a8f0c2 100755 --- a/modules.json +++ b/modules.json @@ -8,289 +8,202 @@ "bcftools/concat": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/sort": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bedtools/merge": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep", - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] }, "fastqc": { "branch": "master", "git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/applybqsr": { "branch": "master", "git_sha": "f1b92874e0de01dd82fe1bf7c6a7409673578065", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", "git_sha": "85561f483acc3bc6a885667ea431b3bb3fccdecb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/combinegvcfs": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "eab2bd29e589bd05da2b47c9bf95ef10b9508699", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", "git_sha": "bc93a4b8904472ce64c6bb50b1fb0a1659b9cf78", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/splitncigarreads": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gffread": { "branch": "master", "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep_snpeff", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff", "vcf_annotate_snpeff"] }, "star/align": { "branch": "master", "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep", - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -299,26 +212,20 @@ "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From e7943b84bf008db524cf627c06135020a36dc795 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 15:53:14 +0200 Subject: [PATCH 110/275] lint --- workflows/rnavar.nf | 132 ++++++++++++++++++++++---------------------- 1 file changed, 66 insertions(+), 66 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 15702f4a..814de207 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -455,75 +455,75 @@ workflow RNAVAR { ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) if (!params.generate_gvcf){ - // - // MODULE: MergeVCFS from GATK4 - // Merge multiple VCF files into one VCF - // - GATK4_MERGEVCFS( - ch_haplotypecaller_raw, - PREPARE_GENOME.out.dict - ) - ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf - ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) - - // - // MODULE: Index the VCF using TABIX - // - TABIX( - ch_haplotypecaller_vcf - ) - - ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf - .join(TABIX.out.tbi, by: [0], remainder: true) - .join(TABIX.out.csi, by: [0], remainder: true) - .map{meta, vcf, tbi, csi -> - if (tbi) [meta, vcf, tbi] - else [meta, vcf, csi] - } - - ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) - ch_final_vcf = ch_haplotypecaller_vcf - - // - // MODULE: VariantFiltration from GATK4 - // Filter variant calls based on certain criteria - // - if (!params.skip_variantfiltration && !params.bam_csi_index ) { - - GATK4_VARIANTFILTRATION( - ch_haplotypecaller_vcf_tbi, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict - ) - - ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf - ch_final_vcf = ch_filtered_vcf - ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) - } - - // - // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. - // - if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { - ANNOTATE( - ch_final_vcf, - params.annotate_tools, - ch_snpeff_db, - ch_snpeff_cache, - ch_vep_genome, - ch_vep_species, - ch_vep_cache_version, - ch_vep_cache) - - // Gather QC reports - ch_reports = ch_reports.mix(ANNOTATE.out.reports) - ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) - } + // + // MODULE: MergeVCFS from GATK4 + // Merge multiple VCF files into one VCF + // + GATK4_MERGEVCFS( + ch_haplotypecaller_raw, + PREPARE_GENOME.out.dict + ) + ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf + ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) + + // + // MODULE: Index the VCF using TABIX + // + TABIX( + ch_haplotypecaller_vcf + ) + + ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf + .join(TABIX.out.tbi, by: [0], remainder: true) + .join(TABIX.out.csi, by: [0], remainder: true) + .map{meta, vcf, tbi, csi -> + if (tbi) [meta, vcf, tbi] + else [meta, vcf, csi] + } + + ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) + ch_final_vcf = ch_haplotypecaller_vcf + + // + // MODULE: VariantFiltration from GATK4 + // Filter variant calls based on certain criteria + // + if (!params.skip_variantfiltration && !params.bam_csi_index ) { + + GATK4_VARIANTFILTRATION( + ch_haplotypecaller_vcf_tbi, + PREPARE_GENOME.out.fasta, + PREPARE_GENOME.out.fai, + PREPARE_GENOME.out.dict + ) + + ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf + ch_final_vcf = ch_filtered_vcf + ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) + } + + // + // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. + // + if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { + ANNOTATE( + ch_final_vcf, + params.annotate_tools, + ch_snpeff_db, + ch_snpeff_cache, + ch_vep_genome, + ch_vep_species, + ch_vep_cache_version, + ch_vep_cache) + + // Gather QC reports + ch_reports = ch_reports.mix(ANNOTATE.out.reports) + ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) + } } else{ - ch_haplotypecaller_raw_index = GATK4_HAPLOTYPECALLER.out.tbi + ch_haplotypecaller_raw_index = GATK4_HAPLOTYPECALLER.out.tbi .map{ meta, idx -> meta.id = meta.sample [meta, idx]} From 8be8b3ed3cf7d72463add67409a9ba0c8f3eff80 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 16:03:21 +0200 Subject: [PATCH 111/275] fix merge conflicts --- workflows/rnavar.nf | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 814de207..32e95fb0 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -101,17 +101,6 @@ include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index/ include { TABIX_TABIX as TABIX } from '../modules/nf-core/tabix/tabix/main' include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/tabix/tabix/main' -/* -======================================================================================== - IMPORT NF-CORE SUBWORKFLOWS -======================================================================================== -*/ - -include { ALIGN_STAR } from '../subworkflows/nf-core/align_star' // Align reads to genome and sort and index the alignment file -include { MARKDUPLICATES } from '../subworkflows/nf-core/markduplicates' // Mark duplicates in the BAM file -include { RECALIBRATE } from '../subworkflows/nf-core/recalibrate' // Estimate and correct systematic bias -include { SPLITNCIGAR } from '../subworkflows/nf-core/splitncigar' // Splits reads that contain Ns in their cigar string - /* ======================================================================================== VARIABLES @@ -493,7 +482,7 @@ workflow RNAVAR { GATK4_VARIANTFILTRATION( ch_haplotypecaller_vcf_tbi, PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, + PREPARE_GENOME.out.fasta_fai, PREPARE_GENOME.out.dict ) From 3f028a8a2e3b11536581d608d9237de6c5cae07e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 16:37:30 +0200 Subject: [PATCH 112/275] fix merge conflicts --- workflows/rnavar.nf | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 32e95fb0..2b39b7f5 100755 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -482,7 +482,7 @@ workflow RNAVAR { GATK4_VARIANTFILTRATION( ch_haplotypecaller_vcf_tbi, PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_fai, + PREPARE_GENOME.out.fasta_fai.map{ fasta_fai -> [[id:'genome'], fasta_fai]}, PREPARE_GENOME.out.dict ) @@ -495,19 +495,24 @@ workflow RNAVAR { // SUBWORKFLOW: Annotate variants using snpEff and Ensembl VEP if enabled. // if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { - ANNOTATE( + + vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []] + + VCF_ANNOTATE_ALL( ch_final_vcf, + vep_fasta, params.annotate_tools, - ch_snpeff_db, - ch_snpeff_cache, - ch_vep_genome, - ch_vep_species, - ch_vep_cache_version, - ch_vep_cache) + params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}", + snpeff_cache, + vep_genome, + vep_species, + vep_cache_version, + vep_cache, + vep_extra_files) // Gather QC reports - ch_reports = ch_reports.mix(ANNOTATE.out.reports) - ch_versions = ch_versions.mix(ANNOTATE.out.versions.first().ifEmpty(null)) + ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports) + ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions.first().ifEmpty(null)) } } From fb2586a96420f34797eae2a54ffcd0c254f5bf24 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 16:48:09 +0200 Subject: [PATCH 113/275] fix linting --- .nf-core.yml | 12 + modules.json | 2 +- .../nf-core/samtools/merge/environment.yml | 3 +- modules/nf-core/samtools/merge/main.nf | 5 +- .../nf-core/samtools/merge/tests/main.nf.test | 125 +++++----- .../samtools/merge/tests/main.nf.test.snap | 220 +++++++++++++++--- 6 files changed, 260 insertions(+), 107 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..c025b49e 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,13 @@ repository_type: pipeline +lint: + files_exist: + - lib/NfcoreTemplate.groovy + - lib/Utils.groovy + - lib/WorkflowMain.groovy + - lib/WorkflowRnavar.groovy + files_unchanged: + - .github/CONTRIBUTING.md + - .github/workflows/branch.yml + - .github/workflows/linting.yml + - .github/workflows/linting_comment.yml + - docs/images/nf-core-rnavar_logo_light.png diff --git a/modules.json b/modules.json index b6a8f0c2..097fe61b 100755 --- a/modules.json +++ b/modules.json @@ -157,7 +157,7 @@ }, "samtools/merge": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["modules"] }, "samtools/sort": { diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 1f7fe49f..fc669b1b 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 16f2b07f..a3048c28 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") @@ -32,7 +32,6 @@ process SAMTOOLS_MERGE { samtools \\ merge \\ --threads ${task.cpus-1} \\ - -f \\ $args \\ ${reference} \\ ${prefix}.${file_type} \\ diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test b/modules/nf-core/samtools/merge/tests/main.nf.test index 024f9f70..40b36e82 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test +++ b/modules/nf-core/samtools/merge/tests/main.nf.test @@ -9,21 +9,19 @@ nextflow_process { tag "samtools" tag "samtools/merge" - test("sarscov2 - [bam1, bam2, bam3], [], []") { + test("bams") { config "./index.config" when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] + ]) input[1] = [[],[]] input[2] = [[],[]] """ @@ -33,40 +31,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - file(process.out.csi[0][1]).name, - process.out.crai, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bams_bam") }, + { assert snapshot(process.out.cram).match("bams_cram") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("bams_csi") }, + { assert snapshot(process.out.crai).match("bams_crai") }, + { assert snapshot(process.out.versions).match("bams_versions") } ) } - } - test("homo_sapiens - [cram1, cram2], fasta, fai") { + test("crams") { config "./index.config" when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - ] - ] - input[1] = [ - [id:'genome'], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] - input[2] = [ - [id:'genome'], - file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) """ } } @@ -74,27 +67,24 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.cram[0][1]).name, - process.out.bam, - file(process.out.crai[0][1]).name, - process.out.csi, - process.out.versions - ).match() } + { assert snapshot(file(process.out.cram[0][1]).name).match("crams_cram") }, + { assert snapshot(process.out.bam).match("crams_bam") }, + { assert snapshot(file(process.out.crai[0][1]).name).match("crams_crai") }, + { assert snapshot(process.out.csi).match("crams_csi") }, + { assert snapshot(process.out.versions).match("crams_versions") } ) } - } - test("sarscov2 - bam, [], []") { + test("bam") { when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true) ] + ]) input[1] = [[],[]] input[2] = [[],[]] """ @@ -104,19 +94,16 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - process.out.crai, - process.out.csi, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, + { assert snapshot(process.out.cram).match("bam_cram") }, + { assert snapshot(process.out.crai).match("bam_crai") }, + { assert snapshot(process.out.csi).match("bam_csi") }, + { assert snapshot(process.out.versions).match("bam_versions") } ) } - } - test("sarscov2 - [bam1, bam2, bam3], [], [] - stub") { + test("bams_stub") { config "./index.config" options "-stub" @@ -124,14 +111,12 @@ nextflow_process { when { process { """ - input[0] = [ - [ id: 'test' ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) ] + ]) input[1] = [[],[]] input[2] = [[],[]] """ @@ -141,16 +126,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.cram, - file(process.out.csi[0][1]).name, - process.out.crai, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bams_stub_bam") }, + { assert snapshot(process.out.cram).match("bams_stub_cram") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("bams_stub_csi") }, + { assert snapshot(process.out.crai).match("bams_stub_crai") }, + { assert snapshot(process.out.versions).match("bams_stub_versions") } ) } - } - } diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index 3ab57d81..f7da7699 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -1,68 +1,228 @@ { - "sarscov2 - bam, [], []": { + "crams_cram": { + "content": [ + "test.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:00.647389" + }, + "bams_stub_cram": { "content": [ - "test.bam", [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:19.937013" + }, + "bams_crai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:49:24.928616" + }, + "bams_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:49:24.923289" + }, + "bams_cram": { + "content": [ [ - ], - [ - "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" ] ], - "timestamp": "2023-12-04T17:13:30.244841621" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:49:24.925716" }, - "sarscov2 - [bam1, bam2, bam3], [], [] - stub": { + "crams_csi": { "content": [ - "test.bam", [ - ], - "test.csi", + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:00.655959" + }, + "bam_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:10.319539" + }, + "bam_versions": { + "content": [ + [ + "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:33.782637377" + }, + "bams_csi": { + "content": [ + "test.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:49:24.92719" + }, + "bams_stub_csi": { + "content": [ + "test.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:19.940498" + }, + "bam_crai": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:10.328852" + }, + "bams_stub_versions": { + "content": [ [ - "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" + "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" ] ], - "timestamp": "2023-12-04T17:10:14.861445721" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:42.594476052" }, - "homo_sapiens - [cram1, cram2], fasta, fai": { + "bam_cram": { "content": [ - "test.cram", [ - ], - "test.cram.crai", + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:10.324219" + }, + "bams_stub_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:19.933153" + }, + "bams_versions": { + "content": [ + [ + "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:04.805335656" + }, + "crams_bam": { + "content": [ [ - ], + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:00.650652" + }, + "crams_versions": { + "content": [ [ - "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" + "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" ] ], - "timestamp": "2023-12-04T17:09:29.716002618" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:25.889394689" }, - "sarscov2 - [bam1, bam2, bam3], [], []": { + "bam_csi": { "content": [ - "test.bam", [ - ], - "test.bam.csi", + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:10.33292" + }, + "crams_crai": { + "content": [ + "test.cram.crai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:00.653512" + }, + "bams_stub_crai": { + "content": [ [ - ], - [ - "versions.yml:md5,71986103374bdddb2e3093d20e7d06cb" ] ], - "timestamp": "2023-12-04T17:08:42.329973045" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:50:19.943839" } } \ No newline at end of file From 0ef4c852326636a23bef38f9b2f416a53fa94ddc Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 17:30:05 +0200 Subject: [PATCH 114/275] update contributors --- README.md | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 327a633b..3f1a5060 100644 --- a/README.md +++ b/README.md @@ -58,9 +58,6 @@ > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - Now, you can run the pipeline using: ```console @@ -96,12 +91,22 @@ For more details about the output files and reports, please refer to the nf-core/rnavar was originally written in Nextflow DSL2 for use at the [Barntumörbanken, Karolinska Institutet](https://ki.se/forskning/barntumorbanken), by Praveen Raj ([@praveenraj2018](https://github.com/praveenraj2018)) and Maxime U Garcia ([@maxulysse](https://github.com/maxulysse)). -The pipeline is primarily maintained by Praveen Raj ([@praveenraj2018](https://github.com/praveenraj2018)) from [Barntumörbanken, Karolinska Institutet](https://ki.se/forskning/barntumorbanken) and Maxime U Garcia ([@maxulysse](https://github.com/maxulysse)) from [Seqera Labs](https://seqera/io) +nf-core/rnavar was originally written by Praveen Raj at [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken). +Maxime U Garcia at [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken) helped with development. + +Maintenance is now lead by Maxime U Garcia (now at [Seqera Labs](https://seqera/io)) + +Main developers: + +- [Maxime U Garcia](https://github.com/maxulysse) + +We thank the following people for their extensive assistance in the development of this pipeline: -Many thanks to other who have helped out along the way too, including (but not limited to): -[@ewels](https://github.com/ewels), -[@drpatelh](https://github.com/drpatelh), -[@nschcolnicov](https://github.com/nschcolnicov). +- [Harshil Patel](https://github.com/drpatelh) +- [Nicolás Schcolnicov](https://github.com/nschcolnicov) +- [Phil Ewels](https://github.com/ewels) +- [Praveen Raj](https://github.com/praveenraj2018) +- [Sarah Maman](https://github.com/SarahMaman) ## Contributions and Support From 66a151a464e98f605b6f754fb2795fa32551ad5a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 27 May 2024 17:35:19 +0200 Subject: [PATCH 115/275] update contributors --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 3f1a5060..64a0458b 100644 --- a/README.md +++ b/README.md @@ -104,6 +104,7 @@ We thank the following people for their extensive assistance in the development - [Harshil Patel](https://github.com/drpatelh) - [Nicolás Schcolnicov](https://github.com/nschcolnicov) +- [Ömer An](https://github.com/bounlu) - [Phil Ewels](https://github.com/ewels) - [Praveen Raj](https://github.com/praveenraj2018) - [Sarah Maman](https://github.com/SarahMaman) From dfc222061e6a9fd4707556bf9de88c52fd82e76a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 16:53:59 +0200 Subject: [PATCH 116/275] remove custom_dumpsoftwareversions --- modules.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules.json b/modules.json index d37057de..472a60ec 100755 --- a/modules.json +++ b/modules.json @@ -35,11 +35,6 @@ "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, - "custom/dumpsoftwareversions": { - "branch": "master", - "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] - }, "ensemblvep/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", From 4cf692feea7ac4ae461af89572cb435ceaaa2042 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 17:05:36 +0200 Subject: [PATCH 117/275] fix linting --- nextflow.config | 4 ++-- nextflow_schema.json | 9 ++++++++- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index 7d983bd8..79f7604a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -103,8 +103,8 @@ params { hook_url = null help = false version = false - modules_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/modules/data/' - pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/modules/data/' + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data' // Config options config_profile_name = null diff --git a/nextflow_schema.json b/nextflow_schema.json index f86079cd..c42e4d7d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -710,11 +710,18 @@ "hidden": true, "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." }, + "modules_testdata_base_path": { + "type": "string", + "fa_icon": "far fa-check-circle", + "description": "Base URL or local path to location of pipeline test dataset files", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data", + "hidden": true + }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data", "hidden": true } } From 7885146ed3b9419670bf22dd79054d4331793833 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 17:24:35 +0200 Subject: [PATCH 118/275] more linting updates --- .github/workflows/awsfulltest.yml | 3 --- .nf-core.yml | 3 --- README.md | 4 ++-- assets/methods_description_template.yml | 2 -- nextflow.config | 4 ++-- 5 files changed, 4 insertions(+), 12 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 46a3767e..9096f17a 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -15,9 +15,6 @@ jobs: steps: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 - # TODO nf-core: You can customise AWS full pipeline tests as required - # Add full size test data (but still relatively small datasets for few samples) - # on the `test_full.config` test runs with only one set of parameters with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.nf-core.yml b/.nf-core.yml index ac969c64..e0b85a77 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,5 +1,2 @@ repository_type: pipeline nf_core_version: "2.14.1" -lint: - files_unchanged: - - .github/CONTRIBUTING.md diff --git a/README.md b/README.md index 4dc04e42..7fb6e23d 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results) -[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.6669636-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.6669636) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) @@ -121,7 +121,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/rnavar for your analysis, please cite it using the following doi: [10.5281/zenodo.6669637](https://doi.org/10.5281/zenodo.6669637) +If you use nf-core/rnavar for your analysis, please cite it using the following doi: [10.5281/zenodo.6669636](https://doi.org/10.5281/zenodo.6669636) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 46025e30..01825cfb 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/rnavar Methods Description" section_href: "https://github.com/nf-core/rnavar" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object data: |

    Methods

    Data was processed using nf-core/rnavar v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

    diff --git a/nextflow.config b/nextflow.config index 79f7604a..eff8a185 100644 --- a/nextflow.config +++ b/nextflow.config @@ -315,8 +315,8 @@ manifest { description = """GATK4 RNA variant calling pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0dev' - doi = '10.5281/zenodo.6669637' + version = '2.0.0dev' + doi = '10.5281/zenodo.6669636' } // Load modules.config for DSL2 module specific options From 4f1b40a6a72d9d52df9ba27b12129b0cf7e1a75e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 17:28:43 +0200 Subject: [PATCH 119/275] fix path --- conf/test.config | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/test.config b/conf/test.config index 9efca7d8..8f539c85 100644 --- a/conf/test.config +++ b/conf/test.config @@ -25,18 +25,18 @@ params { // Genome references genome = null - fasta = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' - dict = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict' - gtf = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf' + fasta = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta" + dict = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/genome.dict" + gtf = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" // Known genome resources (optional) - dbsnp = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz' - dbsnp_tbi = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi' - known_indels = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz' - known_indels_tbi = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi' + dbsnp = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_tbi = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + known_indels = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + known_indels_tbi = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" // STAR index (optional) - star_index = params.pipeline_testdata_base_path + 'genomics/homo_sapiens/genome/index/star/star.tar.gz' + star_index = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/index/star/star.tar.gz" // Annotation snpeff_db = '105' From b1891a83a5a5868c9fc2a69830ea61d7ff547b0e Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 28 May 2024 17:31:09 +0200 Subject: [PATCH 120/275] Update assets/schema_input.json --- assets/schema_input.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 90cd27b1..eb0fc954 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -11,7 +11,7 @@ "type": "string", "pattern": "^\\S+$", "errorMessage": "Sample name must be provided and cannot contain spaces", - "meta": ["id"] + "meta": ["sample"] }, "fastq_1": { "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", From 3bce90278f6c0cb73854cdf4ea3b61c78b989dab Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 17:37:23 +0200 Subject: [PATCH 121/275] fix path --- conf/test.config | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/test.config b/conf/test.config index 8f539c85..c82a9e1d 100644 --- a/conf/test.config +++ b/conf/test.config @@ -25,18 +25,18 @@ params { // Genome references genome = null - fasta = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta" - dict = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/genome.dict" - gtf = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" + fasta = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta" + dict = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.dict" + gtf = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" // Known genome resources (optional) - dbsnp = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" - dbsnp_tbi = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" - known_indels = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" - known_indels_tbi = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" + dbsnp = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" + dbsnp_tbi = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" + known_indels = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz" + known_indels_tbi = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi" // STAR index (optional) - star_index = "${params.pipeline_testdata_base_path}/genomics/homo_sapiens/genome/index/star/star.tar.gz" + star_index = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/index/star/star.tar.gz" // Annotation snpeff_db = '105' From 7c05e358fc875edf31961aac3af634a4e5ecd0f2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 17:40:33 +0200 Subject: [PATCH 122/275] update CHANGELOG --- CHANGELOG.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index aa82163a..a23056fa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [1.1.0dev] nfcore/rnavar +## [2.0.0dev] nfcore/rnavar ### Added @@ -16,6 +16,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#109](https://github.com/nf-core/rnavar/pull/109) - Update all modules - [#111](https://github.com/nf-core/rnavar/pull/111) - Template update from nf-core/tools 2.11 - [#117](https://github.com/nf-core/rnavar/pull/117) - Template update from nf-core/tools 2.11.1 +- [#120](https://github.com/nf-core/rnavar/pull/120) - Template update from nf-core/tools 2.12 +- [#140](https://github.com/nf-core/rnavar/pull/140) - Template update from nf-core/tools 2.14.1 ### Fixed @@ -25,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables - [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir - [#136](https://github.com/nf-core/rnavar/pull/136) - Replaced unzip module with gunzip, removed unzip module +- [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF ### Dependencies From 51790a26c1f23e4095b9bc88963891b97e81f560 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 18:45:25 +0200 Subject: [PATCH 123/275] fix syntax errors (and a couple of extra stuff) --- assets/schema_input.json | 6 +- main.nf | 33 +-- modules.json | 5 + .../nf-core/bcftools/annotate/environment.yml | 7 + modules/nf-core/bcftools/annotate/main.nf | 65 ++++++ modules/nf-core/bcftools/annotate/meta.yml | 56 +++++ .../bcftools/annotate/tests/bcf.config | 6 + .../bcftools/annotate/tests/main.nf.test | 108 ++++++++++ .../bcftools/annotate/tests/main.nf.test.snap | 79 +++++++ .../nf-core/bcftools/annotate/tests/tags.yml | 2 + .../bcftools/annotate/tests/vcf.config | 6 + nextflow_schema.json | 1 - subworkflows/local/prepare_genome/main.nf | 4 + .../utils_nfcore_rnavar_pipeline/main.nf | 56 +++-- workflows/rnavar/main.nf | 201 ++++++++---------- 15 files changed, 475 insertions(+), 160 deletions(-) create mode 100644 modules/nf-core/bcftools/annotate/environment.yml create mode 100644 modules/nf-core/bcftools/annotate/main.nf create mode 100644 modules/nf-core/bcftools/annotate/meta.yml create mode 100644 modules/nf-core/bcftools/annotate/tests/bcf.config create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/annotate/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/annotate/tests/tags.yml create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf.config diff --git a/assets/schema_input.json b/assets/schema_input.json index eb0fc954..9f3c4cb8 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -11,16 +11,14 @@ "type": "string", "pattern": "^\\S+$", "errorMessage": "Sample name must be provided and cannot contain spaces", - "meta": ["sample"] + "meta": ["id"] }, "fastq_1": { "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.f(ast)?q\\.gz$", - "format": "file-path", - "exists": true + "pattern": "^\\S+\\.f(ast)?q\\.gz$" }, "fastq_2": { "type": "string", diff --git a/main.nf b/main.nf index 59a6ed26..4d339824 100644 --- a/main.nf +++ b/main.nf @@ -80,11 +80,6 @@ workflow NFCORE_RNAVAR { seq_center = params.seq_center ?: [] // Initialize value channels based on params, defined in the params.genomes[params.genome] scope - ascat_genome = params.ascat_genome ?: Channel.empty() - dbsnp_vqsr = params.dbsnp_vqsr ? Channel.value(params.dbsnp_vqsr) : Channel.empty() - known_indels_vqsr = params.known_indels_vqsr ? Channel.value(params.known_indels_vqsr) : Channel.empty() - known_snps_vqsr = params.known_snps_vqsr ? Channel.value(params.known_snps_vqsr) : Channel.empty() - ngscheckmate_bed = params.ngscheckmate_bed ? Channel.value(params.ngscheckmate_bed) : Channel.empty() snpeff_db = params.snpeff_db ?: Channel.empty() vep_cache_version = params.vep_cache_version ?: Channel.empty() vep_genome = params.vep_genome ?: Channel.empty() @@ -108,8 +103,12 @@ workflow NFCORE_RNAVAR { ch_fasta_raw, ch_gff, ch_gtf_raw, - feature_type) + ch_dbsnp, + ch_known_indels, + params.feature_type) + ch_fasta = PREPARE_GENOME.out.fasta + ch_star_index = PREPARE_GENOME.out.star_index ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect() @@ -118,8 +117,6 @@ workflow NFCORE_RNAVAR { : PREPARE_GENOME.out.exon_bed ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ it -> [ [id:'gtf'], it ] }.collect() : PREPARE_GENOME.out.gtf - ch_star_index = params.star_index ? Channel.fromPath(params.star_index).map{ it -> [ [id:'star_index'], it ] }.collect() - : PREPARE_GENOME.out.star_index ch_dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([]) ch_known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() @@ -138,11 +135,11 @@ workflow NFCORE_RNAVAR { } else { // Looks for cache information either locally or on the cloud ANNOTATION_CACHE_INITIALISATION( - (params.snpeff_cache && params.tools && (params.tools.split(',').contains("snpeff") || params.tools.split(',').contains('merge'))), + (params.snpeff_cache && params.annotate_tools && (params.annotate_tools.split(',').contains("snpeff") || params.annotate_tools.split(',').contains('merge'))), params.snpeff_cache, params.snpeff_genome, params.snpeff_db, - (params.vep_cache && params.tools && (params.tools.split(',').contains("vep") || params.tools.split(',').contains('merge'))), + (params.vep_cache && params.annotate_tools && (params.annotate_tools.split(',').contains("vep") || params.annotate_tools.split(',').contains('merge'))), params.vep_cache, params.vep_species, params.vep_cache_version, @@ -156,9 +153,19 @@ workflow NFCORE_RNAVAR { // // WORKFLOW: Run pipeline // - RNAVAR ( - samplesheet - ) + RNAVAR(samplesheet, + ch_dbsnp, + ch_dbsnp_tbi, + ch_dict, + ch_exon_bed, + ch_fasta, + ch_fasta_fai, + ch_gtf, + ch_known_indels, + ch_known_indels_tbi, + ch_star_index, + seq_center, + seq_platform) emit: multiqc_report = RNAVAR.out.multiqc_report // channel: /path/to/multiqc_report.html diff --git a/modules.json b/modules.json index 472a60ec..98179092 100755 --- a/modules.json +++ b/modules.json @@ -5,6 +5,11 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "bcftools/annotate": { + "branch": "master", + "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c", + "installed_by": ["modules"] + }, "bcftools/concat": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml new file mode 100644 index 00000000..e0abc8d2 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -0,0 +1,7 @@ +name: bcftools_annotate +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bcftools=1.18 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf new file mode 100644 index 00000000..64e7ec76 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -0,0 +1,65 @@ +process BCFTOOLS_ANNOTATE { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': + 'biocontainers/bcftools:1.18--h8b25389_0' }" + + input: + tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) + + output: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def header_file = header_lines ? "--header-lines ${header_lines}" : '' + def annotations_file = annotations ? "--annotations ${annotations}" : '' + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + """ + bcftools \\ + annotate \\ + $args \\ + $annotations_file \\ + $header_file \\ + --output ${prefix}.${extension} \\ + --threads $task.cpus \\ + $input + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + """ + ${create_cmd} ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml new file mode 100644 index 00000000..f3aa463b --- /dev/null +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -0,0 +1,56 @@ +name: bcftools_annotate +description: Add or remove annotations. +keywords: + - bcftools + - annotate + - vcf + - remove + - add +tools: + - annotate: + description: Add or remove annotations. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: https://samtools.github.io/bcftools/bcftools.html#annotate + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Query VCF or BCF file, can be either uncompressed or compressed + - index: + type: file + description: Index of the query VCF or BCF file + - annotations: + type: file + description: Bgzip-compressed file with annotations + - annotations_index: + type: file + description: Index of the annotations file + - header_lines: + type: file + description: Contains lines to append to the output VCF header +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf: + type: file + description: Compressed annotated VCF file + pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" +authors: + - "@projectoriented" + - "@ramprasadn" +maintainers: + - "@projectoriented" + - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/bcf.config b/modules/nf-core/bcftools/annotate/tests/bcf.config new file mode 100644 index 00000000..b8496b33 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/bcf.config @@ -0,0 +1,6 @@ +process { + withName: 'BCFTOOLS_ANNOTATE' { + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type u" + ext.prefix = { "${meta.id}_ann" } + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test new file mode 100644 index 00000000..9abf9475 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_process { + + name "Test Process BCFTOOLS_ANNOTATE" + script "../main.nf" + process "BCFTOOLS_ANNOTATE" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/annotate" + + test("sarscov2 - [vcf, tbi, vcf2, tbi2, []] - vcf_output") { + + config "./vcf.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("vcf") } + ) + } + + } + + + test("sarscov2 - [vcf, [], [], [], header] - bcf_output") { + + config "./bcf.config" + + when { + process { + """ + vcf = Channel.of([ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + [], + [], + [] + ]) + + header = Channel.of( + '##INFO=', + '##INFO=' + ) + .collectFile(name:"headers.vcf", newLine:true) + + input[0] = vcf.combine(header) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("bcf") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, vcf2, tbi2, []] - stub") { + + config "./vcf.config" + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("stub") } + ) + } + + } + +} diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap new file mode 100644 index 00000000..72b06878 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -0,0 +1,79 @@ +{ + "bcf": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_ann.bcf" + ] + ], + [ + "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-03T09:21:58.526449656" + }, + "vcf": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-02T16:47:47.127427579" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-02T16:43:43.707474961" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/tags.yml b/modules/nf-core/bcftools/annotate/tests/tags.yml new file mode 100644 index 00000000..f97a1afc --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/annotate: + - "modules/nf-core/bcftools/annotate/**" diff --git a/modules/nf-core/bcftools/annotate/tests/vcf.config b/modules/nf-core/bcftools/annotate/tests/vcf.config new file mode 100644 index 00000000..cb809f61 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf.config @@ -0,0 +1,6 @@ +process { + withName: 'BCFTOOLS_ANNOTATE' { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type z" + } +} diff --git a/nextflow_schema.json b/nextflow_schema.json index c42e4d7d..b3de2e1a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -16,7 +16,6 @@ "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/rnavar/usage#input).", "fa_icon": "fas fa-file-csv", - "schema": "assets/schema_input.json", "type": "string", "format": "file-path", "exists": true, diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 478ff351..6b5a7d3b 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -19,6 +19,8 @@ workflow PREPARE_GENOME { ch_fasta_raw // file: /path/to/genome.fasta ch_gff // file: /path/to/genome.gff ch_gtf_raw // file: /path/to/genome.gtf + ch_dbsnp + ch_known_indels feature_type main: @@ -47,6 +49,8 @@ workflow PREPARE_GENOME { GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) GFFREAD(ch_gff) SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) + TABIX_DBSNP(ch_dbsnp.flatten().map{ it -> [ [ id:it.baseName ], it ] }) + TABIX_KNOWN_INDELS(ch_known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) ch_gtf = ch_gtf.mix(GFFREAD.out.gtf) diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 313a5066..76473c54 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -93,32 +93,20 @@ workflow PIPELINE_INITIALISATION { params.star_index ] - // only check if we are using the tools - if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) checkPathParamList.add(params.snpeff_cache) - if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) checkPathParamList.add(params.vep_cache) + // only check if we are using the annotate_tools + if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) checkPathParamList.add(params.snpeff_cache) + if (params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge'))) checkPathParamList.add(params.vep_cache) // // Create channel from input file provided through params.input // - Channel - .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() - .map { - validateInputSamplesheet(it) - } - .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } + + if (params.input) ch_samplesheet = Channel.fromSamplesheet("input") + .map{ meta, fastq_1, fastq_2 -> + if (!fastq_2) [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + else [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + }.groupTuple().map{validateInputSamplesheet(it)} + .map { meta, fastqs -> [ meta, fastqs.flatten() ] } emit: samplesheet = ch_samplesheet @@ -192,16 +180,26 @@ def validateInputSamplesheet(input) { return [ metas[0], fastqs ] } + // -// Get attribute from genome config file e.g. fasta +// Function to check samples are internally consistent after being grouped // -def getGenomeAttribute(attribute) { - if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { - if (params.genomes[ params.genome ].containsKey(attribute)) { - return params.genomes[ params.genome ][ attribute ] - } +def checkSamplesAfterGrouping(input) { + def (metas, fastqs) = input[1..2] + + // Check that multiple runs of the same sample are of the same strandedness + def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1 + if (!strandedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}") } - return null + + // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end + def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + if (!endedness_ok) { + error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") + } + + return [ metas[0], fastqs ] } // diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 1a95ecdf..cbcf70a6 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -4,34 +4,33 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryMap } from 'plugin/nf-validation' -include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' - -include { ALIGN_STAR } from '../../subworkflows/local/align_star' -include { BAM_MARKDUPLICATES } from '../../subworkflows/local/bam_markduplicates' -include { GTF2BED } from '../../modules/local/gtf2bed' -include { PREPARE_CACHE } from '../../subworkflows/local/prepare_cache' -include { PREPARE_GENOME } from '../../subworkflows/local/prepare_genome' -include { RECALIBRATE } from '../../subworkflows/local/recalibrate' -include { SPLITNCIGAR } from '../../subworkflows/local/splitncigar' -include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all' - -include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq' -include { FASTQC } from '../../modules/nf-core/fastqc' -include { GATK4_BASERECALIBRATOR } from '../../modules/nf-core/gatk4/baserecalibrator' -include { GATK4_BEDTOINTERVALLIST } from '../../modules/nf-core/gatk4/bedtointervallist' -include { GATK4_COMBINEGVCFS } from '../../modules/nf-core/gatk4/combinegvcfs' -include { GATK4_HAPLOTYPECALLER } from '../../modules/nf-core/gatk4/haplotypecaller' -include { GATK4_INDEXFEATUREFILE } from '../../modules/nf-core/gatk4/indexfeaturefile' -include { GATK4_INTERVALLISTTOOLS } from '../../modules/nf-core/gatk4/intervallisttools' -include { GATK4_MERGEVCFS } from '../../modules/nf-core/gatk4/mergevcfs' -include { GATK4_VARIANTFILTRATION } from '../../modules/nf-core/gatk4/variantfiltration' -include { MULTIQC } from '../../modules/nf-core/multiqc' -include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index' -include { TABIX_TABIX as TABIX } from '../../modules/nf-core/tabix/tabix' -include { TABIX_TABIX as TABIXGVCF } from '../../modules/nf-core/tabix/tabix' +include { paramsSummaryMap } from 'plugin/nf-validation' +include { checkSamplesAfterGrouping } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' + +include { ALIGN_STAR } from '../../subworkflows/local/align_star' +include { BAM_MARKDUPLICATES } from '../../subworkflows/local/bam_markduplicates' +include { GTF2BED } from '../../modules/local/gtf2bed' +include { RECALIBRATE } from '../../subworkflows/local/recalibrate' +include { SPLITNCIGAR } from '../../subworkflows/local/splitncigar' +include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all' + +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq' +include { FASTQC } from '../../modules/nf-core/fastqc' +include { GATK4_BASERECALIBRATOR } from '../../modules/nf-core/gatk4/baserecalibrator' +include { GATK4_BEDTOINTERVALLIST } from '../../modules/nf-core/gatk4/bedtointervallist' +include { GATK4_COMBINEGVCFS } from '../../modules/nf-core/gatk4/combinegvcfs' +include { GATK4_HAPLOTYPECALLER } from '../../modules/nf-core/gatk4/haplotypecaller' +include { GATK4_INDEXFEATUREFILE } from '../../modules/nf-core/gatk4/indexfeaturefile' +include { GATK4_INTERVALLISTTOOLS } from '../../modules/nf-core/gatk4/intervallisttools' +include { GATK4_MERGEVCFS } from '../../modules/nf-core/gatk4/mergevcfs' +include { GATK4_VARIANTFILTRATION } from '../../modules/nf-core/gatk4/variantfiltration' +include { MULTIQC } from '../../modules/nf-core/multiqc' +include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index' +include { TABIX_TABIX as TABIX } from '../../modules/nf-core/tabix/tabix' +include { TABIX_TABIX as TABIXGVCF } from '../../modules/nf-core/tabix/tabix' /* ======================================================================================== @@ -40,84 +39,60 @@ include { TABIX_TABIX as TABIXGVCF } from '../../modules/nf-core/tabix/tabix' */ workflow RNAVAR { + take: + ch_input + ch_dbsnp + ch_dbsnp_tbi + ch_dict + ch_exon_bed + ch_fasta + ch_fasta_fai + ch_gtf + ch_known_indels + ch_known_indels_tbi + ch_star_index + seq_center + seq_platform + + main: + + ch_fastq = Channel.fromSamplesheet("input").map{meta, fastq_1, fastq_2 -> + if (!fastq_2) [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] + else [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + }.groupTuple().map{ checkSamplesAfterGrouping(it) } + .branch{ meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [ meta, fastqs.flatten() ] + } + // To gather all QC reports for MultiQC ch_reports = Channel.empty() // To gather used softwares versions for MultiQC ch_versions = Channel.empty() - ch_input = Channel.empty() - - if (params.input) ch_input = Channel.fromSamplesheet("input") - - ch_input = ch_input.map{ meta, fastq_1, fastq_2 -> - if (fastq_2) return [ meta + [id: meta.sample], [ fastq_1, fastq_2 ] ] - else return [ meta + [id: meta.sample], [ fastq_1 ] ] - }.groupTuple() - .branch { meta, fastq -> - single : fastq.size() == 1 - return [ meta + [single_end:true], fastq.flatten() ] - multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - - // Download cache if needed - // Assuming that if the cache is provided, the user has already downloaded it - ensemblvep_info = params.vep_cache ? [] : Channel.of([ [ id:"${params.vep_cache_version}_${params.vep_genome}" ], params.vep_genome, params.vep_species, params.vep_cache_version ]) - snpeff_info = params.snpeff_cache ? [] : Channel.of([ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], params.snpeff_genome, params.snpeff_db ]) - - if (params.download_cache) { - PREPARE_CACHE(ensemblvep_info, snpeff_info) - snpeff_cache = PREPARE_CACHE.out.snpeff_cache - vep_cache = PREPARE_CACHE.out.ensemblvep_cache.map{ meta, cache -> [ cache ] } - - ch_versions = ch_versions.mix(PREPARE_CACHE.out.versions) - } - - // Prepare reference genome files - - PREPARE_GENOME( - ch_fasta_raw, - ch_gff, - ch_gtf_raw, - params.feature_type - ) - ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) - - ch_genome_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() - : PREPARE_GENOME.out.exon_bed - ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() - : PREPARE_GENOME.out.dict - - ch_fasta = params.fasta.endsWith('.gz') ? PREPARE_GENOME.out.fasta - : ch_fasta_raw - - ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).collect() - : PREPARE_GENOME.out.fasta_fai - - ch_gtf = params.gtf.endsWith('.gz') ? PREPARE_GENOME.out.gtf - : ch_gtf_raw - // MODULE: Concatenate FastQ files from same sample if required - CAT_FASTQ(ch_input.multiple) + CAT_FASTQ(ch_fastq.multiple) - ch_fastq = CAT_FASTQ.out.reads.mix(ch_input.single) + ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_fastq.single) - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) // MODULE: Generate QC summary using FastQC - FASTQC(ch_fastq) + FASTQC(ch_cat_fastq) ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ meta, logs -> logs }) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + ch_versions = ch_versions.mix(FASTQC.out.versions) // // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList // - GATK4_BEDTOINTERVALLIST(ch_genome_bed, ch_dict) + GATK4_BEDTOINTERVALLIST(ch_exon_bed, ch_dict) ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list - ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions) // // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools @@ -142,14 +117,13 @@ workflow RNAVAR { ch_aligner_clustering_multiqc = Channel.empty() if (params.aligner == 'star') { - ALIGN_STAR( - ch_fastq, - PREPARE_GENOME.out.star_index.first(), - PREPARE_GENOME.out.gtf.first(), + ALIGN_STAR(ch_cat_fastq, + ch_star_index, + ch_gtf, params.star_ignore_sjdbgtf, seq_platform, - seq_center - ) + seq_center) + ch_genome_bam = ALIGN_STAR.out.bam ch_genome_bam_index = ALIGN_STAR.out.bai ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript @@ -157,7 +131,7 @@ workflow RNAVAR { // Gather QC reports ch_reports = ch_reports.mix(ALIGN_STAR.out.reports) ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(ALIGN_STAR.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(ALIGN_STAR.out.versions) // // SUBWORKFLOW: Mark duplicates with GATK4 @@ -172,7 +146,7 @@ workflow RNAVAR { //Gather QC reports ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.reports.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions) // // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals @@ -187,7 +161,7 @@ workflow RNAVAR { ch_interval_list_split ) ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai - ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions) // // MODULE: BaseRecalibrator from GATK4 @@ -218,7 +192,7 @@ workflow RNAVAR { // Gather QC reports ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) - ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions) ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table) ch_bam_recalibrated_qc = Channel.empty() @@ -245,7 +219,7 @@ workflow RNAVAR { // Gather QC reports ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(RECALIBRATE.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(RECALIBRATE.out.versions) } else { ch_bam_variant_calling = ch_splitncigar_bam_bai } @@ -283,7 +257,7 @@ workflow RNAVAR { [meta, vcf]} .groupTuple() - ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions) if (!params.generate_gvcf){ // @@ -292,10 +266,10 @@ workflow RNAVAR { // GATK4_MERGEVCFS( ch_haplotypecaller_raw, - PREPARE_GENOME.out.dict + ch_dict ) ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf - ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions) // // MODULE: Index the VCF using TABIX @@ -312,7 +286,7 @@ workflow RNAVAR { else [meta, vcf, csi] } - ch_versions = ch_versions.mix(TABIX.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(TABIX.out.versions) ch_final_vcf = ch_haplotypecaller_vcf // @@ -323,14 +297,14 @@ workflow RNAVAR { GATK4_VARIANTFILTRATION( ch_haplotypecaller_vcf_tbi, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_fai.map{ fasta_fai -> [[id:'genome'], fasta_fai]}, - PREPARE_GENOME.out.dict + ch_fasta, + ch_fasta_fai.map{ fasta_fai -> [[id:'genome'], fasta_fai]}, + ch_dict ) ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf ch_final_vcf = ch_filtered_vcf - ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions) } // @@ -354,7 +328,7 @@ workflow RNAVAR { // Gather QC reports ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports) - ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions) } } @@ -372,12 +346,12 @@ workflow RNAVAR { GATK4_COMBINEGVCFS( ch_haplotypecaller_raw, ch_haplotypecaller_raw_index, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fai, - PREPARE_GENOME.out.dict + ch_fasta, + ch_fai, + ch_dict ) ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf - ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions) // // MODULE: Index the VCF using TABIX @@ -392,7 +366,7 @@ workflow RNAVAR { else [meta, vcf, csi] } - ch_versions = ch_versions.mix(TABIXGVCF.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(TABIXGVCF.out.versions) } } @@ -407,6 +381,8 @@ workflow RNAVAR { // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report // if (!params.skip_multiqc){ + ch_multiqc_files = Channel.empty() + ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() @@ -428,7 +404,6 @@ workflow RNAVAR { multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) } -} emit: multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html From 2123303cc0b6a5aca5b913ee67f6f782385f09dd Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 28 May 2024 18:51:52 +0200 Subject: [PATCH 124/275] fix version --- main.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 4d339824..c38d75ec 100644 --- a/main.nf +++ b/main.nf @@ -61,6 +61,8 @@ workflow NFCORE_RNAVAR { main: + ch_versions = Channel.empty() + // Initialize fasta file with meta map: ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() @@ -131,7 +133,7 @@ workflow NFCORE_RNAVAR { snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache vep_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ meta, cache -> [ cache ] } - versions = versions.mix(DOWNLOAD_CACHE_SNPEFF_VEP.out.versions) + ch_versions = ch_versions.mix(DOWNLOAD_CACHE_SNPEFF_VEP.out.versions) } else { // Looks for cache information either locally or on the cloud ANNOTATION_CACHE_INITIALISATION( From 957ea6800040386990e1f173a58b285d643a739d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 29 May 2024 09:28:26 +0200 Subject: [PATCH 125/275] update all modules --- conf/modules/annotate.config | 60 ++- conf/modules/prepare_cache.config | 10 +- main.nf | 6 + modules.json | 80 +-- modules/nf-core/bcftools/concat/main.nf | 2 +- .../bcftools/concat/tests/main.nf.test | 15 +- .../bcftools/concat/tests/main.nf.test.snap | 112 +++- modules/nf-core/bcftools/sort/main.nf | 4 +- .../nf-core/bcftools/sort/tests/main.nf.test | 54 ++ .../bcftools/sort/tests/main.nf.test.snap | 68 +++ modules/nf-core/bcftools/sort/tests/tags.yml | 2 + modules/nf-core/bedtools/merge/meta.yml | 4 +- .../nf-core/bedtools/merge/tests/main.nf.test | 34 ++ .../bedtools/merge/tests/main.nf.test.snap | 35 ++ .../bedtools/merge/tests/nextflow.config | 7 + modules/nf-core/bedtools/merge/tests/tags.yml | 2 + modules/nf-core/bedtools/sort/meta.yml | 4 +- .../nf-core/bedtools/sort/tests/main.nf.test | 58 +++ .../bedtools/sort/tests/main.nf.test.snap | 68 +++ .../bedtools/sort/tests/nextflow.config | 8 + modules/nf-core/bedtools/sort/tests/tags.yml | 2 + modules/nf-core/cat/fastq/environment.yml | 2 +- modules/nf-core/cat/fastq/main.nf | 1 - modules/nf-core/cat/fastq/tests/main.nf.test | 65 ++- .../nf-core/cat/fastq/tests/main.nf.test.snap | 185 +++++-- .../ensemblvep/download/environment.yml | 2 +- modules/nf-core/ensemblvep/download/main.nf | 14 +- .../ensemblvep/download/tests/main.nf.test | 60 +++ .../download/tests/main.nf.test.snap | 322 ++++++++++++ .../ensemblvep/download/tests/nextflow.config | 12 + .../ensemblvep/download/tests/tags.yml | 2 + .../nf-core/ensemblvep/vep/environment.yml | 2 +- modules/nf-core/ensemblvep/vep/main.nf | 15 +- .../nf-core/ensemblvep/vep/tests/main.nf.test | 114 ++++ .../ensemblvep/vep/tests/main.nf.test.snap | 26 + .../ensemblvep/vep/tests/nextflow.config | 12 + .../ensemblvep/vep/tests/tab.gz.config | 5 + modules/nf-core/ensemblvep/vep/tests/tags.yml | 2 + .../nf-core/ensemblvep/vep/tests/vcf.config | 5 + .../nf-core/gatk4/applybqsr/environment.yml | 2 +- modules/nf-core/gatk4/applybqsr/main.nf | 4 +- .../gatk4/applybqsr/tests/main.nf.test | 40 +- .../gatk4/applybqsr/tests/main.nf.test.snap | 40 +- .../gatk4/baserecalibrator/environment.yml | 2 +- .../nf-core/gatk4/baserecalibrator/main.nf | 4 +- .../gatk4/baserecalibrator/tests/main.nf.test | 62 +-- .../baserecalibrator/tests/main.nf.test.snap | 50 +- .../gatk4/bedtointervallist/environment.yml | 2 +- .../nf-core/gatk4/bedtointervallist/main.nf | 4 +- .../bedtointervallist/tests/main.nf.test | 38 ++ .../bedtointervallist/tests/main.nf.test.snap | 35 ++ .../gatk4/bedtointervallist/tests/tags.yml | 2 + .../gatk4/combinegvcfs/environment.yml | 2 +- modules/nf-core/gatk4/combinegvcfs/main.nf | 4 +- modules/nf-core/gatk4/combinegvcfs/meta.yml | 2 +- .../gatk4/combinegvcfs/tests/main.nf.test | 38 ++ .../combinegvcfs/tests/main.nf.test.snap | 146 ++++++ .../nf-core/gatk4/combinegvcfs/tests/tags.yml | 2 + .../createsequencedictionary/environment.yml | 2 +- .../gatk4/createsequencedictionary/main.nf | 4 +- .../tests/main.nf.test | 56 ++ .../tests/main.nf.test.snap | 68 +++ .../createsequencedictionary/tests/tags.yml | 2 + .../gatk4/haplotypecaller/environment.yml | 2 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 4 +- .../nf-core/gatk4/haplotypecaller/meta.yml | 10 +- .../gatk4/haplotypecaller/tests/main.nf.test | 28 +- .../haplotypecaller/tests/main.nf.test.snap | 80 ++- .../gatk4/indexfeaturefile/environment.yml | 2 +- .../nf-core/gatk4/indexfeaturefile/main.nf | 4 +- .../gatk4/indexfeaturefile/tests/main.nf.test | 105 ++++ .../indexfeaturefile/tests/main.nf.test.snap | 132 +++++ .../gatk4/indexfeaturefile/tests/tags.yml | 2 + .../gatk4/intervallisttools/environment.yml | 2 +- .../nf-core/gatk4/intervallisttools/main.nf | 4 +- .../intervallisttools/tests/main.nf.test | 72 +++ .../intervallisttools/tests/main.nf.test.snap | 88 ++++ .../intervallisttools/tests/nextflow.config | 5 + .../gatk4/intervallisttools/tests/tags.yml | 2 + .../gatk4/markduplicates/environment.yml | 5 +- modules/nf-core/gatk4/markduplicates/main.nf | 4 +- .../gatk4/markduplicates/tests/main.nf.test | 14 +- .../markduplicates/tests/main.nf.test.snap | 72 ++- .../nf-core/gatk4/mergevcfs/environment.yml | 2 +- modules/nf-core/gatk4/mergevcfs/main.nf | 4 +- modules/nf-core/gatk4/mergevcfs/meta.yml | 2 +- .../gatk4/mergevcfs/tests/main.nf.test | 87 ++++ .../gatk4/mergevcfs/tests/main.nf.test.snap | 35 ++ .../nf-core/gatk4/mergevcfs/tests/tags.yml | 2 + .../gatk4/splitncigarreads/environment.yml | 2 +- .../nf-core/gatk4/splitncigarreads/main.nf | 10 +- .../nf-core/gatk4/splitncigarreads/meta.yml | 15 + .../gatk4/splitncigarreads/tests/main.nf.test | 80 +++ .../splitncigarreads/tests/main.nf.test.snap | 32 ++ .../gatk4/splitncigarreads/tests/tags.yml | 2 + .../gatk4/variantfiltration/environment.yml | 2 +- .../nf-core/gatk4/variantfiltration/main.nf | 4 +- .../variantfiltration/tests/main.nf.test | 87 ++++ .../variantfiltration/tests/main.nf.test.snap | 30 ++ .../gatk4/variantfiltration/tests/tags.yml | 2 + modules/nf-core/gffread/environment.yml | 2 +- modules/nf-core/gffread/main.nf | 49 +- modules/nf-core/gffread/meta.yml | 25 +- modules/nf-core/gffread/tests/main.nf.test | 182 ++++++- .../nf-core/gffread/tests/main.nf.test.snap | 240 ++++++++- .../gffread/tests/nextflow-fasta.config | 5 + .../gffread/tests/nextflow-gff3.config | 5 + modules/nf-core/gunzip/tests/main.nf.test | 9 +- modules/nf-core/mosdepth/environment.yml | 2 +- modules/nf-core/mosdepth/main.nf | 12 +- modules/nf-core/mosdepth/tests/main.nf.test | 16 +- .../nf-core/mosdepth/tests/main.nf.test.snap | 423 +++++++++++---- .../nf-core/samtools/faidx/environment.yml | 5 +- modules/nf-core/samtools/faidx/main.nf | 4 +- modules/nf-core/samtools/faidx/meta.yml | 4 + .../nf-core/samtools/faidx/tests/main.nf.test | 122 +++++ .../samtools/faidx/tests/main.nf.test.snap | 249 +++++++++ .../samtools/faidx/tests/nextflow.config | 7 + .../samtools/faidx/tests/nextflow2.config | 6 + modules/nf-core/samtools/faidx/tests/tags.yml | 2 + .../nf-core/samtools/flagstat/environment.yml | 3 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test | 12 +- .../samtools/flagstat/tests/main.nf.test.snap | 20 +- .../nf-core/samtools/idxstats/environment.yml | 3 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test | 14 +- .../samtools/idxstats/tests/main.nf.test.snap | 20 +- .../nf-core/samtools/index/environment.yml | 3 +- modules/nf-core/samtools/index/main.nf | 4 +- .../nf-core/samtools/index/tests/main.nf.test | 36 +- .../samtools/index/tests/main.nf.test.snap | 54 +- modules/nf-core/samtools/sort/environment.yml | 3 +- modules/nf-core/samtools/sort/main.nf | 32 +- modules/nf-core/samtools/sort/meta.yml | 32 +- .../nf-core/samtools/sort/tests/main.nf.test | 71 ++- .../samtools/sort/tests/main.nf.test.snap | 128 ++++- .../samtools/sort/tests/nextflow.config | 3 +- .../nf-core/samtools/stats/environment.yml | 3 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../nf-core/samtools/stats/tests/main.nf.test | 53 +- .../samtools/stats/tests/main.nf.test.snap | 32 +- modules/nf-core/snpeff/snpeff/main.nf | 10 +- .../nf-core/snpeff/snpeff/tests/main.nf.test | 50 ++ .../snpeff/snpeff/tests/main.nf.test.snap | 31 ++ .../snpeff/snpeff/tests/nextflow.config | 4 + modules/nf-core/snpeff/snpeff/tests/tags.yml | 2 + modules/nf-core/star/align/environment.yml | 1 + modules/nf-core/star/align/tests/main.nf.test | 141 ++--- .../star/genomegenerate/environment.yml | 3 +- .../star/genomegenerate/tests/main.nf.test | 40 +- .../genomegenerate/tests/main.nf.test.snap | 80 ++- .../nf-core/tabix/bgziptabix/environment.yml | 1 + modules/nf-core/tabix/bgziptabix/main.nf | 6 +- .../tabix/bgziptabix/tests/main.nf.test | 94 ++++ .../tabix/bgziptabix/tests/main.nf.test.snap | 143 +++++ .../tabix/bgziptabix/tests/tabix_csi.config | 5 + .../tabix/bgziptabix/tests/tabix_tbi.config | 5 + .../nf-core/tabix/bgziptabix/tests/tags.yml | 2 + modules/nf-core/tabix/tabix/environment.yml | 1 + modules/nf-core/tabix/tabix/main.nf | 6 +- .../nf-core/tabix/tabix/tests/main.nf.test | 142 +++++ .../tabix/tabix/tests/main.nf.test.snap | 217 ++++++++ .../tabix/tabix/tests/tabix_bed.config | 5 + .../tabix/tabix/tests/tabix_gff.config | 5 + .../tabix/tabix/tests/tabix_vcf_csi.config | 5 + .../tabix/tabix/tests/tabix_vcf_tbi.config | 5 + modules/nf-core/tabix/tabix/tests/tags.yml | 2 + modules/nf-core/untar/environment.yml | 4 +- modules/nf-core/untar/tests/main.nf.test | 34 +- modules/nf-core/untar/tests/main.nf.test.snap | 491 +----------------- workflows/rnavar/main.nf | 19 +- 172 files changed, 5243 insertions(+), 1345 deletions(-) create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/sort/tests/tags.yml create mode 100644 modules/nf-core/bedtools/merge/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/merge/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/merge/tests/tags.yml create mode 100644 modules/nf-core/bedtools/sort/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/sort/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/sort/tests/tags.yml create mode 100644 modules/nf-core/ensemblvep/download/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/download/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/download/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/download/tests/tags.yml create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test create mode 100644 modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap create mode 100644 modules/nf-core/ensemblvep/vep/tests/nextflow.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tab.gz.config create mode 100644 modules/nf-core/ensemblvep/vep/tests/tags.yml create mode 100644 modules/nf-core/ensemblvep/vep/tests/vcf.config create mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/bedtointervallist/tests/tags.yml create mode 100644 modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/combinegvcfs/tests/tags.yml create mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml create mode 100644 modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/nextflow.config create mode 100644 modules/nf-core/gatk4/intervallisttools/tests/tags.yml create mode 100644 modules/nf-core/gatk4/mergevcfs/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/mergevcfs/tests/tags.yml create mode 100644 modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/splitncigarreads/tests/tags.yml create mode 100644 modules/nf-core/gatk4/variantfiltration/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/variantfiltration/tests/tags.yml create mode 100644 modules/nf-core/gffread/tests/nextflow-fasta.config create mode 100644 modules/nf-core/gffread/tests/nextflow-gff3.config create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test create mode 100644 modules/nf-core/samtools/faidx/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow.config create mode 100644 modules/nf-core/samtools/faidx/tests/nextflow2.config create mode 100644 modules/nf-core/samtools/faidx/tests/tags.yml create mode 100644 modules/nf-core/snpeff/snpeff/tests/main.nf.test create mode 100644 modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap create mode 100644 modules/nf-core/snpeff/snpeff/tests/nextflow.config create mode 100644 modules/nf-core/snpeff/snpeff/tests/tags.yml create mode 100644 modules/nf-core/tabix/bgziptabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config create mode 100644 modules/nf-core/tabix/bgziptabix/tests/tags.yml create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test create mode 100644 modules/nf-core/tabix/tabix/tests/main.nf.test.snap create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_bed.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_gff.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config create mode 100644 modules/nf-core/tabix/tabix/tests/tags.yml diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 9ac57687..ea4f921e 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -18,9 +18,9 @@ process { // SNPEFF if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) { withName: 'SNPEFF_SNPEFF' { - ext.prefix = { vcf.baseName - ".vcf" + "_snpEff" } - ext.args = '-nodownload -canon -v' - publishDir = [ + ext.args = { '-nodownload -canon -v' } + ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' } + publishDir = [ [ mode: params.publish_dir_mode, path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" }, @@ -34,18 +34,19 @@ process { // VEP if (params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge'))) { withName: 'ENSEMBLVEP_VEP' { - ext.args = { [ + ext.args = { [ + "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html", (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', (params.vep_custom_args) ?: '' ].join(' ').trim() } // If just VEP: _VEP.ann.vcf - ext.prefix = { vcf.baseName - ".vcf" + "_VEP.ann" } - publishDir = [ + ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' } + publishDir = [ [ mode: params.publish_dir_mode, path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" }, @@ -53,28 +54,51 @@ process { ], [ mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_annotation/${meta.id}/" }, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, pattern: "*{gz}" ] ] } } + // BCFTOOLS ANNOTATE + if (params.annotate_tools && params.annotate_tools.split(',').contains('bcfann')) { + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' { + ext.args = { '--output-type z' } + ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{gz}" + ] + } + } + // SNPEFF THEN VEP if (params.annotate_tools && params.annotate_tools.split(',').contains('merge')) { - withName: "NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP" { + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' { + ext.args = { [ + "--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html", + (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', + (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', + (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', + (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', + (params.vep_custom_args) ?: '' + ].join(' ').trim() } // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab - ext.prefix = { vcf.baseName - ".ann.vcf" + "_VEP.ann" } + ext.prefix = { vcf.baseName - '.ann.vcf' + '_VEP.ann' } } } - // ALL ANNOTATION annotate_TOOLS - if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge'))) { - withName: "NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)" { - ext.prefix = { input.name - ".vcf" } - publishDir = [ + // ALL ANNOTATION TOOLS + if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge') || params.annotate_tools.split(',').contains('bcfann'))) { + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' { + ext.prefix = { input.name - '.vcf' } + publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_annotation/${meta.id}/" }, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, pattern: "*{gz.tbi}" ] } @@ -82,9 +106,9 @@ process { if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) { withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' { - publishDir = [ + publishDir = [ mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_annotation/${meta.id}/" }, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, pattern: "*{gz,gz.tbi}", saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null } ] diff --git a/conf/modules/prepare_cache.config b/conf/modules/prepare_cache.config index b0523949..7329d0ab 100644 --- a/conf/modules/prepare_cache.config +++ b/conf/modules/prepare_cache.config @@ -17,8 +17,8 @@ process { // SNPEFF withName: 'SNPEFF_DOWNLOAD' { - ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge')) } - publishDir = [ + ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge')) } + publishDir = [ mode: params.publish_dir_mode, path: { params.outdir_cache ? "${params.outdir_cache}/": "${params.outdir}/cache/" } ] @@ -26,9 +26,9 @@ process { // VEP withName: 'ENSEMBLVEP_DOWNLOAD' { - ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge')) } - ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' - publishDir = [ + ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge')) } + ext.args = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' } + publishDir = [ mode: params.publish_dir_mode, path: { params.outdir_cache ? "${params.outdir_cache}/": "${params.outdir}/cache/" } ] diff --git a/main.nf b/main.nf index c38d75ec..6e638a85 100644 --- a/main.nf +++ b/main.nf @@ -166,6 +166,12 @@ workflow NFCORE_RNAVAR { ch_known_indels, ch_known_indels_tbi, ch_star_index, + snpeff_cache, + params.vep_genome, + params.vep_species, + params.vep_cache_version, + vep_cache, + vep_extra_files, seq_center, seq_platform) diff --git a/modules.json b/modules.json index 98179092..852e55d4 100755 --- a/modules.json +++ b/modules.json @@ -12,43 +12,43 @@ }, "bcftools/concat": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bcftools/sort": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bedtools/merge": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "a5377837fe9013bde89de8689829e83e84086536", "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", + "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831", "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] + "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "fastqc": { "branch": "master", @@ -57,77 +57,77 @@ }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "f1b92874e0de01dd82fe1bf7c6a7409673578065", + "git_sha": "af273ea6618c50e82c372abe18b0a225e84fe6f7", "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", - "git_sha": "85561f483acc3bc6a885667ea431b3bb3fccdecb", + "git_sha": "8a223e11d4e6deb36484e01891eae9c1cacb5f5d", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "d3f215802f696f7993f25c759781d2db91232015", "installed_by": ["modules"] }, "gatk4/combinegvcfs": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "fe3d7aac1b62efe4fd05cc9629d192e9cdfc3ccb", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "eab2bd29e589bd05da2b47c9bf95ef10b9508699", + "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "108e1f5bafc045ac19890852a41e8d95ae12aa67", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105", "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "bc93a4b8904472ce64c6bb50b1fb0a1659b9cf78", + "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", "installed_by": ["modules"] }, "gatk4/splitncigarreads": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "1e15ad71d9022293985dd02e24186e5e496a0b3c", "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "00409369b2aff69bded4f0a9e7a80e17d933b426", "installed_by": ["modules"] }, "gffread": { "branch": "master", - "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8", + "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65", + "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", "installed_by": ["modules"] }, "multiqc": { @@ -137,22 +137,22 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f153f1f10e1083c49935565844cccb7453021682", "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["modules"] }, "samtools/idxstats": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["modules"] }, "samtools/merge": { @@ -162,12 +162,12 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": ["modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", "installed_by": ["modules"] }, "snpeff/download": { @@ -177,32 +177,32 @@ }, "snpeff/snpeff": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff", "vcf_annotate_snpeff"] + "git_sha": "2f3db6f45147ebbb56b371536e31bdf622b5bfee", + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "star/align": { "branch": "master", - "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", + "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", + "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"] + "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", + "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "untar": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index a5830a25..d64640b3 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -36,7 +36,7 @@ process BCFTOOLS_CONCAT { stub: prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index bf1a5f3f..d5d9f787 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -34,10 +34,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.vcf, - process.out.versions - ).match() } + { assert snapshot(process.out).match() } ) } @@ -63,10 +60,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.vcf, - process.out.versions - ).match() } + { assert snapshot(process.out).match() } ) } @@ -96,10 +90,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.vcf[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 7344e6e3..90d3fc06 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,43 +1,101 @@ { "sarscov2 - [[vcf1, vcf2], []]": { "content": [ - [ - [ - { - "id": "test3" - }, - "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" ] - ], - [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" - ] + } ], - "timestamp": "2023-11-29T13:52:27.03724666" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-03T13:22:49.766749302" }, "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ - [ - [ - { - "id": "test3" - }, - "test3.vcf.gz:md5,4bcd0afd89f56c5d433f6b6abc44d0a6" + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" ] - ], - [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" - ] + } ], - "timestamp": "2023-11-29T13:52:21.468988293" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-03T13:22:41.119912312" }, "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ - "test3.vcf.gz", - [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" - ] + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + ] + } ], - "timestamp": "2023-11-29T13:41:04.716017811" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-03T13:22:59.90466392" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index c982944c..246148d6 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -49,9 +49,9 @@ process BCFTOOLS_SORT { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" - + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" """ - touch ${prefix}.${extension} + ${create_cmd} ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test new file mode 100644 index 00000000..8a496dda --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -0,0 +1,54 @@ +nextflow_process { + + name "Test Process BCFTOOLS_SORT" + script "../main.nf" + process "BCFTOOLS_SORT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/sort" + + test("sarscov2 - vcf") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("vcf") } + ) + } + + } + + test("sarscov2 - vcf - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..6200cc42 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-02T16:55:21.237927554" + }, + "sarscov2 - vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-05-03T12:32:50.506309198" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/tags.yml b/modules/nf-core/bcftools/sort/tests/tags.yml new file mode 100644 index 00000000..6e9520dd --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/sort: + - "modules/nf-core/bcftools/sort/**" diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index 5565ce48..d7463e3d 100644 --- a/modules/nf-core/bedtools/merge/meta.yml +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -36,10 +36,10 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" maintainers: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test new file mode 100644 index 00000000..95dba8e5 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test @@ -0,0 +1,34 @@ +nextflow_process { + + name "Test Process BEDTOOLS_MERGE" + script "../main.nf" + config "./nextflow.config" + process "BEDTOOLS_MERGE" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/merge" + + test("test_bedtools_merge") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test.snap b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..ee6c4e63 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test_bedtools_merge": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "1": [ + "versions.yml:md5,2d134badb4cd1e4e903696c7967f28d6" + ], + "bed": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,0cf6ed2b6f470cd44a247da74ca4fe4e" + ] + ], + "versions": [ + "versions.yml:md5,2d134badb4cd1e4e903696c7967f28d6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T17:07:09.721153" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/merge/tests/nextflow.config b/modules/nf-core/bedtools/merge/tests/nextflow.config new file mode 100644 index 00000000..16444e98 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: BEDTOOLS_MERGE { + ext.prefix = { "${meta.id}_out" } + } + +} diff --git a/modules/nf-core/bedtools/merge/tests/tags.yml b/modules/nf-core/bedtools/merge/tests/tags.yml new file mode 100644 index 00000000..60c8cad1 --- /dev/null +++ b/modules/nf-core/bedtools/merge/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/merge: + - "modules/nf-core/bedtools/merge/**" diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 9ad70b11..7c915f5f 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -41,13 +41,13 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" - "@chris-cheshire" - "@adamrtalbot" maintainers: - - "@Emiller88" + - "@edmundmiller" - "@sruthipsuresh" - "@drpatelh" - "@chris-cheshire" diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test b/modules/nf-core/bedtools/sort/tests/main.nf.test new file mode 100644 index 00000000..b1f36dd9 --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process BEDTOOLS_SORT" + script "../main.nf" + config "./nextflow.config" + process "BEDTOOLS_SORT" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/sort" + + test("test_bedtools_sort") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + + test("test_bedtools_sort_with_genome") { + + when { + process { + """ + input[0] = [ [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/sort/tests/main.nf.test.snap b/modules/nf-core/bedtools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..f10e8b98 --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test_bedtools_sort_with_genome": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "1": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "versions": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T10:13:11.830452" + }, + "test_bedtools_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "1": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test_out.testtext:md5,fe4053cf4de3aebbdfc3be2efb125a74" + ] + ], + "versions": [ + "versions.yml:md5,cdbae2c7ebc41e534aaf0835779061f8" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T10:16:40.535947" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/sort/tests/nextflow.config b/modules/nf-core/bedtools/sort/tests/nextflow.config new file mode 100644 index 00000000..f203c99c --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + + withName: BEDTOOLS_SORT { + ext.prefix = { "${meta.id}_out" } + ext.suffix = "testtext" + } + +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/sort/tests/tags.yml b/modules/nf-core/bedtools/sort/tests/tags.yml new file mode 100644 index 00000000..47c85eea --- /dev/null +++ b/modules/nf-core/bedtools/sort/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/sort: + - "modules/nf-core/bedtools/sort/**" diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index bff93add..8c69b121 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 3d963784..f132b2ad 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -76,5 +76,4 @@ process CAT_FASTQ { """ } } - } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index f5f94182..a71dcb8d 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -1,3 +1,5 @@ +// NOTE The version snaps may not be consistant +// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035 nextflow_process { name "Test Process CAT_FASTQ" @@ -16,11 +18,11 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -28,8 +30,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -42,13 +43,13 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -56,8 +57,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -70,11 +70,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -82,8 +82,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -96,13 +95,13 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -110,8 +109,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } @@ -124,10 +122,10 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] - ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) """ } } @@ -135,8 +133,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.reads).match() }, - { assert path(process.out.versions.get(0)).getText().contains("cat") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index ec2342e5..43dfe28f 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -1,78 +1,169 @@ { "test_cat_fastq_single_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:12.990284837" + "timestamp": "2024-01-17T17:30:39.816981" }, "test_cat_fastq_single_end_same_name": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:31.554568147" + "timestamp": "2024-01-17T17:32:35.229332" }, "test_cat_fastq_single_end_single_file": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.merged.fastq.gz:md5,e325ef7deb4023447a1f074e285761af" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:49.629360033" + "timestamp": "2024-01-17T17:34:00.058829" }, "test_cat_fastq_paired_end_same_name": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ [ - "test_1.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66", - "test_2.merged.fastq.gz:md5,fe9f266f43a6fc3dcab690a18419a56e" + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" ] - ] + } ], - "timestamp": "2023-10-17T23:19:40.711617539" + "timestamp": "2024-01-17T17:33:33.031555" }, "test_cat_fastq_paired_end": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + 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b/modules/nf-core/ensemblvep/download/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ensembl-vep=110.0 + - bioconda::ensembl-vep=111.0 diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index a770cbfc..f9e025a5 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -4,24 +4,25 @@ process ENSEMBLVEP_DOWNLOAD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }" input: tuple val(meta), val(assembly), val(species), val(cache_version) output: - tuple val(meta), path("vep_cache"), emit: cache - path "versions.yml" , emit: versions + tuple val(meta), path(prefix), emit: cache + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: 'vep_cache' """ vep_install \\ - --CACHEDIR vep_cache \\ + --CACHEDIR $prefix \\ --SPECIES $species \\ --ASSEMBLY $assembly \\ --CACHE_VERSION $cache_version \\ @@ -34,8 +35,9 @@ process ENSEMBLVEP_DOWNLOAD { """ stub: + prefix = task.ext.prefix ?: 'vep_cache' """ - mkdir vep_cache + mkdir $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test new file mode 100644 index 00000000..760c9d56 --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_DOWNLOAD" + script "../main.nf" + process "ENSEMBLVEP_DOWNLOAD" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/download" + + test("celegans - download") { + + when { + process { + """ + input[0] = Channel.of([ + [id:"111_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("celegans - download - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id:"111_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap new file mode 100644 index 00000000..6ea596fb --- /dev/null +++ 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] + ], + "versions": [ + "versions.yml:md5,954fd177c394ba167d575a6aac47390b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-04-15T18:09:54.909036" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config new file mode 100644 index 00000000..882bce41 --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config @@ -0,0 +1,12 @@ +params { + vep_cache_version = "111" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} + +process { + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" } + } +} diff --git a/modules/nf-core/ensemblvep/download/tests/tags.yml b/modules/nf-core/ensemblvep/download/tests/tags.yml new file mode 100644 index 00000000..26671f3d --- /dev/null +++ b/modules/nf-core/ensemblvep/download/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/download: + - "modules/nf-core/ensemblvep/download/**" diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 7a127746..91457c05 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::ensembl-vep=110.0 + - bioconda::ensembl-vep=111.0 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index 3a2b7423..e82471aa 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:110.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:110.0--pl5321h2a3209d_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) @@ -20,7 +20,7 @@ process ENSEMBLVEP_VEP { tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf tuple val(meta), path("*.tab.gz") , optional:true, emit: tab tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , emit: report + path "*.summary.html" , optional:true, emit: report path "versions.yml" , emit: versions when: @@ -45,8 +45,7 @@ process ENSEMBLVEP_VEP { --cache \\ --cache_version $cache_version \\ --dir_cache $dir_cache \\ - --fork $task.cpus \\ - --stats_file ${prefix}.summary.html \\ + --fork $task.cpus cat <<-END_VERSIONS > versions.yml @@ -58,9 +57,9 @@ process ENSEMBLVEP_VEP { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz - touch ${prefix}.tab.gz - touch ${prefix}.json.gz + echo "" | gzip > ${prefix}.vcf.gz + echo "" | gzip > ${prefix}.tab.gz + echo "" | gzip > ${prefix}.json.gz touch ${prefix}.summary.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test new file mode 100644 index 00000000..4aff84a3 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -0,0 +1,114 @@ +nextflow_process { + + name "Test Process ENSEMBLVEP_VEP" + script "../main.nf" + process "ENSEMBLVEP_VEP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ensemblvep" + tag "ensemblvep/vep" + tag "ensemblvep/download" + + test("test_ensemblvep_vep_fasta_vcf") { + config "./vcf.config" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"111_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") } + ) + } + + } + + test("test_ensemblvep_vep_fasta_tab_gz") { + config "./tab.gz.config" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"111_WBcel235"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] + ]) + input[1] = params.vep_genome + input[2] = params.vep_species + input[3] = params.vep_cache_version + input[4] = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] } + input[5] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v111.0") } + ) + } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap new file mode 100644 index 00000000..f937b299 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -0,0 +1,26 @@ +{ + "test_ensemblvep_vep_fasta_tab_gz": { + "content": [ + [ + "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-04-15T17:35:20.694114" + }, + "test_ensemblvep_vep_fasta_vcf": { + "content": [ + [ + "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.03.0" + }, + "timestamp": "2024-04-15T17:34:41.093843" + } +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config new file mode 100644 index 00000000..882bce41 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -0,0 +1,12 @@ +params { + vep_cache_version = "111" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" +} + +process { + withName: ENSEMBLVEP_DOWNLOAD { + ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' + ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" } + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tab.gz.config b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config new file mode 100644 index 00000000..40eb03e5 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tab.gz.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--tab --compress_output bgzip' + } +} diff --git a/modules/nf-core/ensemblvep/vep/tests/tags.yml b/modules/nf-core/ensemblvep/vep/tests/tags.yml new file mode 100644 index 00000000..4aa4aa45 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/tags.yml @@ -0,0 +1,2 @@ +ensemblvep/vep: + - "modules/nf-core/ensemblvep/vep/**" diff --git a/modules/nf-core/ensemblvep/vep/tests/vcf.config b/modules/nf-core/ensemblvep/vep/tests/vcf.config new file mode 100644 index 00000000..ad8955a3 --- /dev/null +++ b/modules/nf-core/ensemblvep/vep/tests/vcf.config @@ -0,0 +1,5 @@ +process { + withName: ENSEMBLVEP_VEP { + ext.args = '--vcf' + } +} diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index a6900991..80c811e6 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 7e495637..78db9d7f 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test index 5ee53d5c..3d9c6204 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test @@ -16,14 +16,14 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), [] ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) """ } } @@ -44,14 +44,14 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) """ } } @@ -71,14 +71,14 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index 1473d66a..a387039d 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -7,45 +7,57 @@ { "id": "test" }, - "test.bam:md5,13f8358467c9cda8a95194a1498ce605" + "test.bam:md5,096d269e17f4ae53f765013479240db8" ] ], "1": [ ], "2": [ - "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,13f8358467c9cda8a95194a1498ce605" + "test.bam:md5,096d269e17f4ae53f765013479240db8" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" ] } ], - "timestamp": "2023-12-09T03:10:32.612468954" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:21:48.144461" }, "sarscov2 - cram": { "content": [ [ - "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" ] ], - "timestamp": "2023-12-09T03:10:46.692732651" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:22:09.308602" }, "test.cram": { "content": [ "test.cram" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-09T03:10:46.70859771" }, "sarscov2 - bam": { @@ -56,31 +68,35 @@ { "id": "test" }, - "test.bam:md5,e025e4351c5a3ff426bb5521cb353e0f" + "test.bam:md5,022271b9ce0a07579282a2a5c1186513" ] ], "1": [ ], "2": [ - "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,e025e4351c5a3ff426bb5521cb353e0f" + "test.bam:md5,022271b9ce0a07579282a2a5c1186513" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,369f8733e6ead8380588819a648acf7a" + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" ] } ], - "timestamp": "2023-12-09T03:10:19.704738169" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:21:28.719225" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 6863fb17..365e5c63 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index b4af1f33..1a299862 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,8 +4,8 @@ process GATK4_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test index 1262b694..fbd91bea 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -15,15 +15,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - input[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) """ } @@ -45,15 +45,15 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) - input[4] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) """ } @@ -75,20 +75,20 @@ nextflow_process { input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] - input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) input[4] = [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) ] input[5] = [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] """ @@ -141,15 +141,15 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] ] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - input[3] = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) - input[4] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) - input[5] = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap index 0d96f660..8291304b 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ], "table": [ [ @@ -22,11 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ] } ], - "timestamp": "2023-12-14T20:42:32.991100186" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:16:00.04396" }, "sarscov2 - bam - intervals": { "content": [ @@ -40,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ], "table": [ [ @@ -51,11 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ] } ], - "timestamp": "2023-12-14T20:42:07.697600853" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:15:17.899391" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -69,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ], "table": [ [ @@ -80,11 +88,15 @@ ] ], "versions": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ] } ], - "timestamp": "2023-12-14T20:42:21.374942189" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:15:47.770383" }, "homo_sapiens - cram ": { "content": [ @@ -98,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ], "table": [ [ @@ -109,11 +121,15 @@ ] ], "versions": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ] } ], - "timestamp": "2023-12-14T20:42:49.148196543" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:16:42.135898" }, "sarscov2 - bam": { "content": [ @@ -127,7 +143,7 @@ ] ], "1": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ], "table": [ [ @@ -138,10 +154,14 @@ ] ], "versions": [ - "versions.yml:md5,8b4c1f3950eb01822c4589c15aa54847" + "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" ] } ], - "timestamp": "2023-12-14T20:41:53.870942331" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T16:14:57.629443" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index e7cb4280..d6fbe2e7 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 88b24b1a..68863d67 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process GATK4_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test new file mode 100644 index 00000000..2289f73f --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process GATK4_BEDTOINTERVALLIST" + script "../main.nf" + process "GATK4_BEDTOINTERVALLIST" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/bedtointervallist" + + test("test_gatk4_bedtointervallist") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + input[1] = [ [ id:'dict' ], // meta map + [file(params.modules_testdata_base_path + + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap new file mode 100644 index 00000000..48c322fd --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test_gatk4_bedtointervallist": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" + ] + ], + "1": [ + "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + ], + "interval_list": [ + [ + { + "id": "test" + }, + "test.interval_list:md5,e51101c9357fb2d59fd30e370eefa39c" + ] + ], + "versions": [ + "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T14:20:12.168775" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml b/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml new file mode 100644 index 00000000..b4d54f12 --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/bedtointervallist: + - "modules/nf-core/gatk4/bedtointervallist/**" diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index c1205a35..e4510f97 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index ed658f1c..df8ade11 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_COMBINEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_idx) diff --git a/modules/nf-core/gatk4/combinegvcfs/meta.yml b/modules/nf-core/gatk4/combinegvcfs/meta.yml index 477b7c6d..f13ddde7 100644 --- a/modules/nf-core/gatk4/combinegvcfs/meta.yml +++ b/modules/nf-core/gatk4/combinegvcfs/meta.yml @@ -41,7 +41,7 @@ input: description: FASTA dictionary file pattern: "*.dict" output: - - gvcf: + - combined_gvcf: type: file description: Compressed Combined GVCF file pattern: "*.combined.g.vcf.gz" diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test new file mode 100644 index 00000000..56f54d0f --- /dev/null +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process GATK4_COMBINEGVCFS" + script "../main.nf" + process "GATK4_COMBINEGVCFS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/combinegvcfs" + + test("test_gatk4_combinegvcfs") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + // File has a timestamp in it and is in binary format, need to compare only a portion of the file (after header) + { assert snapshot(path(process.out.combined_gvcf[0][1]).linesGzip[102..-1], + process.out.versions + ).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap new file mode 100644 index 00000000..1f04b8bd --- /dev/null +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap @@ -0,0 +1,146 @@ +{ + "test_gatk4_combinegvcfs": { + "content": [ + [ + "chr22\t1\t.\tA\t\t.\t.\tEND=1951\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0", + "chr22\t1952\t.\tT\t\t.\t.\tEND=1953\tGT:DP:GQ:MIN_DP:PL\t./.:1:3:1:0,3,25", + "chr22\t1954\t.\tT\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:1:0:1:0,0,0", + "chr22\t1955\t.\tT\t\t.\t.\tEND=1956\tGT:DP:GQ:MIN_DP:PL\t./.:1:3:1:0,3,33", + "chr22\t1957\t.\tT\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:2:6:2:0,6,68", + "chr22\t1958\t.\tA\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:1:3:1:0,3,34", + "chr22\t1959\t.\tA\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:3:9:3:0,9,101", + "chr22\t1960\t.\tA\t\t.\t.\tEND=1961\tGT:DP:GQ:MIN_DP:PL\t./.:3:6:2:0,6,58", + 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"chr22\t4585\t.\tT\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:34:42:34:0,42,630", + "chr22\t4586\t.\tC\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:32:24:32:0,24,360", + "chr22\t4587\t.\tA\t\t.\t.\tEND=4597\tGT:DP:GQ:MIN_DP:PL\t./.:16:12:4:0,12,99", + "chr22\t4598\t.\tT\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:2:6:2:0,6,49", + "chr22\t4599\t.\tG\t\t.\t.\tEND=4604\tGT:DP:GQ:MIN_DP:PL\t./.:4:12:4:0,12,98", + "chr22\t4605\t.\tG\t\t.\t.\t.\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0", + "chr22\t4606\t.\tT\t\t.\t.\tEND=4607\tGT:DP:GQ:MIN_DP:PL\t./.:2:6:2:0,6,49", + "chr22\t4608\t.\tA\t\t.\t.\tEND=40001\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0" + ], + [ + "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T15:41:25.316932" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/tags.yml b/modules/nf-core/gatk4/combinegvcfs/tests/tags.yml new file mode 100644 index 00000000..26885b46 --- /dev/null +++ b/modules/nf-core/gatk4/combinegvcfs/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/combinegvcfs: + - "modules/nf-core/gatk4/combinegvcfs/**" diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index db663e14..78822ad0 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index b47ad162..c7f1d75b 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test new file mode 100644 index 00000000..a8a9c6d2 --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test @@ -0,0 +1,56 @@ +nextflow_process { + + name "Test Process GATK4_CREATESEQUENCEDICTIONARY" + script "../main.nf" + process "GATK4_CREATESEQUENCEDICTIONARY" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/createsequencedictionary" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap new file mode 100644 index 00000000..16735f95 --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ], + "dict": [ + [ + { + "id": "test" + }, + "genome.dict:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-16T10:16:16.34453" + }, + "sarscov2 - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.dict:md5,7362679f176e0f52add03c08f457f646" + ] + ], + "1": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ], + "dict": [ + [ + { + "id": "test" + }, + "genome.dict:md5,7362679f176e0f52add03c08f457f646" + ] + ], + "versions": [ + "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-05-16T13:58:25.822068" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml b/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml new file mode 100644 index 00000000..035c5e4c --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/createsequencedictionary: + - "modules/nf-core/gatk4/createsequencedictionary/**" diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index 0c8f32fa..d4e8d360 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index a6a71d56..3043ee07 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,8 +4,8 @@ process GATK4_HAPLOTYPECALLER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 2085c2db..703b99a0 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -39,7 +39,7 @@ input: type: map description: | Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test_reference' ] - fasta: type: file description: The reference fasta file @@ -48,7 +48,7 @@ input: type: map description: | Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test_reference' ] - fai: type: file description: Index of reference fasta file @@ -57,7 +57,7 @@ input: type: map description: | Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test_reference' ] - dict: type: file description: GATK sequence dictionary @@ -66,7 +66,7 @@ input: type: map description: | Groovy Map containing dbsnp information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test_dbsnp' ] - dbsnp: type: file description: VCF file containing known sites (optional) @@ -74,7 +74,7 @@ input: type: map description: | Groovy Map containing dbsnp information - e.g. [ id:'test', single_end:false ] + e.g. [ id:'test_dbsnp' ] - dbsnp_tbi: type: file description: VCF index of dbsnp (optional) diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test index 8d6ed4cf..a124bff5 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test_bam' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), [], @@ -36,9 +36,8 @@ nextflow_process { assertAll( { assert process.success }, // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, - { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") }, ) } @@ -50,7 +49,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test_cram' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], @@ -69,9 +68,8 @@ nextflow_process { assertAll( { assert process.success }, // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, - { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") }, ) } @@ -83,7 +81,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test_cram_sites' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], @@ -102,9 +100,8 @@ nextflow_process { assertAll( { assert process.success }, // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, - { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") }, ) } @@ -116,7 +113,7 @@ nextflow_process { process { """ input[0] = [ - [ id:'test' ], // meta map + [ id:'test_cram_sites_dragstr' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], @@ -135,9 +132,8 @@ nextflow_process { assertAll( { assert process.success }, // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("output/gatk4/test.vcf.gz") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("output/gatk4/test.vcf.gz.tbi") }, - { assert snapshot(file(process.out.versions.get(0)).name).match("output/gatk4/versions.yml") }, + { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") }, + { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") }, ) } diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index e5349c2d..375025ee 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -1,20 +1,82 @@ { - "output/gatk4/versions.yml": { + "gatk_hc_vcf_cram_dragstr_input_with_sites": { "content": [ - "versions.yml" + "test_cram_sites_dragstr.vcf.gz" ], - "timestamp": "2023-11-24T12:59:29.843116" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:24:45.142682" }, - "output/gatk4/test.vcf.gz.tbi": { + "gatk_hc_vcf_bam_input": { "content": [ - "test.vcf.gz.tbi" + "test_bam.vcf.gz" ], - "timestamp": "2023-11-24T12:59:29.840834" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:23:19.203837" }, - "output/gatk4/test.vcf.gz": { + "gatk_hc_vcf_cram_input": { "content": [ - "test.vcf.gz" + "test_cram.vcf.gz" ], - "timestamp": "2023-11-24T12:59:29.832106" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:23:48.434615" + }, + "gatk_hc_vcf_cram_input_with_sites": { + "content": [ + "test_cram_sites.vcf.gz" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:24:17.147745" + }, + "gatk_hc_vcf_tbi_bam_input": { + "content": [ + "test_bam.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:23:19.23048" + }, + "gatk_hc_vcf_tbi_cram_input": { + "content": [ + "test_cram.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:23:48.45958" + }, + "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": { + "content": [ + "test_cram_sites_dragstr.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:24:45.154818" + }, + "gatk_hc_vcf_tbi_cram_input_with_sites": { + "content": [ + "test_cram_sites.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-20T13:24:17.158138" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index 95beac68..dccdb15e 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index d7f52e5f..b1a2698c 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,8 +4,8 @@ process GATK4_INDEXFEATUREFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test new file mode 100644 index 00000000..ee99a541 --- /dev/null +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test @@ -0,0 +1,105 @@ +// nf-core modules test gatk4/indexfeaturefile +nextflow_process { + + name "Test Process GATK4_INDEXFEATUREFILE" + script "../main.nf" + process "GATK4_INDEXFEATUREFILE" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/indexfeaturefile" + + test("test_gatk4_indexfeaturefile_bed") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("geneome.bed.idx") }, + ) + } + + } + + test("test_gatk4_indexfeaturefile_bed_gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("genome.bed.gz.tbi") }, + ) + } + + } + + test("test_gatk4_indexfeaturefile_vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("test.genome.vcf.idx") }, + ) + } + + } + + test("test_gatk4_indexfeaturefile_vcf_gz") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot(file(process.out.index.get(0).get(1)).name).match("test.genome.vcf.gz.tbi") }, + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap new file mode 100644 index 00000000..fc193336 --- /dev/null +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap @@ -0,0 +1,132 @@ +{ + "genome.bed.gz.tbi": { + "content": [ + "genome.bed.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:03.068725" + }, + "test_gatk4_indexfeaturefile_vcf": { + "content": [ + [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:20.602472" + }, + "geneome.bed.idx": { + "content": [ + "genome.bed.idx" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:56:46.988441" + }, + "test.genome.vcf.gz.tbi": { + "content": [ + "test.genome.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:51.898472" + }, + "test_gatk4_indexfeaturefile_bed_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "genome.bed.gz.tbi:md5,4bc51e2351a6e83f20e13be75861f941" + ] + ], + "1": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ], + "index": [ + [ + { + "id": "test" + }, + "genome.bed.gz.tbi:md5,4bc51e2351a6e83f20e13be75861f941" + ] + ], + "versions": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:03.058351" + }, + "test_gatk4_indexfeaturefile_vcf_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.genome.vcf.gz.tbi:md5,fedd68eaddf8d31257853d9da8325bd3" + ] + ], + "1": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ], + "index": [ + [ + { + "id": "test" + }, + "test.genome.vcf.gz.tbi:md5,fedd68eaddf8d31257853d9da8325bd3" + ] + ], + "versions": [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:51.861697" + }, + "test.genome.vcf.idx": { + "content": [ + "test.genome.vcf.idx" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:57:20.624337" + }, + "test_gatk4_indexfeaturefile_bed": { + "content": [ + [ + "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T18:56:46.885162" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml b/modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml new file mode 100644 index 00000000..041bd3d3 --- /dev/null +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/indexfeaturefile: + - "modules/nf-core/gatk4/indexfeaturefile/**" diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index b70e5e14..a4026f98 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 10baa752..400fa038 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -4,8 +4,8 @@ process GATK4_INTERVALLISTTOOLS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test new file mode 100644 index 00000000..2891bf9e --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test @@ -0,0 +1,72 @@ +nextflow_process { + + name "Test Process GATK4_INTERVALLISTTOOLS" + script "../main.nf" + process "GATK4_INTERVALLISTTOOLS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/bedtointervallist" + tag "gatk4/intervallisttools" + + setup { + run("GATK4_BEDTOINTERVALLIST") { + script "../../bedtointervallist/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)] + ] + input[1] = [ + [ id:'dict' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)] + ] + """ + } + } + } + + test("test_gatk4_intervallisttools") { + + when { + process { + """ + input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("test_gatk4_intervallisttools -stub") { + + options "-stub" + + when { + process { + """ + input[0] = GATK4_BEDTOINTERVALLIST.out.interval_list + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap new file mode 100644 index 00000000..7718ed00 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -0,0 +1,88 @@ +{ + "test_gatk4_intervallisttools": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995", + "2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5", + "3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53", + "4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498" + ] + ] + ], + "1": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ], + "interval_list": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,64f6665f9fbd257e4a300ec602f4e995", + "2scattered.interval_list:md5,f515c3da0c6accfd8e7dc33df50855c5", + "3scattered.interval_list:md5,7a918e8c9211b54334587793e8cbae53", + "4scattered.interval_list:md5,1b93105227a7dc81f07101a1efd31498" + ] + ] + ], + "versions": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T21:26:22.252885" + }, + "test_gatk4_intervallisttools -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ], + "interval_list": [ + [ + { + "id": "test" + }, + [ + "1scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "2scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "3scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e", + "4scattered.interval_list:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T22:15:11.772344" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config b/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config new file mode 100644 index 00000000..b24b20db --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GATK4_INTERVALLISTTOOLS { + ext.args = '--SCATTER_COUNT 6 --SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW --UNIQUE true --SORT true' + } +} diff --git a/modules/nf-core/gatk4/intervallisttools/tests/tags.yml b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml new file mode 100644 index 00000000..bf85ff5f --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/intervallisttools: + - "modules/nf-core/gatk4/intervallisttools/**" diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 9af4f568..7362eea6 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -4,5 +4,6 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 - - bioconda::samtools=1.18 + - bioconda::gatk4=4.5.0.0 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 790af889..baadefef 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -4,8 +4,8 @@ process GATK4_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-13342043031ce2dd38cd19135a0754154f3d5dcf:5b8e58304eeed40565ed7894b208444fc5c852fa-0': - 'biocontainers/mulled-v2-13342043031ce2dd38cd19135a0754154f3d5dcf:5b8e58304eeed40565ed7894b208444fc5c852fa-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:7cc3d06cbf42e28c5e2ebfc7c858654c7340a9d5-0': + 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:7cc3d06cbf42e28c5e2ebfc7c858654c7340a9d5-0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test index d243b19a..bbcf74db 100644 --- a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test +++ b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:false ], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ] input[1] = [] input[2] = [] @@ -45,8 +45,8 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] ] input[1] = [] @@ -76,12 +76,12 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) ] ] - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[2] = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) """ } } diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap index a89fe989..336bb373 100644 --- a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap @@ -7,16 +7,24 @@ "id": "test", "single_end": false }, - "test.bam:md5,f178378cbc335ab2447f49f32b767083" + "test.bam:md5,8a808b1a94d2627c4d659a2151c4cb9f" ] ] ], - "timestamp": "2023-12-12T17:43:11.703789701" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T15:21:36.059923" }, "multi crai": { "content": [ "test.cram.crai" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-12T17:43:37.780426007" }, "multi bai": { @@ -27,24 +35,36 @@ "id": "test", "single_end": false }, - "test.bai:md5,529fbbad54edf512a1249c9be4258fba" + "test.bai:md5,38b99c5f771895ecf5324c3186b9d452" ] ] ], - "timestamp": "2023-12-12T17:43:11.71311291" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T15:21:36.09642" }, "versions": { "content": [ [ - "versions.yml:md5,ea27c5dfbc6df51aff34d5bf4b7a0eca" + "versions.yml:md5,c58bf16c6e3786cc4d17bb7249f9ffe5" ] ], - "timestamp": "2023-12-12T17:42:39.657705497" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T15:21:08.710549" }, "multi test.metrics": { "content": [ "test.bam.metrics" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-12T17:43:11.732892667" }, "bai": { @@ -59,34 +79,54 @@ ] ] ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-12T17:42:39.651888758" }, "multi cram versions": { "content": [ [ - "versions.yml:md5,ea27c5dfbc6df51aff34d5bf4b7a0eca" + "versions.yml:md5,c58bf16c6e3786cc4d17bb7249f9ffe5" ] ], - "timestamp": "2023-12-12T17:43:37.789135196" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T15:21:56.966376" }, "multi versions": { "content": [ [ - "versions.yml:md5,ea27c5dfbc6df51aff34d5bf4b7a0eca" + "versions.yml:md5,c58bf16c6e3786cc4d17bb7249f9ffe5" ] ], - "timestamp": "2023-12-12T17:43:11.722133619" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T15:21:36.138095" }, "multi cram test.metrics": { "content": [ "test.cram.metrics" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-12T17:43:37.798977444" }, "multi cram": { "content": [ "test.cram" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-12T17:43:37.771137858" }, "bam": { @@ -97,16 +137,24 @@ "id": "test", "single_end": false }, - "test.bam:md5,2e17dfa6db576fd87be8b36fa2133c73" + "test.bam:md5,75d914ba8804eaf2acf02ab432197ec9" ] ] ], - "timestamp": "2023-12-12T17:42:39.64008431" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, + "timestamp": "2024-02-13T15:21:08.645892" }, "test.metrics": { "content": [ "test.bam.metrics" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.0" + }, "timestamp": "2023-12-12T17:42:39.672508385" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index d6c3e51a..efd9faa2 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 3362c2bd..9e8d4391 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_MERGEVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml index 30290a85..996053fc 100644 --- a/modules/nf-core/gatk4/mergevcfs/meta.yml +++ b/modules/nf-core/gatk4/mergevcfs/meta.yml @@ -29,7 +29,7 @@ input: description: | Groovy Map containing reference information e.g. [ id:'genome'] - - ref_dict: + - dict: type: file description: Optional Sequence Dictionary as input pattern: "*.dict" diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test new file mode 100644 index 00000000..77ace10a --- /dev/null +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process GATK4_MERGEVCFS" + script "../main.nf" + process "GATK4_MERGEVCFS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/mergevcfs" + + test("test_gatk4_mergevcfs") { + when { + process { + """ + input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] + input[1] = [ [], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)] + """ + } + } + + then { + assertAll( + { assert process.success }, + { + assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name + ).match("test_gatk4_mergevcfs") + }, + ) + } + + } + + test("test_gatk4_mergevcfs_no_dict") { + when { + process { + """ + input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] + input[1] = [ [],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { + assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name + ).match("test_gatk4_mergevcfs_no_dict") + }, + ) + } + + } + + test("test_gatk4_mergevcfs_no_dict_stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz', checkIfExists: true) ]] + input[1] = [ [],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { + assert snapshot( + file(process.out.vcf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name + ).match("test_gatk4_mergevcfs_no_dict_stub") + }, + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap new file mode 100644 index 00000000..62cceed5 --- /dev/null +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -0,0 +1,35 @@ +{ + "test_gatk4_mergevcfs_no_dict_stub": { + "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T14:57:40.784590995" + }, + "test_gatk4_mergevcfs": { + "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T14:56:42.178255913" + }, + "test_gatk4_mergevcfs_no_dict": { + "content": [ + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-14T14:57:11.404322124" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/tests/tags.yml b/modules/nf-core/gatk4/mergevcfs/tests/tags.yml new file mode 100644 index 00000000..d2a74ba2 --- /dev/null +++ b/modules/nf-core/gatk4/mergevcfs/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/mergevcfs: + - "modules/nf-core/gatk4/mergevcfs/**" diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 50b79217..834d2486 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index 9d32e748..e2c287a0 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -4,14 +4,14 @@ process GATK4_SPLITNCIGARREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(intervals) - path fasta - path fai - path dict + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) output: tuple val(meta), path('*.bam'), emit: bam diff --git a/modules/nf-core/gatk4/splitncigarreads/meta.yml b/modules/nf-core/gatk4/splitncigarreads/meta.yml index e1efde0c..f8132746 100644 --- a/modules/nf-core/gatk4/splitncigarreads/meta.yml +++ b/modules/nf-core/gatk4/splitncigarreads/meta.yml @@ -31,14 +31,29 @@ input: - intervals: type: file description: Bed file with the genomic regions included in the library (optional) + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] - fasta: type: file description: The reference fasta file pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] - fai: type: file description: Index of reference fasta file pattern: "*.fasta.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] - dict: type: file description: GATK sequence dictionary diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test new file mode 100644 index 00000000..b4910126 --- /dev/null +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_process { + + name "Test Process GATK4_SPLITNCIGARREADS" + script "../main.nf" + process "GATK4_SPLITNCIGARREADS" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/splitncigarreads" + + test("test_gatk4_splitncigarreads") { + + when { + process { + """ + input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), []] + input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads") } + ) + } + + } + + test("test_gatk4_splitncigarreads_intervals") { + + when { + process { + """ + input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)] + input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_intervals") } + ) + } + + } + + test("test_gatk4_splitncigarreads_stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), [], []] + input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_stub") } + ) + } + + } + +} diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap new file mode 100644 index 00000000..3e581ceb --- /dev/null +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap @@ -0,0 +1,32 @@ +{ + "test_gatk4_splitncigarreads_intervals": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T08:26:10.91960579" + }, + "test_gatk4_splitncigarreads_stub": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T08:26:32.322712467" + }, + "test_gatk4_splitncigarreads": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T08:25:53.532205456" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/tags.yml b/modules/nf-core/gatk4/splitncigarreads/tests/tags.yml new file mode 100644 index 00000000..b5d95313 --- /dev/null +++ b/modules/nf-core/gatk4/splitncigarreads/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/splitncigarreads: + - "modules/nf-core/gatk4/splitncigarreads/**" diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index cc16bc0e..0812b6f2 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gatk4=4.4.0.0 + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 1c4d8ad0..388c60ab 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -4,8 +4,8 @@ process GATK4_VARIANTFILTRATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test new file mode 100644 index 00000000..36b7438d --- /dev/null +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process GATK4_VARIANTFILTRATION" + script "../main.nf" + process "GATK4_VARIANTFILTRATION" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/variantfiltration" + + test("test_gatk4_variantfiltration_vcf_input") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions, + file(process.out.vcf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name).match() }, + ) + } + + } + + test("test_gatk4_variantfiltration_gz_input") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions, + file(process.out.vcf.get(0).get(1)).name, + file(process.out.tbi.get(0).get(1)).name).match() }, + ) + } + + } + +} + diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap new file mode 100644 index 00000000..36c03f7c --- /dev/null +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "test_gatk4_variantfiltration_gz_input": { + "content": [ + [ + "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" + ], + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T22:43:27.609784" + }, + "test_gatk4_variantfiltration_vcf_input": { + "content": [ + [ + "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" + ], + "test.vcf.gz", + "test.vcf.gz.tbi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T22:42:55.316294" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/variantfiltration/tests/tags.yml b/modules/nf-core/gatk4/variantfiltration/tests/tags.yml new file mode 100644 index 00000000..4818037d --- /dev/null +++ b/modules/nf-core/gatk4/variantfiltration/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/variantfiltration: + - "modules/nf-core/gatk4/variantfiltration/**" diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index 5398f71c..c6df58ad 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::gffread=0.12.1 + - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index d8a473e0..da55cbab 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -1,32 +1,57 @@ process GFFREAD { - tag "$gff" + tag "$meta.id" label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : - 'biocontainers/gffread:0.12.1--h8b12597_0' }" + 'https://depot.galaxyproject.org/singularity/gffread:0.12.7--hdcf5f25_4' : + 'biocontainers/gffread:0.12.7--hdcf5f25_4' }" input: - path gff + tuple val(meta), path(gff) + path fasta output: - path "*.gtf" , emit: gtf , optional: true - path "*.gff3" , emit: gffread_gff , optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.gtf") , emit: gtf , optional: true + tuple val(meta), path("*.gff3") , emit: gffread_gff , optional: true + tuple val(meta), path("*.fasta"), emit: gffread_fasta , optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${gff.baseName}" - def extension = args.contains("-T") ? 'gtf' : 'gffread.gff3' + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("-T") ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' ) + def fasta_arg = fasta ? "-g $fasta" : '' + def output_name = "${prefix}.${extension}" + def output = extension == "fasta" ? "$output_name" : "-o $output_name" + def args_sorted = args.replaceAll(/(.*)(-[wxy])(.*)/) { all, pre, param, post -> "$pre $post $param" }.trim() + // args_sorted = Move '-w', '-x', and '-y' to the end of the args string as gffread expects the file name after these parameters + if ( "$output_name" in [ "$gff", "$fasta" ] ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ gffread \\ $gff \\ - $args \\ - -o ${prefix}.${extension} + $fasta_arg \\ + $args_sorted \\ + $output + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gffread: \$(gffread --version 2>&1) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("-T") ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' ) + def output_name = "${prefix}.${extension}" + if ( "$output_name" in [ "$gff", "$fasta" ] ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch $output_name + cat <<-END_VERSIONS > versions.yml "${task.process}": gffread: \$(gffread --version 2>&1) diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index 27ac3105..c0602820 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -13,11 +13,25 @@ tools: doi: 10.12688/f1000research.23297.1 licence: ["MIT"] input: + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] - gff: type: file description: A reference file in either the GFF3, GFF2 or GTF format. pattern: "*.{gff, gtf}" + - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] - gtf: type: file description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present @@ -25,12 +39,17 @@ output: - gffread_gff: type: file description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.{gff3}" + pattern: "*.gff3" + - gffread_fasta: + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters is present + pattern: "*.fasta" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - - "@emiller88" + - "@edmundmiller" maintainers: - - "@emiller88" + - "@edmundmiller" + - "@gallvp" diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index 3c064b31..4cd13dcd 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -18,17 +18,52 @@ nextflow_process { } process { """ - input[0] = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = [] """ } } then { assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() }, - { assert process.out.gtf != null }, - { assert process.out.gffread_gff == [] } + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gffread_gff == [] }, + { assert process.out.gffread_fasta == [] } + ) + } + + } + + test("sarscov2-gff3-gtf-stub") { + + options '-stub' + config "./nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gffread_gff == [] }, + { assert process.out.gffread_fasta == [] } ) } @@ -36,23 +71,150 @@ nextflow_process { test("sarscov2-gff3-gff3") { + config "./nextflow-gff3.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf == [] }, + { assert process.out.gffread_fasta == [] } + ) + } + + } + + test("sarscov2-gff3-gff3-stub") { + + options '-stub' + config "./nextflow-gff3.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf == [] }, + { assert process.out.gffread_fasta == [] } + ) + } + + } + + test("sarscov2-gff3-fasta") { + + config "./nextflow-fasta.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf == [] }, + { assert process.out.gffread_gff == [] } + ) + } + + } + + test("sarscov2-gff3-fasta-stub") { + + options '-stub' + config "./nextflow-fasta.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf == [] }, + { assert process.out.gffread_gff == [] } + ) + } + + } + + test("sarscov2-gff3-fasta-fail-catch") { + + options '-stub' + config "./nextflow-fasta.config" + when { params { outdir = "$outputDir" } process { """ - input[0] = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + input[0] = [ + [id: 'genome'], + file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) """ } } then { assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() }, - { assert process.out.gtf == [] }, - { assert process.out.gffread_gff != null }, + { assert ! process.success }, + { assert process.stdout.toString().contains("Input and output names are the same") } ) } diff --git a/modules/nf-core/gffread/tests/main.nf.test.snap b/modules/nf-core/gffread/tests/main.nf.test.snap index 1f1342e1..15262320 100644 --- a/modules/nf-core/gffread/tests/main.nf.test.snap +++ b/modules/nf-core/gffread/tests/main.nf.test.snap @@ -3,26 +3,46 @@ "content": [ { "0": [ - "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3" + [ + { + "id": "test" + }, + "test.gtf:md5,1ea0ae98d3388e0576407dc4a24ef428" + ] ], "1": [ ], "2": [ - "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + + ], + "3": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ], + "gffread_fasta": [ + ], "gffread_gff": [ ], "gtf": [ - "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3" + [ + { + "id": "test" + }, + "test.gtf:md5,1ea0ae98d3388e0576407dc4a24ef428" + ] ], "versions": [ - "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" ] } ], - "timestamp": "2023-11-29T15:39:30.006985" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-09T10:48:56.496187" }, "sarscov2-gff3-gff3": { "content": [ @@ -31,22 +51,222 @@ ], "1": [ - "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d" + [ + { + "id": "test" + }, + "test.gff3:md5,c4e5da6267c6bee5899a2c204ae1ad91" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ], + "gffread_fasta": [ + + ], + "gffread_gff": [ + [ + { + "id": "test" + }, + "test.gff3:md5,c4e5da6267c6bee5899a2c204ae1ad91" + ] + ], + "gtf": [ + + ], + "versions": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-09T10:49:00.892782" + }, + "sarscov2-gff3-gtf-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ], + "gffread_fasta": [ + + ], + "gffread_gff": [ + + ], + "gtf": [ + [ + { + "id": "test" + }, + "test.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-09T11:11:26.975666" + }, + "sarscov2-gff3-fasta-stub": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ], + "gffread_fasta": [ + [ + { + "id": "test" + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gffread_gff": [ + + ], + "gtf": [ + + ], + "versions": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-09T11:11:44.34792" + }, + "sarscov2-gff3-gff3-stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ], + "gffread_fasta": [ + + ], + "gffread_gff": [ + [ + { + "id": "test" + }, + "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gtf": [ + + ], + "versions": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-09T11:11:35.221671" + }, + "sarscov2-gff3-fasta": { + "content": [ + { + "0": [ + + ], + "1": [ + ], "2": [ - "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + [ + { + "id": "test" + }, + "test.fasta:md5,5f8108fb51739a0588ccf0a251de919a" + ] + ], + "3": [ + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" + ], + "gffread_fasta": [ + [ + { + "id": "test" + }, + "test.fasta:md5,5f8108fb51739a0588ccf0a251de919a" + ] ], "gffread_gff": [ - "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d" + ], "gtf": [ ], "versions": [ - "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + "versions.yml:md5,05f671c6c6e530acedad0af0a5948dbd" ] } ], - "timestamp": "2023-11-29T15:39:34.636061" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-09T10:54:02.88143" } } \ No newline at end of file diff --git a/modules/nf-core/gffread/tests/nextflow-fasta.config b/modules/nf-core/gffread/tests/nextflow-fasta.config new file mode 100644 index 00000000..ac6cb148 --- /dev/null +++ b/modules/nf-core/gffread/tests/nextflow-fasta.config @@ -0,0 +1,5 @@ +process { + withName: GFFREAD { + ext.args = '-w -S' + } +} diff --git a/modules/nf-core/gffread/tests/nextflow-gff3.config b/modules/nf-core/gffread/tests/nextflow-gff3.config new file mode 100644 index 00000000..afe0830e --- /dev/null +++ b/modules/nf-core/gffread/tests/nextflow-gff3.config @@ -0,0 +1,5 @@ +process { + withName: GFFREAD { + ext.args = '' + } +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test index d0317922..6406008e 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -15,10 +15,11 @@ nextflow_process { } process { """ - input[0] = [ - [], - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) """ } } diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index 88c7126c..bcb9d64a 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -5,4 +5,4 @@ channels: - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.6 + - mosdepth=0.3.8 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index c7e24303..6f4a8383 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.6--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.6--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : + 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" input: tuple val(meta), path(bam), path(bai), path(bed) @@ -63,13 +63,13 @@ process MOSDEPTH { touch ${prefix}.region.dist.txt touch ${prefix}.summary.txt touch ${prefix}.per-base.d4 - touch ${prefix}.per-base.bed.gz + echo "" | gzip > ${prefix}.per-base.bed.gz touch ${prefix}.per-base.bed.gz.csi - touch ${prefix}.regions.bed.gz + echo "" | gzip > ${prefix}.regions.bed.gz touch ${prefix}.regions.bed.gz.csi - touch ${prefix}.quantized.bed.gz + echo "" | gzip > ${prefix}.quantized.bed.gz touch ${prefix}.quantized.bed.gz.csi - touch ${prefix}.thresholds.bed.gz + echo "" | gzip > ${prefix}.thresholds.bed.gz touch ${prefix}.thresholds.bed.gz.csi cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index d991f819..21eebc1f 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -237,21 +237,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - file(process.out.global_txt[0][1]).name, - file(process.out.summary_txt[0][1]).name, - file(process.out.regions_txt[0][1]).name, - file(process.out.per_base_d4[0][1]).name, - file(process.out.per_base_bed[0][1]).name, - file(process.out.per_base_csi[0][1]).name, - file(process.out.regions_bed[0][1]).name, - file(process.out.regions_csi[0][1]).name, - file(process.out.quantized_bed[0][1]).name, - file(process.out.quantized_csi[0][1]).name, - file(process.out.thresholds_bed[0][1]).name, - file(process.out.thresholds_csi[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index dc4d9508..c604540b 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -1,23 +1,236 @@ { "homo_sapiens - bam, bai, [] - stub": { "content": [ - "test.global.dist.txt", - "test.summary.txt", - "test.region.dist.txt", - "test.per-base.d4", - "test.per-base.bed.gz", - "test.per-base.bed.gz.csi", - "test.regions.bed.gz", - "test.regions.bed.gz.csi", - "test.quantized.bed.gz", - "test.quantized.bed.gz.csi", - "test.thresholds.bed.gz", - "test.thresholds.bed.gz.csi", - [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "11": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "global_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "per_base_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "per_base_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "per_base_d4": [ + [ + { + "id": "test", + "single_end": true + }, + "test.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "quantized_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "quantized_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "regions_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "regions_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "regions_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary_txt": [ + [ + { + "id": "test", + "single_end": true + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "thresholds_bed": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "thresholds_csi": [ + [ + { + "id": "test", + "single_end": true + }, + "test.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + ] + } ], - "timestamp": "2023-11-27T15:14:34.897155161" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:16.953408231" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -47,7 +260,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -67,7 +280,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -76,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -85,7 +298,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -94,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -118,7 +331,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -127,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -145,7 +358,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -154,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -182,11 +395,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:18.171150781" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:50.160217828" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -216,7 +433,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -230,7 +447,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -239,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -254,7 +471,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz:md5,3e434a8bafcf59a67841ae3d4d752838" + "test.quantized.bed.gz:md5,f037c215449d361112efc10108fcc17c" ] ], "9": [ @@ -263,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "global_txt": [ @@ -281,7 +498,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -290,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -302,7 +519,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz:md5,3e434a8bafcf59a67841ae3d4d752838" + "test.quantized.bed.gz:md5,f037c215449d361112efc10108fcc17c" ] ], "quantized_csi": [ @@ -311,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" + "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" ] ], "regions_bed": [ @@ -339,11 +556,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:29.228103864" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:01.164885111" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -373,7 +594,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -393,7 +614,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -402,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -411,7 +632,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -420,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -444,7 +665,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -453,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -471,7 +692,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -480,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -508,11 +729,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:04.537716314" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:39.071657456" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -542,7 +767,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -550,7 +775,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "3": [ @@ -562,7 +787,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -571,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -580,7 +805,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,f02e2cb49cc050e13d76942d6960827a" + "test.regions.bed.gz:md5,34f48d16fcdd61e44d812e29e02c77b8" ] ], "7": [ @@ -589,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "8": [ @@ -613,7 +838,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -622,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -640,7 +865,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,f02e2cb49cc050e13d76942d6960827a" + "test.regions.bed.gz:md5,34f48d16fcdd61e44d812e29e02c77b8" ] ], "regions_csi": [ @@ -649,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" + "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" ] ], "regions_txt": [ @@ -658,7 +883,7 @@ "id": "test", "single_end": true }, - "test.mosdepth.region.dist.txt:md5,39e0e707ec32feb5176fd20a95f1f468" + "test.mosdepth.region.dist.txt:md5,0b6ea9f0da1228252d9aef2d3b6f7f76" ] ], "summary_txt": [ @@ -677,11 +902,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:23.708536171" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:55.631776118" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -711,7 +940,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -725,7 +954,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -734,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -764,7 +993,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -773,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -810,11 +1039,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:46:56.975710077" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:33.642125299" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -844,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ @@ -858,7 +1091,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -867,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -897,7 +1130,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -906,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -943,11 +1176,15 @@ ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:47:12.09259995" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:32:44.704920941" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -976,7 +1213,7 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz:md5,13101e326eea3cbfa1d569b69f494f4c" + "test.thresholds.bed.gz:md5,fe70ae728cd10726c42a2bcd44adfc9d" ] ], "11": [ @@ -985,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "12": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ], "2": [ [ @@ -1009,7 +1246,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "5": [ @@ -1018,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "6": [ @@ -1027,7 +1264,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "7": [ @@ -1036,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "8": [ @@ -1060,7 +1297,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz:md5,bc1df47d46f818fee5275975925d769a" + "test.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa" ] ], "per_base_csi": [ @@ -1069,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" + "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" ] ], "per_base_d4": [ @@ -1087,7 +1324,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz:md5,5d398caf7171ec4406278e2add3009ae" + "test.regions.bed.gz:md5,9ded0397623fda26a6a3514d6a0e2a2c" ] ], "regions_csi": [ @@ -1096,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" + "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" ] ], "regions_txt": [ @@ -1123,7 +1360,7 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz:md5,13101e326eea3cbfa1d569b69f494f4c" + "test.thresholds.bed.gz:md5,fe70ae728cd10726c42a2bcd44adfc9d" ] ], "thresholds_csi": [ @@ -1132,14 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" + "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" ] ], "versions": [ - "versions.yml:md5,f8b1896c9c6784181f1234e87225f0e8" + "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" ] } ], - "timestamp": "2023-11-27T14:49:44.311847326" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-04-29T13:33:06.737266831" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 01ccbcc7..9c24eb0a 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,7 +1,10 @@ name: samtools_faidx + channels: - conda-forge - bioconda - defaults + dependencies: - - bioconda::samtools=1.18 + - bioconda::htslib=1.19.1 + - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index d3461627..cfe7ad95 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index e189af28..f3c25de2 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -39,6 +39,10 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - fa: + type: file + description: FASTA file + pattern: "*.{fa}" - fai: type: file description: FASTA index file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test b/modules/nf-core/samtools/faidx/tests/main.nf.test new file mode 100644 index 00000000..17244ef2 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process SAMTOOLS_FAIDX" + script "../main.nf" + process "SAMTOOLS_FAIDX" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/faidx" + + test("test_samtools_faidx") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_bgzip") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true)] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_fasta") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fasta") { + + config "./nextflow2.config" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_samtools_faidx_stub_fai") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap new file mode 100644 index 00000000..3e651ef6 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -0,0 +1,249 @@ +{ + "test_samtools_faidx": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:22:39.412601" + }, + "test_samtools_faidx_bgzip": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.gz.gzi:md5,7dea362b3fac8e00956a4952a3d4f474" + ] + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:23:22.427966" + }, + "test_samtools_faidx_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,6a0774a0ad937ba0bfd2ac7457d90f36" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:24:04.107537" + }, + "test_samtools_faidx_stub_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + [ + { + "id": "test", + "single_end": false + }, + "extract.fa:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "fai": [ + + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:24:45.868463" + }, + "test_samtools_faidx_stub_fai": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ], + "fa": [ + + ], + "fai": [ + [ + { + "id": "test", + "single_end": false + }, + "genome.fasta.fai:md5,9da2a56e2853dc8c0b86a9e7229c9fe5" + ] + ], + "gzi": [ + + ], + "versions": [ + "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-18T16:25:27.550554" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/tests/nextflow.config b/modules/nf-core/samtools/faidx/tests/nextflow.config new file mode 100644 index 00000000..f76a3ba0 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = 'MT192765.1 -o extract.fa' + } + +} diff --git a/modules/nf-core/samtools/faidx/tests/nextflow2.config b/modules/nf-core/samtools/faidx/tests/nextflow2.config new file mode 100644 index 00000000..33ebbd5d --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/nextflow2.config @@ -0,0 +1,6 @@ +process { + + withName: SAMTOOLS_FAIDX { + ext.args = '-o extract.fa' + } +} diff --git a/modules/nf-core/samtools/faidx/tests/tags.yml b/modules/nf-core/samtools/faidx/tests/tags.yml new file mode 100644 index 00000000..e4a83948 --- /dev/null +++ b/modules/nf-core/samtools/faidx/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/faidx: + - modules/nf-core/samtools/faidx/** diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 5efae053..bd57cb54 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index f1893d7c..eb5f5252 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index c8dd8dc9..24c3c04b 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -16,11 +16,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) """ } } @@ -28,8 +28,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.flagstat).match() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.flagstat).match("flagstat") }, + { assert snapshot(process.out.versions).match("versions") } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 880019f2..a76fc27e 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "BAM": { + "flagstat": { "content": [ [ [ @@ -11,6 +11,22 @@ ] ] ], - "timestamp": "2023-11-14T15:49:22.577133" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:31:37.783927" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,fd0030ce49ab3a92091ad80260226452" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:11:44.299617452" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 2401db0f..174973b8 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 00d916bb..a544026f 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index f6c92150..a2dcb27c 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/idxstats" - test("BAM") { + test("bam") { when { params { @@ -16,11 +16,11 @@ nextflow_process { } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) """ } } @@ -28,8 +28,8 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.idxstats).match() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.idxstats).match("idxstats") }, + { assert snapshot(process.out.versions).match("versions") } ) } } diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index 4c6c12bd..a7050bdc 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -1,5 +1,17 @@ { - "BAM": { + "versions": { + "content": [ + [ + "versions.yml:md5,613dde56f108418039ffcdeeddba397a" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:16:50.147462763" + }, + "idxstats": { "content": [ [ [ @@ -11,6 +23,10 @@ ] ] ], - "timestamp": "2023-11-14T15:52:19.875194" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:36:41.561026" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 296ed99e..a5e50649 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8ad18fdc..dc14f98d 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index c76a9169..bb7756d1 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "samtools" tag "samtools/index" - test("sarscov2 [BAI]") { + test("bai") { when { params { @@ -16,10 +16,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) """ } } @@ -28,12 +28,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot(process.out.bai).match("bai") }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("bai_versions") } ) } } - test("homo_sapiens [CRAI]") { + test("crai") { when { params { @@ -41,10 +41,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) """ } } @@ -53,12 +53,12 @@ nextflow_process { assertAll ( { assert process.success }, { assert snapshot(process.out.crai).match("crai") }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("crai_versions") } ) } } - test("homo_sapiens [CSI]") { + test("csi") { config "./csi.nextflow.config" @@ -68,10 +68,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) """ } } @@ -80,7 +80,7 @@ nextflow_process { assertAll ( { assert process.success }, { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert path(process.out.versions.get(0)).getText().contains("samtools") } + { assert snapshot(process.out.versions).match("csi_versions") } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index b3baee7f..3dc8e7de 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,28 +1,74 @@ { + "crai_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:00.324667957" + }, + "csi_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:12:07.885103162" + }, "crai": { "content": [ [ [ { - "id": "test" + "id": "test", + "single_end": false }, "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" ] ] ], - "timestamp": "2023-11-15T15:17:37.30801" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:41:38.446424" }, "bai": { "content": [ [ [ { - "id": "test" + "id": "test", + "single_end": false }, "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" ] ] ], - "timestamp": "2023-11-15T15:17:30.869234" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T18:40:46.579747" + }, + "bai_versions": { + "content": [ + [ + "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:11:51.641425452" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index cd50868c..4d898e48 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 4a666d42..fc374f98 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,15 +4,18 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: - tuple val(meta), path(bam) + tuple val(meta) , path(bam) + tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam - tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -21,14 +24,24 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + def reference = fasta ? "--reference ${fasta}" : "" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + samtools cat \\ + --threads $task.cpus \\ + ${bam} \\ + | \\ samtools sort \\ $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam + -T ${prefix} \\ + --threads $task.cpus \\ + ${reference} \\ + -o ${prefix}.${extension} \\ + - cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -40,6 +53,7 @@ process SAMTOOLS_SORT { def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam + touch ${prefix}.bam.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 2200de72..341a7d0e 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -23,8 +23,18 @@ input: e.g. [ id:'test', single_end:false ] - bam: type: file - description: BAM/CRAM/SAM file + description: BAM/CRAM/SAM file(s) pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - meta: type: map @@ -33,19 +43,29 @@ output: e.g. [ id:'test', single_end:false ] - bam: type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - versions: + description: Sorted BAM file + pattern: "*.{bam}" + - cram: type: file - description: File containing software versions - pattern: "versions.yml" + description: Sorted CRAM file + pattern: "*.{cram}" + - crai: + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: type: file description: BAM index file (optional) pattern: "*.csi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" + - "@matthdsm" maintainers: - "@drpatelh" - "@ewels" + - "@matthdsm" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index abb80978..8360e2b1 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -8,22 +8,21 @@ nextflow_process { tag "samtools" tag "samtools/sort" - test("test_samtools_sort") { + test("bam") { config "./nextflow.config" when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -34,13 +33,39 @@ nextflow_process { { assert snapshot(process.out).match() } ) } + } + + test("cram") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } } - test("test_samtools_sort_stub") { + test("bam_stub") { config "./nextflow.config" - options "-stub-run" + options "-stub" when { params { @@ -48,12 +73,14 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -61,13 +88,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot( - file(process.out.bam[0][1]).name, - process.out.versions - ).match() } + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, + { assert snapshot(process.out.versions).match("bam_stub_versions") } ) } - } - } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index ff722259..38477656 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_samtools_sort": { + "cram": { "content": [ { "0": [ @@ -8,14 +8,26 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" ] ], "1": [ ], "2": [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "4": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ], "bam": [ [ @@ -23,26 +35,120 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,ea6a0fef94eb534e901f107a05a33a06" + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" ] ], - "csi": [ + "crai": [ + + ], + "cram": [ + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] ], "versions": [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ] } ], - "timestamp": "2023-12-04T11:11:22.005628301" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-04T15:08:00.830294" + }, + "bam_stub_bam": { + "content": [ + "test.sorted.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:21:04.364044" }, - "test_samtools_sort_stub": { + "bam_stub_versions": { "content": [ - "test.sorted.bam", [ - "versions.yml:md5,33b6a403dc19a0d28e4219ccab0a1d80" + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ] ], - "timestamp": "2023-12-04T17:47:22.314445935" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:00.20800281" + }, + "bam": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "4": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "versions": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-04T15:07:48.773803" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config index d0f35086..f642771f 100644 --- a/modules/nf-core/samtools/sort/tests/nextflow.config +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -1,7 +1,8 @@ process { withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index" } } diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index b89ce647..67bb0ca4 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -4,4 +4,5 @@ channels: - bioconda - defaults dependencies: - - bioconda::samtools=1.18 + - bioconda::samtools=1.19.2 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 7539140a..52b00f4b 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : - 'biocontainers/samtools:1.18--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : + 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index 20c3efe1..e3d5cb14 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -8,71 +8,58 @@ nextflow_process { tag "samtools" tag "samtools/stats" - test("SAMTOOLS STATS Should run without failures") { + test("bam") { when { params { - outdir = "$outputDir" } process { """ - // define inputs of the process here. - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) input[1] = [[],[]] """ - } } then { assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + {assert process.success}, + {assert snapshot(process.out).match()} ) } - } - test("SAMTOOLS CRAM Should run without failures") { + test("cram") { when { params { - outdir = "$outputDir" } process { """ - // define inputs of the process here - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) - - ] - input[1] = [ - [ id:'genome' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) """ } - - } then { assertAll( - {assert process.success}, - {assert snapshot(process.out).match()} + {assert process.success}, + {assert snapshot(process.out).match()} ) } - } - - } diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 025c83a5..1b7c9ba4 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "SAMTOOLS STATS Should run without failures": { + "cram": { "content": [ { "0": [ @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" + "test.stats:md5,01812900aa4027532906c5d431114233" ] ], "1": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ], "stats": [ [ @@ -20,17 +20,21 @@ "id": "test", "single_end": false }, - "test.stats:md5,045a48208b1c6f5b8af4347fe31f4def" + "test.stats:md5,01812900aa4027532906c5d431114233" ] ], "versions": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ] } ], - "timestamp": "2023-12-04T11:07:28.26821485" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:25.562429714" }, - "SAMTOOLS CRAM Should run without failures": { + "bam": { "content": [ { "0": [ @@ -39,11 +43,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" + "test.stats:md5,5d8681bf541199898c042bf400391d59" ] ], "1": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ], "stats": [ [ @@ -51,14 +55,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,dfbfa130d4a6925ddd1931dcd8354a43" + "test.stats:md5,5d8681bf541199898c042bf400391d59" ] ], "versions": [ - "versions.yml:md5,650a365c6635001436008350ae83337c" + "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" ] } ], - "timestamp": "2023-12-04T11:07:50.356233402" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:15:07.857611509" } } \ No newline at end of file diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index cc4f2ccb..28d13826 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -13,11 +13,11 @@ process SNPEFF_SNPEFF { tuple val(meta2), path(cache) output: - tuple val(meta), path("*.ann.vcf"), emit: vcf - path "*.csv" , emit: report - path "*.html" , emit: summary_html - path "*.genes.txt" , emit: genes_txt - path "versions.yml" , emit: versions + tuple val(meta), path("*.ann.vcf"), emit: vcf + tuple val(meta), path("*.csv"), emit: report + tuple val(meta), path("*.html"), emit: summary_html + tuple val(meta), path("*.genes.txt"), emit: genes_txt + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test new file mode 100644 index 00000000..dd37f275 --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -0,0 +1,50 @@ +nextflow_process { + + name "Test Process SNPEFF_SNPEFF" + script "../main.nf" + process "SNPEFF_SNPEFF" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "snpeff" + tag "snpeff/download" + tag "snpeff/snpeff" + + test("test_SNPEFF_SNPEFF") { + + setup { + run("SNPEFF_DOWNLOAD") { + script "../../download/main.nf" + process { + """ + input[0] = Channel.of([[id:params.snpeff_genome + '.' + params.snpeff_cache_version], params.snpeff_genome, params.snpeff_cache_version]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = params.snpeff_genome + '.' + params.snpeff_cache_version + input[2] = SNPEFF_DOWNLOAD.out.cache + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report[0][1]).exists() }, + { assert path(process.out.summary_html[0][1]).exists() }, + { assert path(process.out.vcf[0][1]).exists() }, + { assert snapshot(process.out.genes_txt).match("genes_txt") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap new file mode 100644 index 00000000..0891b844 --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,25d44a118d558b331d51ec00be0d997c" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-03-18T17:37:18.879477" + }, + "genes_txt": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.genes.txt:md5,130536bf0237d7f3f746d32aaa32840a" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.02.0" + }, + "timestamp": "2024-03-18T17:37:18.874822" + } +} \ No newline at end of file diff --git a/modules/nf-core/snpeff/snpeff/tests/nextflow.config b/modules/nf-core/snpeff/snpeff/tests/nextflow.config new file mode 100644 index 00000000..d31ebf6b --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/nextflow.config @@ -0,0 +1,4 @@ +params { + snpeff_cache_version = "105" + snpeff_genome = "WBcel235" +} diff --git a/modules/nf-core/snpeff/snpeff/tests/tags.yml b/modules/nf-core/snpeff/snpeff/tests/tags.yml new file mode 100644 index 00000000..427b588d --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/tests/tags.yml @@ -0,0 +1,2 @@ +snpeff/snpeff: + - "modules/nf-core/snpeff/snpeff/**" diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 36fcd022..8bd58cff 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -6,4 +6,5 @@ channels: dependencies: - bioconda::star=2.7.10a - bioconda::samtools=1.18 + - bioconda::htslib=1.18 - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 4c878474..6ecd7786 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -7,39 +7,40 @@ nextflow_process { tag "modules_nfcore" tag "star" tag "star/align" + tag "star/genomegenerate" - test("homo_sapiens - single_end") { - config "./nextflow.config" - - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ } } + } + + test("homo_sapiens - single_end") { + config "./nextflow.config" when { process { """ input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -74,38 +75,20 @@ nextflow_process { test("homo_sapiens - paired_end") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -140,38 +123,20 @@ nextflow_process { test("homo_sapiens - paired_end - arriba") { config "./nextflow.arriba.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -206,38 +171,20 @@ nextflow_process { test("homo_sapiens - paired_end - starfusion") { config "./nextflow.starfusion.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' @@ -272,40 +219,22 @@ nextflow_process { test("homo_sapiens - paired_end - multiple") { config "./nextflow.config" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" - process { - """ - input[0] = Channel.of([ - [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] - ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] - ]) - """ - } - } - } - when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) ] ]) input[1] = STAR_GENOMEGENERATE.out.index input[2] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) input[3] = false input[4] = 'illumina' diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 93e4476a..791f255e 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,11 +1,10 @@ name: star_genomegenerate - channels: - conda-forge - bioconda - defaults - dependencies: - bioconda::samtools=1.18 + - bioconda::htslib=1.18 - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index af0c9421..c17c8ba4 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -8,18 +8,18 @@ nextflow_process { tag "star" tag "star/genomegenerate" - test("homo_sapiens") { + test("fasta_gtf") { when { process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) """ } @@ -28,14 +28,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") }, + { assert snapshot(process.out.versions).match("fasta_gtf_versions") } ) } - } - test("homo_sapiens-stub") { + test("fasta_gtf_stub") { options '-stub' @@ -44,11 +43,11 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [ id:'test_gtf' ], - [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) """ } @@ -57,21 +56,20 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") }, + { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") } ) } - } - test("homo_sapiens-without_gtf") { + test("fasta") { when { process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [], [] ]) """ @@ -81,14 +79,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") }, + { assert snapshot(process.out.versions).match("fasta_versions") } ) } } - test("homo_sapiens-without_gtf-stub") { + test("fasta_stub") { options '-stub' @@ -97,7 +95,7 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test_fasta' ], - [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) input[1] = Channel.of([ [], [] ]) """ @@ -107,11 +105,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") }, + { assert snapshot(process.out.versions).match("fasta_stub_versions") } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 9de08c74..5653d6e6 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -1,22 +1,90 @@ { - "versions": { + "fasta_gtf_versions": { "content": [ [ "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" ] ], - "timestamp": "2023-12-19T11:05:51.741109" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:31.798555" }, - "index_with_gtf": { + "fasta_stub_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:55:07.521209" + }, + "fasta_gtf_stub_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:46.478098" + }, + "fasta_gtf_stub_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:46.491657" + }, + "fasta_index": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:57.552329" + }, + "fasta_versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:57.560541" + }, + "fasta_gtf_index": { "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" ], - "timestamp": "2023-12-19T11:38:14.551548" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:54:31.786814" }, - "index_without_gtf": { + "fasta_stub_index": { "content": [ "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" ], - "timestamp": "2023-12-19T11:38:22.382905" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-01T15:55:07.517472" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index 028461c9..c4235872 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index f9482690..bcdcf2a6 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : + 'biocontainers/htslib:1.19.1--h81da01d_1' }" input: tuple val(meta), path(input) @@ -35,7 +35,7 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.${input.getExtension()}.gz + echo "" | gzip > ${prefix}.${input.getExtension()}.gz touch ${prefix}.${input.getExtension()}.gz.tbi touch ${prefix}.${input.getExtension()}.gz.csi diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test new file mode 100644 index 00000000..87ea2c84 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -0,0 +1,94 @@ +nextflow_process { + + name "Test Process TABIX_BGZIPTABIX" + script "modules/nf-core/tabix/bgziptabix/main.nf" + process "TABIX_BGZIPTABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/bgziptabix" + + test("sarscov2_bed_tbi") { + config "./tabix_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'tbi_test' ], + [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_test") + } + ) + } + } + + test("sarscov2_bed_csi") { + config "./tabix_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'csi_test' ], + [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_test") + } + ) + } + + } + + test("sarscov2_bed_csi_stub") { + config "./tabix_csi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_csi[0][1]).name + ).match("csi_stub") + } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap new file mode 100644 index 00000000..fcecb2e4 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -0,0 +1,143 @@ +{ + "sarscov2_bed_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "tbi_test" + }, + "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4" + ] + ], + "versions": [ + "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + ] + } + ], + "timestamp": "2024-02-19T14:50:51.513838" + }, + "sarscov2_bed_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43" + ] + ], + "2": [ + "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + ], + "gz_csi": [ + [ + { + "id": "csi_test" + }, + "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", + "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43" + ] + ], + "gz_tbi": [ + + ], + "versions": [ + "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + ] + } + ], + "timestamp": "2024-02-19T14:51:00.513777" + }, + "csi_test": { + "content": [ + "csi_test.bed.gz" + ], + "timestamp": "2024-02-19T14:51:00.548801" + }, + "csi_stub": { + "content": [ + "test.bed.gz" + ], + "timestamp": "2024-02-19T14:51:09.218454" + }, + "tbi_test": { + "content": [ + "tbi_test.bed.gz" + ], + "timestamp": "2024-02-19T14:50:51.579654" + }, + "sarscov2_bed_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + ], + "gz_csi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + ] + } + ], + "timestamp": "2024-02-19T14:51:09.164254" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config new file mode 100644 index 00000000..fb41a314 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config new file mode 100644 index 00000000..c1915dc4 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tabix_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_BGZIPTABIX { + ext.args2 = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/tests/tags.yml b/modules/nf-core/tabix/bgziptabix/tests/tags.yml new file mode 100644 index 00000000..5052b4d7 --- /dev/null +++ b/modules/nf-core/tabix/bgziptabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/bgziptabix: + - "modules/nf-core/tabix/bgziptabix/**" diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 7167fb87..76b45e16 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -5,3 +5,4 @@ channels: - defaults dependencies: - bioconda::tabix=1.11 + - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index c304a8a3..1737141d 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,8 +4,8 @@ process TABIX_TABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' : - 'biocontainers/tabix:1.11--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : + 'biocontainers/htslib:1.19.1--h81da01d_1' }" input: tuple val(meta), path(tab) @@ -30,9 +30,9 @@ process TABIX_TABIX { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${tab}.tbi + touch ${tab}.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test new file mode 100644 index 00000000..3a150c70 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -0,0 +1,142 @@ +nextflow_process { + + name "Test Process TABIX_TABIX" + script "modules/nf-core/tabix/tabix/main.nf" + process "TABIX_TABIX" + + tag "modules" + tag "modules_nfcore" + tag "tabix" + tag "tabix/tabix" + + test("sarscov2_bedgz_tbi") { + config "./tabix_bed.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_bed' ], + [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.tbi[0][1]).name + ).match("tbi_bed") + } + ) + } + } + + test("sarscov2_gff_tbi") { + config "./tabix_gff.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_gff' ], + [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.tbi[0][1]).name + ).match("tbi_gff") + } + ) + } + + } + + test("sarscov2_vcf_tbi") { + config "./tabix_vcf_tbi.config" + when { + process { + """ + input[0] = [ + [ id:'tbi_vcf' ], + [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.tbi[0][1]).name + ).match("tbi_vcf") + } + ) + } + + } + + test("sarscov2_vcf_csi") { + config "./tabix_vcf_csi.config" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi' ], + [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.csi[0][1]).name + ).match("vcf_csi") + } + ) + } + + } + + test("sarscov2_vcf_csi_stub") { + config "./tabix_vcf_csi.config" + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'vcf_csi_stub' ], + [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.csi[0][1]).name + ).match("vcf_csi_stub") + } + ) + } + + } + +} diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap new file mode 100644 index 00000000..034e38b6 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -0,0 +1,217 @@ +{ + "vcf_csi_stub": { + "content": [ + "test.vcf.gz.csi" + ], + "timestamp": "2024-03-04T14:51:59.788002" + }, + "tbi_gff": { + "content": [ + "genome.gff3.gz.tbi" + ], + "timestamp": "2024-02-19T14:53:37.420216" + }, + "sarscov2_gff_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_gff" + }, + "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178" + ] + ], + "versions": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ] + } + ], + "timestamp": "2024-02-19T14:53:37.388157" + }, + "sarscov2_bedgz_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_bed" + }, + "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8" + ] + ], + "versions": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ] + } + ], + "timestamp": "2024-02-19T14:53:28.879408" + }, + "tbi_vcf": { + "content": [ + "test.vcf.gz.tbi" + ], + "timestamp": "2024-02-19T14:53:46.402522" + }, + "vcf_csi": { + "content": [ + "test.vcf.gz.csi" + ], + "timestamp": "2024-02-19T14:53:54.921189" + }, + "sarscov2_vcf_tbi": { + "content": [ + { + "0": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "tbi_vcf" + }, + "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf" + ] + ], + "versions": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ] + } + ], + "timestamp": "2024-02-19T14:53:46.370358" + }, + "sarscov2_vcf_csi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,3d45df6d80883bad358631069a2940fd" + ], + "csi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + [ + { + "id": "vcf_csi_stub" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3d45df6d80883bad358631069a2940fd" + ] + } + ], + "timestamp": "2024-03-04T14:51:59.766184" + }, + "sarscov2_vcf_csi": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03" + ] + ], + "2": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ], + "csi": [ + [ + { + "id": "vcf_csi" + }, + "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + ] + } + ], + "timestamp": "2024-02-19T14:53:54.886876" + }, + "tbi_bed": { + "content": [ + "test.bed.gz.tbi" + ], + "timestamp": "2024-02-19T14:53:28.947628" + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_bed.config b/modules/nf-core/tabix/tabix/tests/tabix_bed.config new file mode 100644 index 00000000..7ff05905 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_bed.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p bed' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_gff.config b/modules/nf-core/tabix/tabix/tests/tabix_gff.config new file mode 100644 index 00000000..20c0a1e3 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_gff.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p gff' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config new file mode 100644 index 00000000..eb4f2d7e --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_csi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf --csi' + } +} diff --git a/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config new file mode 100644 index 00000000..2774c8a9 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tabix_vcf_tbi.config @@ -0,0 +1,5 @@ +process { + withName: TABIX_TABIX { + ext.args = '-p vcf' + } +} \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/tests/tags.yml b/modules/nf-core/tabix/tabix/tests/tags.yml new file mode 100644 index 00000000..6eda0653 --- /dev/null +++ b/modules/nf-core/tabix/tabix/tests/tags.yml @@ -0,0 +1,2 @@ +tabix/tabix: + - "modules/nf-core/tabix/tabix/**" diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index d6917da3..0c9cbb10 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,9 +1,11 @@ name: untar + channels: - conda-forge - bioconda - defaults + dependencies: - - conda-forge::sed=4.7 - conda-forge::grep=3.11 + - conda-forge::sed=4.7 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index d40db13d..2a7c97bf 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -3,20 +3,15 @@ nextflow_process { name "Test Process UNTAR" script "../main.nf" process "UNTAR" - tag "modules" tag "modules_nfcore" tag "untar" - test("test_untar") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ] + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] """ } } @@ -30,37 +25,12 @@ nextflow_process { } - test("test_untar_different_output_path") { - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = [ [], file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) ] - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_different_output_path") }, - ) - } - - } - test("test_untar_onlyfiles") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ [], file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) ] + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] """ } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 146c8678..64550292 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,483 +1,4 @@ { - "test_untar_different_output_path": { - "content": [ - [ - [ - [ - - ], - [ - [ - [ - [ - [ - [ - "s_1_1101.bcl:md5,ad01889e2ff43e2f194224e20bdb600c", - 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newline at end of file diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index cbcf70a6..ac691b49 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -51,6 +51,12 @@ workflow RNAVAR { ch_known_indels ch_known_indels_tbi ch_star_index + snpeff_cache + vep_genome + vep_species + vep_cache_version + vep_cache + vep_extra_files seq_center seq_platform @@ -315,7 +321,7 @@ workflow RNAVAR { vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []] VCF_ANNOTATE_ALL( - ch_final_vcf, + ch_final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, vep_fasta, params.annotate_tools, params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}", @@ -324,7 +330,10 @@ workflow RNAVAR { vep_species, vep_cache_version, vep_cache, - vep_extra_files) + vep_extra_files, + [], // bcftools_annotations, + [], //bcftools_annotations_tbi, + []) //bcftools_header_lines) // Gather QC reports ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports) @@ -380,6 +389,8 @@ workflow RNAVAR { // MODULE: MultiQC // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report // + multiqc_report = Channel.empty() + if (!params.skip_multiqc){ ch_multiqc_files = Channel.empty() @@ -406,8 +417,8 @@ workflow RNAVAR { } emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [ path(versions.yml) ] + multiqc_report // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 233361c0b6086396cbe05b01443a079dbf62a498 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 29 May 2024 13:11:27 +0200 Subject: [PATCH 126/275] update subworkflows --- modules.json | 27 +- subworkflows/local/align_star/main.nf | 58 - subworkflows/local/bam_markduplicates/main.nf | 8 +- subworkflows/local/bam_stats_samtools/main.nf | 32 - subworkflows/local/prepare_genome/main.nf | 2 +- subworkflows/local/splitncigar/main.nf | 6 +- .../bam_sort_stats_samtools}/main.nf | 25 +- .../nf-core/bam_sort_stats_samtools/meta.yml | 70 ++ .../tests/main.nf.test | 82 ++ .../tests/main.nf.test.snap | 110 ++ .../bam_sort_stats_samtools/tests/tags.yml | 2 + .../nf-core/bam_stats_samtools/main.nf | 32 + .../nf-core/bam_stats_samtools/meta.yml | 43 + .../bam_stats_samtools/tests/main.nf.test | 108 ++ .../tests/main.nf.test.snap | 164 +++ .../nf-core/bam_stats_samtools/tests/tags.yml | 2 + subworkflows/nf-core/fastq_align_star/main.nf | 68 ++ .../nf-core/fastq_align_star/meta.yml | 133 +++ .../nf-core/fastq_align_star/nextflow.config | 10 + .../fastq_align_star/tests/main.nf.test | 262 +++++ .../fastq_align_star/tests/main.nf.test.snap | 1010 +++++++++++++++++ .../fastq_align_star/tests/nextflow.config | 21 + .../nf-core/fastq_align_star/tests/tags.yml | 2 + .../tests/with_transcripts.config | 21 + workflows/rnavar/main.nf | 22 +- 25 files changed, 2193 insertions(+), 127 deletions(-) delete mode 100644 subworkflows/local/align_star/main.nf delete mode 100644 subworkflows/local/bam_stats_samtools/main.nf rename subworkflows/{local/bam_sort_samtools => nf-core/bam_sort_stats_samtools}/main.nf (71%) create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/meta.yml create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml create mode 100644 subworkflows/nf-core/bam_stats_samtools/main.nf create mode 100644 subworkflows/nf-core/bam_stats_samtools/meta.yml create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_stats_samtools/tests/tags.yml create mode 100644 subworkflows/nf-core/fastq_align_star/main.nf create mode 100644 subworkflows/nf-core/fastq_align_star/meta.yml create mode 100644 subworkflows/nf-core/fastq_align_star/nextflow.config create mode 100644 subworkflows/nf-core/fastq_align_star/tests/main.nf.test create mode 100644 subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/fastq_align_star/tests/nextflow.config create mode 100644 subworkflows/nf-core/fastq_align_star/tests/tags.yml create mode 100644 subworkflows/nf-core/fastq_align_star/tests/with_transcripts.config diff --git a/modules.json b/modules.json index 852e55d4..cd08ab16 100755 --- a/modules.json +++ b/modules.json @@ -143,17 +143,17 @@ "samtools/flagstat": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/idxstats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/index": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/merge": { "branch": "master", @@ -163,12 +163,12 @@ "samtools/sort": { "branch": "master", "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", - "installed_by": ["modules"] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"] + "installed_by": ["bam_stats_samtools", "modules"] }, "snpeff/download": { "branch": "master", @@ -183,7 +183,7 @@ "star/align": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["modules"] + "installed_by": ["fastq_align_star", "modules"] }, "star/genomegenerate": { "branch": "master", @@ -209,6 +209,21 @@ }, "subworkflows": { "nf-core": { + "bam_sort_stats_samtools": { + "branch": "master", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", + "installed_by": ["fastq_align_star", "subworkflows"] + }, + "bam_stats_samtools": { + "branch": "master", + "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "installed_by": ["bam_sort_stats_samtools"] + }, + "fastq_align_star": { + "branch": "master", + "git_sha": "1d1d7df613ff53223259c14185858cd742cd4743", + "installed_by": ["subworkflows"] + }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf deleted file mode 100644 index 4949686f..00000000 --- a/subworkflows/local/align_star/main.nf +++ /dev/null @@ -1,58 +0,0 @@ -// -// Alignment with STAR -// - -include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main' -include { BAM_SORT_SAMTOOLS } from '../bam_sort_samtools/main' - -workflow ALIGN_STAR { - take: - reads // channel: [ val(meta), [ reads ] ] - index // channel: /path/to/star/index/ - gtf // channel: /path/to/genome.gtf - star_ignore_sjdbgtf // value: ignore gtf - seq_platform // value: sequencing platform - seq_center // value: sequencing centre - - main: - - ch_versions = Channel.empty() - - // - // Map reads with STAR - // - STAR_ALIGN ( - reads, - index, - gtf, - star_ignore_sjdbgtf, - seq_platform, - seq_center - ) - ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first()) - - // - // Sort, index BAM file and run samtools stats, flagstat and idxstats - // - BAM_SORT_SAMTOOLS ( - STAR_ALIGN.out.bam - ) - ch_versions = ch_versions.mix(BAM_SORT_SAMTOOLS.out.versions.first()) - - emit: - orig_bam = STAR_ALIGN.out.bam // channel: [ val(meta), bam ] - log_final = STAR_ALIGN.out.log_final // channel: [ val(meta), log_final ] - log_out = STAR_ALIGN.out.log_out // channel: [ val(meta), log_out ] - log_progress = STAR_ALIGN.out.log_progress // channel: [ val(meta), log_progress ] - bam_sorted = STAR_ALIGN.out.bam_sorted // channel: [ val(meta), bam_sorted ] - bam_transcript = STAR_ALIGN.out.bam_transcript // channel: [ val(meta), bam_transcript ] - fastq = STAR_ALIGN.out.fastq // channel: [ val(meta), fastq ] - tab = STAR_ALIGN.out.tab // channel: [ val(meta), tab ] - - bam = BAM_SORT_SAMTOOLS.out.bam // channel: [ val(meta), [ bam ] ] - bai = BAM_SORT_SAMTOOLS.out.bai // channel: [ val(meta), [ bai ] ] - csi = BAM_SORT_SAMTOOLS.out.csi // channel: [ val(meta), [ csi ] ] - reports = BAM_SORT_SAMTOOLS.out.reports - versions = ch_versions // channel: [ versions.yml ] - -} diff --git a/subworkflows/local/bam_markduplicates/main.nf b/subworkflows/local/bam_markduplicates/main.nf index 37d901b9..aa361fa3 100644 --- a/subworkflows/local/bam_markduplicates/main.nf +++ b/subworkflows/local/bam_markduplicates/main.nf @@ -4,7 +4,7 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' +include { BAM_STATS_SAMTOOLS } from '../../nf-core/bam_stats_samtools' include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main' include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' @@ -32,11 +32,13 @@ workflow BAM_MARKDUPLICATES { else [meta, bam, csi] } - BAM_STATS_SAMTOOLS(ch_bam_index) + BAM_STATS_SAMTOOLS(ch_bam_index, fasta) // Gather all reports generated ch_reports = ch_reports.mix(GATK4_MARKDUPLICATES.out.metrics) - ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.reports) + ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.stats) + ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.flagstat) + ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.idxstats) // Gather versions of all tools used ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) diff --git a/subworkflows/local/bam_stats_samtools/main.nf b/subworkflows/local/bam_stats_samtools/main.nf deleted file mode 100644 index 09fdd265..00000000 --- a/subworkflows/local/bam_stats_samtools/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -// -// Run SAMtools stats, flagstat and idxstats -// - -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' -include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' - -workflow BAM_STATS_SAMTOOLS { - take: - ch_bam_bai // channel: [ val(meta), [ bam ], [bai/csi] ] - - main: - ch_versions = Channel.empty() - ch_reports = Channel.empty() - - SAMTOOLS_FLAGSTAT(ch_bam_bai) - SAMTOOLS_IDXSTATS(ch_bam_bai) - SAMTOOLS_STATS(ch_bam_bai, [[],[]]) - - ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first()) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) - - ch_reports = ch_reports.mix(SAMTOOLS_STATS.out.stats) - ch_reports = ch_reports.mix(SAMTOOLS_FLAGSTAT.out.flagstat) - ch_reports = ch_reports.mix(SAMTOOLS_IDXSTATS.out.idxstats) - - emit: - reports = ch_reports - versions = ch_versions // channel: [ versions.yml ] -} diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 6b5a7d3b..a568e1a8 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -47,7 +47,7 @@ workflow PREPARE_GENOME { } GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) - GFFREAD(ch_gff) + GFFREAD(ch_gff, ch_fasta) SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) TABIX_DBSNP(ch_dbsnp.flatten().map{ it -> [ [ id:it.baseName ], it ] }) TABIX_KNOWN_INDELS(ch_known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index e479d34b..4040e8bb 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -10,7 +10,7 @@ workflow SPLITNCIGAR { take: bam // channel: [ val(meta), [ bam ], [bai] ] ch_fasta // channel: [ fasta ] - ch_fai // channel: [ fai ] + ch_fai // channel: [ fai ] ch_dict // channel: [ dict ] intervals // channel: [ interval_list] @@ -26,9 +26,9 @@ workflow SPLITNCIGAR { GATK4_SPLITNCIGARREADS( bam_interval, - ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta.map{ fasta -> [[id:'genome'], fasta] }, ch_fai, - ch_dict.map{ meta, dict -> [dict] }, + ch_dict ) bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions.first()) diff --git a/subworkflows/local/bam_sort_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf similarity index 71% rename from subworkflows/local/bam_sort_samtools/main.nf rename to subworkflows/nf-core/bam_sort_stats_samtools/main.nf index feabd8c9..b716375b 100644 --- a/subworkflows/local/bam_sort_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -6,22 +6,19 @@ include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' -workflow BAM_SORT_SAMTOOLS { +workflow BAM_SORT_STATS_SAMTOOLS { take: - ch_bam // channel: [ val(meta), [ bam ] ] + ch_bam // channel: [ val(meta), [ bam ] ] + ch_fasta // channel: [ val(meta), path(fasta) ] main: ch_versions = Channel.empty() - SAMTOOLS_SORT ( - ch_bam - ) + SAMTOOLS_SORT ( ch_bam, ch_fasta ) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) - SAMTOOLS_INDEX ( - SAMTOOLS_SORT.out.bam - ) + SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) SAMTOOLS_SORT.out.bam @@ -37,17 +34,17 @@ workflow BAM_SORT_SAMTOOLS { } .set { ch_bam_bai } - BAM_STATS_SAMTOOLS(ch_bam_bai) - - reports = BAM_STATS_SAMTOOLS.out.reports.map{meta, logs -> [logs] } - - ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions.first()) + BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta ) + ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) emit: bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), [ csi ] ] - reports + stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ] + flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ] + idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml new file mode 100644 index 00000000..e01f9ccf --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml @@ -0,0 +1,70 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: bam_sort_stats_samtools +description: Sort SAM/BAM/CRAM file +keywords: + - sort + - bam + - sam + - cram +components: + - samtools/sort + - samtools/index + - samtools/stats + - samtools/idxstats + - samtools/flagstat + - bam_stats_samtools +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" +# TODO Update when we decide on a standard for subworkflow docs +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - crai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - stats: + type: file + description: File containing samtools stats output + pattern: "*.{stats}" + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@ewels" +maintainers: + - "@drpatelh" + - "@ewels" diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test new file mode 100644 index 00000000..75b5b934 --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -0,0 +1,82 @@ +nextflow_workflow { + + name "Test Workflow BAM_SORT_STATS_SAMTOOLS" + script "../main.nf" + workflow "BAM_SORT_STATS_SAMTOOLS" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/bam_sort_stats_samtools" + tag "bam_sort_stats_samtools" + tag "subworkflows/bam_stats_samtools" + tag "bam_stats_samtools" + tag "samtools" + tag "samtools/index" + tag "samtools/sort" + tag "samtools/stats" + tag "samtools/idxstats" + tag "samtools/flagstat" + + test("test_bam_sort_stats_samtools_single_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, + { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, + { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_single_end_idxstats") } + ) + } + } + + test("test_bam_sort_stats_samtools_paired_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, + { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, + { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_paired_end_idxstats") } + ) + } + } +} diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap new file mode 100644 index 00000000..6645a092 --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -0,0 +1,110 @@ +{ + "test_bam_sort_stats_samtools_paired_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-10-22T20:25:03.687121177" + }, + "test_bam_sort_stats_samtools_paired_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-10-22T20:25:03.709648916" + }, + "test_bam_sort_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,cb0bf2b79de52fdf0c61e80efcdb0bb4" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:38.553256801" + }, + "test_bam_sort_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:48.355870518" + }, + "test_bam_sort_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:10:02.84631" + }, + "test_bam_sort_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:10:02.829756" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml new file mode 100644 index 00000000..30b69d6a --- /dev/null +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_sort_stats_samtools: + - subworkflows/nf-core/bam_sort_stats_samtools/** diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf new file mode 100644 index 00000000..44d4c010 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/main.nf @@ -0,0 +1,32 @@ +// +// Run SAMtools stats, flagstat and idxstats +// + +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_IDXSTATS } from '../../../modules/nf-core/samtools/idxstats/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' + +workflow BAM_STATS_SAMTOOLS { + take: + ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ] + ch_fasta // channel: [ val(meta), path(fasta) ] + + main: + ch_versions = Channel.empty() + + SAMTOOLS_STATS ( ch_bam_bai, ch_fasta ) + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) + + SAMTOOLS_FLAGSTAT ( ch_bam_bai ) + ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) + + SAMTOOLS_IDXSTATS ( ch_bam_bai ) + ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions) + + emit: + stats = SAMTOOLS_STATS.out.stats // channel: [ val(meta), path(stats) ] + flagstat = SAMTOOLS_FLAGSTAT.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = SAMTOOLS_IDXSTATS.out.idxstats // channel: [ val(meta), path(idxstats) ] + + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml new file mode 100644 index 00000000..809bf736 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -0,0 +1,43 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: bam_stats_samtools +description: Produces comprehensive statistics from SAM/BAM/CRAM file +keywords: + - statistics + - counts + - bam + - sam + - cram +components: + - samtools/stats + - samtools/idxstats + - samtools/flagstat +input: + - ch_bam_bai: + description: | + The input channel containing the BAM/CRAM and it's index + Structure: [ val(meta), path(bam), path(bai) ] + - ch_fasta: + description: | + Reference genome fasta file + Structure: [ path(fasta) ] +output: + - stats: + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] + - flagstat: + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] + - idxstats: + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats)] + - versions: + description: | + Files containing software versions + Structure: [ path(versions.yml) ] +authors: + - "@drpatelh" +maintainers: + - "@drpatelh" diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test new file mode 100644 index 00000000..c8b21f28 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_workflow { + + name "Test Workflow BAM_STATS_SAMTOOLS" + script "../main.nf" + workflow "BAM_STATS_SAMTOOLS" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "bam_stats_samtools" + tag "subworkflows/bam_stats_samtools" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/stats" + + test("test_bam_stats_samtools_single_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_single_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_idxstats") } + ) + } + } + + test("test_bam_stats_samtools_paired_end_cram") { + + when { + params { + outdir = "$outputDir" + } + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_cram_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_cram_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_cram_idxstats") } + ) + } + } + +} diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap new file mode 100644 index 00000000..bf0b0c69 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -0,0 +1,164 @@ +{ + "test_bam_stats_samtools_paired_end_cram_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:31:26.194017574" + }, + "test_bam_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,ddaf8f33fe9c1ebe9b06933213aec8ed" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:45:06.230091746" + }, + "test_bam_stats_samtools_paired_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:17:27.717482" + }, + "test_bam_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:26:10.340046381" + }, + "test_bam_stats_samtools_paired_end_cram_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:31:26.207052003" + }, + "test_bam_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,dc178e1a4956043aba8abc83e203521b" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:44:57.442208382" + }, + "test_bam_stats_samtools_paired_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-01-18T17:17:27.726719" + }, + "test_bam_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2023-11-06T09:26:10.349439801" + }, + "test_bam_stats_samtools_paired_end_cram_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d3345c4887f4a9ea4f7f56405b495db0" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.01.0" + }, + "timestamp": "2024-02-13T16:45:14.997164209" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml new file mode 100644 index 00000000..ec2f2d68 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_samtools/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_stats_samtools: + - subworkflows/nf-core/bam_stats_samtools/** diff --git a/subworkflows/nf-core/fastq_align_star/main.nf b/subworkflows/nf-core/fastq_align_star/main.nf new file mode 100644 index 00000000..00d553d9 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/main.nf @@ -0,0 +1,68 @@ +include { STAR_ALIGN } from '../../../modules/nf-core/star/align/main' +include { BAM_SORT_STATS_SAMTOOLS as BAM_SORT_STATS_SAMTOOLS_GENOME } from '../bam_sort_stats_samtools/main' +include { BAM_SORT_STATS_SAMTOOLS as BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME } from '../bam_sort_stats_samtools/main' + + +workflow FASTQ_ALIGN_STAR { + + take: + ch_reads // channel: [ val(meta), [ path(reads) ] ] + ch_index // channel: [ path(index) ] + ch_gtf // channel: [ path(gtf) ] + val_star_ignore_sjdbgtf // boolean: when using pre-built STAR indices do not re-extract and use splice junctions from the GTF file + val_seq_platform // string : sequencing platform + val_seq_center // string : sequencing center + ch_fasta // channel: [ val(meta), path(fasta) ] + ch_transcripts_fasta // channel: [ val(meta), path(fasta) ] + + main: + + ch_versions = Channel.empty() + + // + // Map reads with STAR + // + STAR_ALIGN ( ch_reads, ch_index, ch_gtf, val_star_ignore_sjdbgtf, val_seq_platform, val_seq_center ) + ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first()) + + // + // Sort, index BAM file and run samtools stats, flagstat and idxstats + // + BAM_SORT_STATS_SAMTOOLS_GENOME ( STAR_ALIGN.out.bam, ch_fasta ) + ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS_GENOME.out.versions) + + // + // Sort, index BAM file and run samtools stats, flagstat and idxstats + // + // Only runs when '--quantMode TranscriptomeSAM' is set in args and + // STAR_ALIGN.out.bam_transcript is populated + // + + BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME ( STAR_ALIGN.out.bam_transcript, ch_transcripts_fasta ) + ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME.out.versions) + + emit: + + orig_bam = STAR_ALIGN.out.bam // channel: [ val(meta), path(bam) ] + log_final = STAR_ALIGN.out.log_final // channel: [ val(meta), path(log_final) ] + log_out = STAR_ALIGN.out.log_out // channel: [ val(meta), path(log_out) ] + log_progress = STAR_ALIGN.out.log_progress // channel: [ val(meta), path(log_progress) ] + bam_sorted = STAR_ALIGN.out.bam_sorted // channel: [ val(meta), path(bam) ] + fastq = STAR_ALIGN.out.fastq // channel: [ val(meta), path(fastq) ] + tab = STAR_ALIGN.out.tab // channel: [ val(meta), path(tab) ] + orig_bam_transcript = STAR_ALIGN.out.bam_transcript // channel: [ val(meta), path(bam) ] + + bam = BAM_SORT_STATS_SAMTOOLS_GENOME.out.bam // channel: [ val(meta), path(bam) ] + bai = BAM_SORT_STATS_SAMTOOLS_GENOME.out.bai // channel: [ val(meta), path(bai) ] + stats = BAM_SORT_STATS_SAMTOOLS_GENOME.out.stats // channel: [ val(meta), path(stats) ] + flagstat = BAM_SORT_STATS_SAMTOOLS_GENOME.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = BAM_SORT_STATS_SAMTOOLS_GENOME.out.idxstats // channel: [ val(meta), path(idxstats) ] + + bam_transcript = BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME.out.bam // channel: [ val(meta), path(bam) ] + bai_transcript = BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME.out.bai // channel: [ val(meta), path(bai) ] + stats_transcript = BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME.out.stats // channel: [ val(meta), path(stats) ] + flagstat_transcript = BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats_transcript = BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME.out.idxstats // channel: [ val(meta), path(idxstats) ] + + versions = ch_versions // channel: [ path(versions.yml) ] +} diff --git a/subworkflows/nf-core/fastq_align_star/meta.yml b/subworkflows/nf-core/fastq_align_star/meta.yml new file mode 100644 index 00000000..796d3e4b --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/meta.yml @@ -0,0 +1,133 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fastq_align_star" +description: Align reads to a reference genome using bowtie2 then sort with samtools +keywords: + - align + - fasta + - genome + - reference +components: + - star/align + - samtools/sort + - samtools/index + - samtools/stats + - samtools/idxstats + - samtools/flagstat + - bam_sort_stats_samtools +input: + - ch_reads: + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + Structure: [ val(meta), [ path(reads) ] ] + - ch_index: + type: directory + description: STAR genome index + pattern: "star" + - ch_gtf: + type: file + description: | + GTF file used to set the splice junctions with the --sjdbGTFfile flag + pattern: "*.gtf" + - val_star_ignore_sjdbgtf: + type: boolean + description: | + If true the --sjdbGTFfile flag is set + pattern: "true|false" + - val_seq_platform: + type: string + description: | + Sequencing platform to be added to the bam header using the --outSAMattrRGline flag + - val_seq_center: + type: string + description: | + Sequencing center to be added to the bam header using the --outSAMattrRGline flag + - ch_fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa,fna}" + - ch_transcripts_fasta: + type: file + description: Optional reference genome fasta file + pattern: "*.{fasta,fa,fna}" +output: + - orig_bam: + description: | + Output BAM file containing read alignments + Structure: [ val(meta), path(bam) ] + - log_final: + description: | + STAR final log file + Structure: [ val(meta), path(log_final) ] + - log_out: + description: | + STAR log out file + Structure: [ val(meta), path(log_out) ] + - log_progress: + description: | + STAR log progress file + Structure: [ val(meta), path(log_progress) ] + - bam_sorted: + description: | + Sorted BAM file of read alignments (optional) + Structure: [ val(meta), path(bam) ] + - orig_bam_transcript: + description: | + Output BAM file of transcriptome alignment (optional) + Structure: [ val(meta), path(bam) ] + - fastq: + description: | + Unmapped FastQ files (optional) + Structure: [ val(meta), path(fastq) ] + - tab: + description: | + STAR output tab file(s) (optional) + Structure: [ val(meta), path(tab) ] + - bam: + description: | + BAM file ordered by samtools + Structure: [ val(meta), path(bam) ] + - bai: + description: | + BAI index of the ordered BAM file + Structure: [ val(meta), path(bai) ] + - stats: + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] + - flagstat: + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] + - idxstats: + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats) ] + - bam_transcript: + description: | + Transcriptome-level BAM file ordered by samtools (optional) + Structure: [ val(meta), path(bam) ] + - bai_transcript: + description: | + Transcriptome-level BAI index of the ordered BAM file (optional) + Structure: [ val(meta), path(bai) ] + - stats_transcript: + description: | + Transcriptome-level file containing samtools stats output (optional) + Structure: [ val(meta), path(stats) ] + - flagstat_transcript: + description: | + Transcriptome-level file containing samtools flagstat output (optional) + Structure: [ val(meta), path(flagstat) ] + - idxstats_transcript: + description: | + Transcriptome-level file containing samtools idxstats output (optional) + Structure: [ val(meta), path(idxstats) ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@JoseEspinosa" +maintainers: + - "@JoseEspinosa" diff --git a/subworkflows/nf-core/fastq_align_star/nextflow.config b/subworkflows/nf-core/fastq_align_star/nextflow.config new file mode 100644 index 00000000..926eae71 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/nextflow.config @@ -0,0 +1,10 @@ +// IMPORTANT: Add this configuration to your modules.config + +process { + withName: ".*:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:.*" { + ext.prefix = {"${meta.id}_genome"} + } + withName: ".*:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:.*" { + ext.prefix = {"${meta.id}_transcriptome"} + } +} diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test new file mode 100644 index 00000000..2c512c96 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test @@ -0,0 +1,262 @@ +nextflow_workflow { + + name "Test Subworkflow FASTQ_ALIGN_STAR" + script "../main.nf" + workflow "FASTQ_ALIGN_STAR" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_align_star" + tag "star/align" + tag "star/genomegenerate" + tag "rsem/preparereference" + tag "subworkflows/bam_sort_stats_samtools" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../../modules/nf-core/star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + test("homo_sapiens - fastq - single_end") { + config "./nextflow.config" + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = true // star_ignore_sjdbgtf + input[4] = 'illumina' // seq_platform + input[5] = false // seq_center + input[6] = Channel.of([ + [ id:'test_fasta' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[7] = Channel.of([[:], []]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.orig_bam).match('orig_bam_single_end')}, + { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_single_end')}, + { assert snapshot(workflow.out.fastq).match('fastq_single_end')}, + { assert snapshot(workflow.out.tab).match('tab_single_end')}, + { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_single_end')}, + { assert snapshot(workflow.out.bam).match('bam_single_end')}, + { assert snapshot(workflow.out.bai).match('bai_single_end')}, + { assert snapshot(workflow.out.stats).match('stats_single_end')}, + { assert snapshot(workflow.out.flagstat).match('flagstat_single_end')}, + { assert snapshot(workflow.out.idxstats).match('idxstats_single_end')}, + { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_single_end')}, + { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_single_end')}, + { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_single_end')}, + { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_single_end')}, + { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_single_end')}, + { assert path(workflow.out.log_out.get(0).get(1)).exists() }, + { assert path(workflow.out.log_final.get(0).get(1)).exists() }, + { assert path(workflow.out.log_progress.get(0).get(1)).exists() } + ) + } + } + + test("homo_sapiens - fastq - paired_end") { + config "./nextflow.config" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = true // star_ignore_sjdbgtf + input[4] = 'illumina' // seq_platform + input[5] = false // seq_center + input[6] = Channel.of([ + [ id:'test_fasta' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[7] = Channel.of([[:], []]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.orig_bam).match('orig_bam_paired_end')}, + { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_paired_end')}, + { assert snapshot(workflow.out.fastq).match('fastq_paired_end')}, + { assert snapshot(workflow.out.tab).match('tab_paired_end')}, + { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_paired_end')}, + { assert snapshot(workflow.out.bam).match('bam_paired_end')}, + { assert snapshot(workflow.out.bai).match('bai_paired_end')}, + { assert snapshot(workflow.out.stats).match('stats_paired_end')}, + { assert snapshot(workflow.out.flagstat).match('flagstat_paired_end')}, + { assert snapshot(workflow.out.idxstats).match('idxstats_paired_end')}, + { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_paired_end')}, + { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_paired_end')}, + { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_paired_end')}, + { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_paired_end')}, + { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_paired_end')}, + { assert snapshot(workflow.out.idxstats_transcript).match('versions_paired_end')}, + { assert path(workflow.out.log_out.get(0).get(1)).exists() }, + { assert path(workflow.out.log_final.get(0).get(1)).exists() }, + { assert path(workflow.out.log_progress.get(0).get(1)).exists() } + ) + } + } + + test("homo_sapiens - fastq - paired_end - with_transcriptome") { + config "./with_transcripts.config" + + setup { + run("RSEM_PREPAREREFERENCE") { + script "../../../../modules/nf-core/rsem/preparereference/main.nf" + process { + """ + input[0] = channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkifexists: true)) + input[1] = channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkifexists: true)) + """ + } + } + } + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = true // star_ignore_sjdbgtf + input[4] = 'illumina' // seq_platform + input[5] = false // seq_center + input[6] = Channel.of([ + [ id:'test_fasta' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[7] = RSEM_PREPAREREFERENCE.out.transcript_fasta.map{[[:], it]} + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.orig_bam).match('orig_bam_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.fastq).match('fastq_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.tab).match('tab_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.bam).match('bam_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.bai).match('bai_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.stats).match('stats_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.flagstat).match('flagstat_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.idxstats).match('idxstats_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_paired_end_with_transcriptome')}, + { assert snapshot(workflow.out.idxstats_transcript).match('versions_paired_end_with_transcriptome')}, + { assert path(workflow.out.log_out.get(0).get(1)).exists() }, + { assert path(workflow.out.log_final.get(0).get(1)).exists() }, + { assert path(workflow.out.log_progress.get(0).get(1)).exists() } + ) + } + } + + test("homo_sapiens - fastq - paired_end - transcripts - no_transcriptome") { + config "./with_transcripts.config" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = true // star_ignore_sjdbgtf + input[4] = 'illumina' // seq_platform + input[5] = false // seq_center + input[6] = Channel.of([ + [ id:'test_fasta' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[7] = Channel.of([[:], []]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.orig_bam).match('orig_bam_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.fastq).match('fastq_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.tab).match('tab_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.bam).match('bam_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.bai).match('bai_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.stats).match('stats_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.flagstat).match('flagstat_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.idxstats).match('idxstats_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_paired_end_transcripts_no_transcriptome')}, + { assert snapshot(workflow.out.idxstats_transcript).match('versions_paired_end_transcripts_no_transcriptome')}, + { assert path(workflow.out.log_out.get(0).get(1)).exists() }, + { assert path(workflow.out.log_final.get(0).get(1)).exists() }, + { assert path(workflow.out.log_progress.get(0).get(1)).exists() } + ) + } + } +} diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap new file mode 100644 index 00000000..989d38a6 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap @@ -0,0 +1,1010 @@ +{ + "flagstat_transcript_paired_end_with_transcriptome": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.flagstat:md5,a204dee59ef8b7cd0f7d952a80119b77" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T11:04:06.836115665" + }, + "orig_bam_paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.out.bam:md5,51d2ef198d5725978a4b6da6fbec17dd" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T19:37:37.493635239" + }, + "tab_paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T19:37:37.62565966" + }, + "stats_single_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.sorted.bam.stats:md5,2b8eb6967b68f03584cc242499658e92" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-16T11:01:51.011841774" + }, + "bam_sorted_single_end": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T19:36:01.366823434" + }, + "idxstats_paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.idxstats:md5,107ca94dd426cc44db316f0d402307c5" + ] + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-15T19:37:37.799888732" + }, + "fastq_paired_end_with_transcriptome": { + "content": [ + [ 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a/subworkflows/nf-core/fastq_align_star/tests/nextflow.config b/subworkflows/nf-core/fastq_align_star/tests/nextflow.config new file mode 100644 index 00000000..6af49d58 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/tests/nextflow.config @@ -0,0 +1,21 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat' + } + + withName: '.*:BAM_SORT_STATS_SAMTOOLS_.*:SAMTOOLS_.*' { + ext.prefix = { "${meta.id}.sorted" } + } + + withName: '.*:BAM_SORT_STATS_SAMTOOLS_.*:BAM_STATS_SAMTOOLS:.*' { + ext.prefix = { "${meta.id}.sorted.bam" } + } + +} diff --git a/subworkflows/nf-core/fastq_align_star/tests/tags.yml b/subworkflows/nf-core/fastq_align_star/tests/tags.yml new file mode 100644 index 00000000..a919a2d1 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/fastq_align_star: + - subworkflows/nf-core/fastq_align_star/** diff --git a/subworkflows/nf-core/fastq_align_star/tests/with_transcripts.config b/subworkflows/nf-core/fastq_align_star/tests/with_transcripts.config new file mode 100644 index 00000000..62f15250 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_star/tests/with_transcripts.config @@ -0,0 +1,21 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --quantMode TranscriptomeSAM' + } + + withName: '.*:BAM_SORT_STATS_SAMTOOLS_.*:SAMTOOLS_.*' { + ext.prefix = { "${meta.id}.sorted" } + } + + withName: '.*:BAM_SORT_STATS_SAMTOOLS_.*:BAM_STATS_SAMTOOLS:.*' { + ext.prefix = { "${meta.id}.sorted.bam" } + } + +} diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index ac691b49..b4c87b9b 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -10,13 +10,13 @@ include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcor include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { ALIGN_STAR } from '../../subworkflows/local/align_star' include { BAM_MARKDUPLICATES } from '../../subworkflows/local/bam_markduplicates' -include { GTF2BED } from '../../modules/local/gtf2bed' include { RECALIBRATE } from '../../subworkflows/local/recalibrate' include { SPLITNCIGAR } from '../../subworkflows/local/splitncigar' include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all' +include { FASTQ_ALIGN_STAR } from '../../subworkflows/nf-core/fastq_align_star' +include { GTF2BED } from '../../modules/local/gtf2bed' include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq' include { FASTQC } from '../../modules/nf-core/fastqc' include { GATK4_BASERECALIBRATOR } from '../../modules/nf-core/gatk4/baserecalibrator' @@ -123,21 +123,23 @@ workflow RNAVAR { ch_aligner_clustering_multiqc = Channel.empty() if (params.aligner == 'star') { - ALIGN_STAR(ch_cat_fastq, + FASTQ_ALIGN_STAR(ch_cat_fastq, ch_star_index, ch_gtf, params.star_ignore_sjdbgtf, seq_platform, - seq_center) + seq_center, + ch_fasta, + [[:],[]]) //ch_transcripts_fasta) - ch_genome_bam = ALIGN_STAR.out.bam - ch_genome_bam_index = ALIGN_STAR.out.bai - ch_transcriptome_bam = ALIGN_STAR.out.bam_transcript + ch_genome_bam = FASTQ_ALIGN_STAR.out.bam + ch_genome_bam_index = FASTQ_ALIGN_STAR.out.bai + ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.bam_transcript // Gather QC reports - ch_reports = ch_reports.mix(ALIGN_STAR.out.reports) - ch_reports = ch_reports.mix(ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(ALIGN_STAR.out.versions) + ch_reports = ch_reports.mix(FASTQ_ALIGN_STAR.out.log_out) + ch_reports = ch_reports.mix(FASTQ_ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) + ch_versions = ch_versions.mix(FASTQ_ALIGN_STAR.out.versions) // // SUBWORKFLOW: Mark duplicates with GATK4 From 993b2596801eb310d11f1ac04e3e2d1984a213f6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 29 May 2024 13:13:25 +0200 Subject: [PATCH 127/275] proper align --- subworkflows/local/vcf_annotate_bcftools/main.nf | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/vcf_annotate_bcftools/main.nf b/subworkflows/local/vcf_annotate_bcftools/main.nf index e54c52aa..f616af8c 100644 --- a/subworkflows/local/vcf_annotate_bcftools/main.nf +++ b/subworkflows/local/vcf_annotate_bcftools/main.nf @@ -3,8 +3,8 @@ // Run BCFtools to annotate VCF files // -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' +include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' +include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow VCF_ANNOTATE_BCFTOOLS { take: @@ -13,7 +13,6 @@ workflow VCF_ANNOTATE_BCFTOOLS { annotations_index // header_lines // - main: ch_versions = Channel.empty() @@ -22,12 +21,11 @@ workflow VCF_ANNOTATE_BCFTOOLS { ch_vcf_tbi = BCFTOOLS_ANNOTATE.out.vcf.join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true) - // Gather versions of all tools used ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) emit: vcf_tbi = ch_vcf_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - versions = ch_versions // path: versions.yml + versions = ch_versions // path: versions.yml } From 3f15db64a6bc519d3cd4629684be9344356a615f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 29 May 2024 14:13:42 +0200 Subject: [PATCH 128/275] fix workflow --- conf/modules.config | 6 +- modules.json | 19 ++- .../gatk4/markduplicates/environment.yml | 9 - modules/nf-core/gatk4/markduplicates/main.nf | 85 ---------- modules/nf-core/gatk4/markduplicates/meta.yml | 71 -------- .../gatk4/markduplicates/tests/bam.config | 8 - .../gatk4/markduplicates/tests/cram.config | 8 - .../gatk4/markduplicates/tests/main.nf.test | 126 -------------- .../markduplicates/tests/main.nf.test.snap | 160 ------------------ .../gatk4/markduplicates/tests/tags.yml | 2 - .../picard/markduplicates/environment.yml | 7 + modules/nf-core/picard/markduplicates/main.nf | 68 ++++++++ .../nf-core/picard/markduplicates/meta.yml | 79 +++++++++ .../picard/markduplicates/tests/main.nf.test | 92 ++++++++++ .../markduplicates/tests/main.nf.test.snap | 110 ++++++++++++ .../markduplicates/tests/nextflow.config | 6 + .../picard/markduplicates/tests/tags.yml | 2 + subworkflows/local/bam_markduplicates/main.nf | 53 ------ .../local/cram_qc_mosdepth_samtools/main.nf | 8 +- subworkflows/local/recalibrate/main.nf | 4 +- subworkflows/local/splitncigar/main.nf | 32 ++-- .../nf-core/bam_markduplicates_picard/main.nf | 54 ++++++ .../bam_markduplicates_picard/meta.yml | 71 ++++++++ .../tests/main.nf.test | 93 ++++++++++ .../tests/main.nf.test.snap | 30 ++++ .../bam_markduplicates_picard/tests/tags.yml | 2 + workflows/rnavar/main.nf | 74 ++++---- 27 files changed, 690 insertions(+), 589 deletions(-) delete mode 100644 modules/nf-core/gatk4/markduplicates/environment.yml delete mode 100644 modules/nf-core/gatk4/markduplicates/main.nf delete mode 100644 modules/nf-core/gatk4/markduplicates/meta.yml delete mode 100644 modules/nf-core/gatk4/markduplicates/tests/bam.config delete mode 100644 modules/nf-core/gatk4/markduplicates/tests/cram.config delete mode 100644 modules/nf-core/gatk4/markduplicates/tests/main.nf.test delete mode 100644 modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap delete mode 100644 modules/nf-core/gatk4/markduplicates/tests/tags.yml create mode 100644 modules/nf-core/picard/markduplicates/environment.yml create mode 100644 modules/nf-core/picard/markduplicates/main.nf create mode 100644 modules/nf-core/picard/markduplicates/meta.yml create mode 100644 modules/nf-core/picard/markduplicates/tests/main.nf.test create mode 100644 modules/nf-core/picard/markduplicates/tests/main.nf.test.snap create mode 100644 modules/nf-core/picard/markduplicates/tests/nextflow.config create mode 100644 modules/nf-core/picard/markduplicates/tests/tags.yml delete mode 100644 subworkflows/local/bam_markduplicates/main.nf create mode 100644 subworkflows/nf-core/bam_markduplicates_picard/main.nf create mode 100644 subworkflows/nf-core/bam_markduplicates_picard/meta.yml create mode 100644 subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test create mode 100644 subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml diff --git a/conf/modules.config b/conf/modules.config index 5280c36d..6890a8ed 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -184,13 +184,13 @@ process { publishDir = [ enabled: false ] } - withName: 'GATK4_MARKDUPLICATES' { + withName: 'PICARD_MARKDUPLICATES' { ext.args = [ '--ASSUME_SORTED true', '--VALIDATION_STRINGENCY LENIENT', params.remove_duplicates ? '--REMOVE_DUPLICATES true' : '' ].join(' ').trim() - ext.prefix = {"${meta.id}.md.bam"} + ext.prefix = {"${meta.id}.md"} publishDir = [ [ path: { "${params.outdir}/preprocessing/${meta.id}" }, @@ -207,7 +207,7 @@ process { ] } - withName: '.*:BAM_MARKDUPLICATES:SAMTOOLS_INDEX' { + withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.md"} publishDir = [ diff --git a/modules.json b/modules.json index cd08ab16..cb3f9bf5 100755 --- a/modules.json +++ b/modules.json @@ -95,11 +95,6 @@ "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105", "installed_by": ["modules"] }, - "gatk4/markduplicates": { - "branch": "master", - "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", - "installed_by": ["modules"] - }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", @@ -135,6 +130,11 @@ "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] }, + "picard/markduplicates": { + "branch": "master", + "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087", + "installed_by": ["bam_markduplicates_picard"] + }, "samtools/faidx": { "branch": "master", "git_sha": "f153f1f10e1083c49935565844cccb7453021682", @@ -153,7 +153,7 @@ "samtools/index": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_sort_stats_samtools", "modules"] + "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"] }, "samtools/merge": { "branch": "master", @@ -209,6 +209,11 @@ }, "subworkflows": { "nf-core": { + "bam_markduplicates_picard": { + "branch": "master", + "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087", + "installed_by": ["subworkflows"] + }, "bam_sort_stats_samtools": { "branch": "master", "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", @@ -217,7 +222,7 @@ "bam_stats_samtools": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"] }, "fastq_align_star": { "branch": "master", diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml deleted file mode 100644 index 7362eea6..00000000 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ -name: gatk4_markduplicates -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::gatk4=4.5.0.0 - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf deleted file mode 100644 index baadefef..00000000 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ /dev/null @@ -1,85 +0,0 @@ -process GATK4_MARKDUPLICATES { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:7cc3d06cbf42e28c5e2ebfc7c858654c7340a9d5-0': - 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:7cc3d06cbf42e28c5e2ebfc7c858654c7340a9d5-0' }" - - input: - tuple val(meta), path(bam) - path fasta - path fasta_fai - - output: - tuple val(meta), path("*cram"), emit: cram, optional: true - tuple val(meta), path("*bam"), emit: bam, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true - tuple val(meta), path("*.metrics"), emit: metrics - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}.bam" - - // If the extension is CRAM, then change it to BAM - prefix_bam = prefix.tokenize('.')[-1] == 'cram' ? "${prefix.substring(0, prefix.lastIndexOf('.'))}.bam" : prefix - - def input_list = bam.collect{"--INPUT $it"}.join(' ') - def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" - - def avail_mem = 3072 - if (!task.memory) { - log.info '[GATK MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() - } - - // Using samtools and not Markduplicates to compress to CRAM speeds up computation: - // https://medium.com/@acarroll.dna/looking-at-trade-offs-in-compression-levels-for-genomics-tools-eec2834e8b94 - """ - gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ - MarkDuplicates \\ - $input_list \\ - --OUTPUT ${prefix_bam} \\ - --METRICS_FILE ${prefix}.metrics \\ - --TMP_DIR . \\ - ${reference} \\ - $args - - # If cram files are wished as output, the run samtools for conversion - if [[ ${prefix} == *.cram ]]; then - samtools view -Ch -T ${fasta} -o ${prefix} ${prefix_bam} - rm ${prefix_bam} - samtools index ${prefix} - fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ - - stub: - prefix = task.ext.prefix ?: "${meta.id}.bam" - prefix_no_suffix = task.ext.prefix ? prefix.tokenize('.')[0] : "${meta.id}" - """ - touch ${prefix_no_suffix}.bam - touch ${prefix_no_suffix}.cram - touch ${prefix_no_suffix}.cram.crai - touch ${prefix_no_suffix}.bai - touch ${prefix}.metrics - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml deleted file mode 100644 index b0f09d4b..00000000 --- a/modules/nf-core/gatk4/markduplicates/meta.yml +++ /dev/null @@ -1,71 +0,0 @@ -name: gatk4_markduplicates -description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. -keywords: - - bam - - gatk4 - - markduplicates - - sort -tools: - - gatk4: - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- - tool_dev_url: https://github.com/broadinstitute/gatk - doi: 10.1158/1538-7445.AM2017-3590 - licence: ["MIT"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta}" - - fasta_fai: - type: file - description: Fasta index file - pattern: "*.{fai}" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Marked duplicates BAM file - pattern: "*.{bam}" - - cram: - type: file - description: Marked duplicates CRAM file - pattern: "*.{cram}" - - bai: - type: file - description: BAM index file - pattern: "*.{bam.bai}" - - crai: - type: file - description: CRAM index file - pattern: "*.{cram.crai}" - - metrics: - type: file - description: Duplicate metrics file generated by GATK - pattern: "*.{metrics.txt}" -authors: - - "@ajodeh-juma" - - "@FriederikeHanssen" - - "@maxulysse" -maintainers: - - "@ajodeh-juma" - - "@FriederikeHanssen" - - "@maxulysse" diff --git a/modules/nf-core/gatk4/markduplicates/tests/bam.config b/modules/nf-core/gatk4/markduplicates/tests/bam.config deleted file mode 100644 index 0bbfbac3..00000000 --- a/modules/nf-core/gatk4/markduplicates/tests/bam.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - withName: GATK4_MARKDUPLICATES { - ext.args = '--CREATE_INDEX true' - ext.prefix = { "${meta.id}.bam" } - } - -} diff --git a/modules/nf-core/gatk4/markduplicates/tests/cram.config b/modules/nf-core/gatk4/markduplicates/tests/cram.config deleted file mode 100644 index 04a9b074..00000000 --- a/modules/nf-core/gatk4/markduplicates/tests/cram.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - withName: GATK4_MARKDUPLICATES { - ext.args = '--CREATE_INDEX true' - ext.prefix = { "${meta.id}.cram" } - } - -} diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test deleted file mode 100644 index bbcf74db..00000000 --- a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test +++ /dev/null @@ -1,126 +0,0 @@ -nextflow_process { - - name "Test Process GATK4_MARKDUPLICATES" - script "../main.nf" - process "GATK4_MARKDUPLICATES" - - tag "modules" - tag "modules_nfcore" - tag "gatk4" - tag "gatk4/markduplicates" - - test("sarscov2 - bam") { - config "./bam.config" - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ] - input[1] = [] - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.bam).match("bam") }, - { assert snapshot(process.out.bai).match("bai") }, - { assert snapshot(process.out.versions).match("versions") }, - { assert snapshot(file(process.out.metrics[0][1]).name).match("test.metrics") } - ) - } - } - - test("homo_sapiens - multiple bam") { - config "./bam.config" - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) - ] - ] - input[1] = [] - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.bam).match("multi bam") }, - { assert snapshot(process.out.bai).match("multi bai") }, - { assert snapshot(process.out.versions).match("multi versions") }, - { assert snapshot(file(process.out.metrics[0][1]).name).match("multi test.metrics") } - ) - } - - } - - test("homo_sapiens - multiple cram") { - config "./cram.config" - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) - ] - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(file(process.out.cram[0][1]).name).match("multi cram")}, - { assert snapshot(file(process.out.crai[0][1]).name).match("multi crai") }, - { assert snapshot(process.out.versions).match("multi cram versions") }, - { assert snapshot(file(process.out.metrics[0][1]).name).match("multi cram test.metrics") } - ) - } - - } - - test("stub") { - config "./bam.config" - options "-stub" - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], - [] - ] - input[1] = [] - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success } - ) - } - - } - -} diff --git a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap b/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap deleted file mode 100644 index 336bb373..00000000 --- a/modules/nf-core/gatk4/markduplicates/tests/main.nf.test.snap +++ /dev/null @@ -1,160 +0,0 @@ -{ - "multi bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,8a808b1a94d2627c4d659a2151c4cb9f" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-02-13T15:21:36.059923" - }, - "multi crai": { - "content": [ - "test.cram.crai" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2023-12-12T17:43:37.780426007" - }, - "multi bai": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bai:md5,38b99c5f771895ecf5324c3186b9d452" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-02-13T15:21:36.09642" - }, - "versions": { - "content": [ - [ - "versions.yml:md5,c58bf16c6e3786cc4d17bb7249f9ffe5" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-02-13T15:21:08.710549" - }, - "multi test.metrics": { - "content": [ - "test.bam.metrics" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2023-12-12T17:43:11.732892667" - }, - "bai": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bai:md5,26001bcdbce12e9f07557d8f7b8d360e" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2023-12-12T17:42:39.651888758" - }, - "multi cram versions": { - "content": [ - [ - "versions.yml:md5,c58bf16c6e3786cc4d17bb7249f9ffe5" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-02-13T15:21:56.966376" - }, - "multi versions": { - "content": [ - [ - "versions.yml:md5,c58bf16c6e3786cc4d17bb7249f9ffe5" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-02-13T15:21:36.138095" - }, - "multi cram test.metrics": { - "content": [ - "test.cram.metrics" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2023-12-12T17:43:37.798977444" - }, - "multi cram": { - "content": [ - "test.cram" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2023-12-12T17:43:37.771137858" - }, - "bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,75d914ba8804eaf2acf02ab432197ec9" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2024-02-13T15:21:08.645892" - }, - "test.metrics": { - "content": [ - "test.bam.metrics" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, - "timestamp": "2023-12-12T17:42:39.672508385" - } -} \ No newline at end of file diff --git a/modules/nf-core/gatk4/markduplicates/tests/tags.yml b/modules/nf-core/gatk4/markduplicates/tests/tags.yml deleted file mode 100644 index 8632e32b..00000000 --- a/modules/nf-core/gatk4/markduplicates/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -gatk4/markduplicates: - - "modules/nf-core/gatk4/markduplicates/**" diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml new file mode 100644 index 00000000..58b795f5 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -0,0 +1,7 @@ +name: picard_markduplicates +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::picard=3.1.1 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf new file mode 100644 index 00000000..ad0b2963 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -0,0 +1,68 @@ +process PICARD_MARKDUPLICATES { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : + 'biocontainers/picard:3.1.1--hdfd78af_0' }" + + input: + tuple val(meta), path(reads) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + + output: + tuple val(meta), path("*.bam") , emit: bam, optional: true + tuple val(meta), path("*.bai") , emit: bai, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.metrics.txt"), emit: metrics + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" + def avail_mem = 3072 + if (!task.memory) { + log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + + if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + + """ + picard \\ + -Xmx${avail_mem}M \\ + MarkDuplicates \\ + $args \\ + --INPUT $reads \\ + --OUTPUT ${prefix}.${suffix} \\ + $reference \\ + --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ?: "${reads.getExtension()}" + if ("$reads" == "${prefix}.${suffix}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.${suffix} + touch ${prefix}.MarkDuplicates.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ +} diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml new file mode 100644 index 00000000..1f0ffe16 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -0,0 +1,79 @@ +name: picard_markduplicates +description: Locate and tag duplicate reads in a BAM file +keywords: + - markduplicates + - pcr + - duplicates + - bam + - sam + - cram +tools: + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://broadinstitute.github.io/picard/ + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file, required for CRAM input + pattern: "*.{fasta,fa}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference genome fasta index + pattern: "*.{fai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" + - bai: + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag + pattern: "*.{bai}" + - cram: + type: file + description: Output CRAM file + pattern: "*.{cram}" + - metrics: + type: file + description: Duplicate metrics file generated by picard + pattern: "*.{metrics.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@projectoriented" + - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@projectoriented" + - "@ramprasadn" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test new file mode 100644 index 00000000..e3e97f6c --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -0,0 +1,92 @@ +nextflow_process { + + name "Test Process PICARD_MARKDUPLICATES" + script "../main.nf" + process "PICARD_MARKDUPLICATES" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/markduplicates" + + test("sarscov2 [unsorted bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("unsorted_bam_name") }, + { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("unsorted_bam_metrics") }, + { assert snapshot(process.out.versions).match("unsorted_bam_versions") } + ) + } + } + + test("sarscov2 [sorted bam]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("sorted_bam_name") }, + { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("sorted_bam_metrics") }, + { assert snapshot(process.out.versions).match("sorted_bam_versions") } + ) + } + } + + test("homo_sapiens [cram]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.cram[0][1]).name).match("cram_name") }, + { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("cram_metrics") }, + { assert snapshot(process.out.versions).match("cram_versions") } + ) + } + } +} diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap new file mode 100644 index 00000000..eb17111e --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -0,0 +1,110 @@ +{ + "sorted_bam_versions": { + "content": [ + [ + "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T15:31:50.928021" + }, + "unsorted_bam_name": { + "content": [ + "test.marked.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-19T10:26:28.100755" + }, + "cram_metrics": { + "content": [ + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T15:25:47.518152" + }, + "sorted_bam_metrics": { + "content": [ + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-21T11:39:10.318331" + }, + "cram_name": { + "content": [ + "test.marked.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T15:25:47.459663" + }, + "cram_versions": { + "content": [ + [ + "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-19T10:27:03.26989" + }, + "unsorted_bam_versions": { + "content": [ + [ + "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T15:31:24.040403" + }, + "unsorted_bam_metrics": { + "content": [ + [ + "## htsjdk.samtools.metrics.StringHeader", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "## htsjdk.samtools.metrics.StringHeader" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-21T10:51:12.831787" + }, + "sorted_bam_name": { + "content": [ + "test.marked.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-01-19T10:26:45.080116" + } +} \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/tests/nextflow.config b/modules/nf-core/picard/markduplicates/tests/nextflow.config new file mode 100644 index 00000000..02818dd6 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: PICARD_MARKDUPLICATES { + ext.prefix = { "${meta.id}.marked" } + ext.args = '--ASSUME_SORT_ORDER queryname' + } +} diff --git a/modules/nf-core/picard/markduplicates/tests/tags.yml b/modules/nf-core/picard/markduplicates/tests/tags.yml new file mode 100644 index 00000000..4f213d62 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/tests/tags.yml @@ -0,0 +1,2 @@ +picard/markduplicates: + - modules/nf-core/picard/markduplicates/** diff --git a/subworkflows/local/bam_markduplicates/main.nf b/subworkflows/local/bam_markduplicates/main.nf deleted file mode 100644 index aa361fa3..00000000 --- a/subworkflows/local/bam_markduplicates/main.nf +++ /dev/null @@ -1,53 +0,0 @@ -// -// MARKDUPLICATES AND QC after mapping -// -// For all modules here: -// A when clause condition is defined in the conf/modules.config to determine if the module should be run - -include { BAM_STATS_SAMTOOLS } from '../../nf-core/bam_stats_samtools' -include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' - -workflow BAM_MARKDUPLICATES { - take: - bam // channel: [mandatory] [ meta, bam ] - fasta // channel: [mandatory] [ fasta ] - fasta_fai // channel: [mandatory] [ fasta_fai ] - intervals_bed_combined // channel: [optional] [ intervals_bed ] - - main: - ch_versions = Channel.empty() - ch_reports = Channel.empty() - - // RUN MARKUPDUPLICATES - GATK4_MARKDUPLICATES(bam, fasta, fasta_fai) - - SAMTOOLS_INDEX(GATK4_MARKDUPLICATES.out.bam) - - ch_bam_index = GATK4_MARKDUPLICATES.out.bam - .join(SAMTOOLS_INDEX.out.bai, remainder: true) - .join(SAMTOOLS_INDEX.out.csi, remainder: true) - .map{meta, bam, bai, csi -> - if (bai) [meta, bam, bai] - else [meta, bam, csi] - } - - BAM_STATS_SAMTOOLS(ch_bam_index, fasta) - - // Gather all reports generated - ch_reports = ch_reports.mix(GATK4_MARKDUPLICATES.out.metrics) - ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.stats) - ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.flagstat) - ch_reports = ch_reports.mix(BAM_STATS_SAMTOOLS.out.idxstats) - - // Gather versions of all tools used - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - ch_versions = ch_versions.mix(GATK4_MARKDUPLICATES.out.versions) - ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) - - emit: - bam = ch_bam_index - reports = ch_reports - - versions = ch_versions // channel: [ versions.yml ] -} diff --git a/subworkflows/local/cram_qc_mosdepth_samtools/main.nf b/subworkflows/local/cram_qc_mosdepth_samtools/main.nf index fd070a68..e2b51418 100644 --- a/subworkflows/local/cram_qc_mosdepth_samtools/main.nf +++ b/subworkflows/local/cram_qc_mosdepth_samtools/main.nf @@ -4,8 +4,8 @@ // For all modules here: // A when clause condition is defined in the conf/modules.config to determine if the module should be run -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' -include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { MOSDEPTH } from '../../../modules/nf-core/mosdepth/main' workflow CRAM_QC_MOSDEPTH_SAMTOOLS { take: @@ -18,9 +18,9 @@ workflow CRAM_QC_MOSDEPTH_SAMTOOLS { reports = Channel.empty() // Reports run on cram - SAMTOOLS_STATS(cram, fasta.map{ it -> [ [ id:'fasta' ], it ] }) + SAMTOOLS_STATS(cram, fasta) - MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed?:[] ] }), fasta.map{ it -> [ [ id:'fasta' ], it ] }) + MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed ?: [] ] }), fasta) // Gather all reports generated reports = reports.mix(SAMTOOLS_STATS.out.stats) diff --git a/subworkflows/local/recalibrate/main.nf b/subworkflows/local/recalibrate/main.nf index 518e9fb2..bbf80e1b 100644 --- a/subworkflows/local/recalibrate/main.nf +++ b/subworkflows/local/recalibrate/main.nf @@ -5,8 +5,8 @@ */ include { GATK4_APPLYBQSR as APPLYBQSR } from '../../../modules/nf-core/gatk4/applybqsr/main' -include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' workflow RECALIBRATE { take: diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 4040e8bb..91524e64 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -17,35 +17,24 @@ workflow SPLITNCIGAR { main: ch_versions = Channel.empty() - bam_interval = bam.combine(intervals).map{ meta, bam, bai, intervals -> - def new_meta = meta.clone() - new_meta.id = meta.id + "_" + intervals.baseName - new_meta.sample = meta.id - [new_meta, bam, bai, intervals] - } + bam_interval = bam.combine(intervals).map{ meta, bam, bai, intervals -> [ meta + [sample:meta.id], bam, bai, intervals ] } + + GATK4_SPLITNCIGARREADS(bam_interval, + ch_fasta, + ch_fai.map{ fai -> [[id:'genome'], fai] }, + ch_dict) - GATK4_SPLITNCIGARREADS( - bam_interval, - ch_fasta.map{ fasta -> [[id:'genome'], fasta] }, - ch_fai, - ch_dict - ) bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam - ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions.first()) + ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions) - bam_splitncigar_interval = bam_splitncigar - .map{ meta, bam -> - def new_meta = meta.clone() - new_meta.id = meta.sample - [new_meta, bam] - }.groupTuple() + bam_splitncigar_interval = bam_splitncigar.map{ meta, bam -> [ meta + [id:meta.sample] - meta.subMap('sample'), bam ] }.groupTuple() SAMTOOLS_MERGE(bam_splitncigar_interval, ch_fasta, ch_fai.map{ fai -> [[id:fai.baseName], fai] }) splitncigar_bam = SAMTOOLS_MERGE.out.bam - ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions.first()) + ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) SAMTOOLS_INDEX(splitncigar_bam) @@ -56,7 +45,8 @@ workflow SPLITNCIGAR { if (bai) [meta, bam, bai] else [meta, bam, csi] } - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) emit: bam_bai = splitncigar_bam_bai diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf new file mode 100644 index 00000000..2de059b8 --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf @@ -0,0 +1,54 @@ +// +// Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats +// + +include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { BAM_STATS_SAMTOOLS } from '../bam_stats_samtools/main' + +workflow BAM_MARKDUPLICATES_PICARD { + + take: + ch_reads // channel: [ val(meta), path(reads) ] + ch_fasta // channel: [ path(fasta) ] + ch_fai // channel: [ path(fai) ] + + main: + + ch_versions = Channel.empty() + + PICARD_MARKDUPLICATES ( ch_reads, ch_fasta, ch_fai ) + ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions.first()) + + ch_markdup = PICARD_MARKDUPLICATES.out.bam.mix(PICARD_MARKDUPLICATES.out.cram) + + SAMTOOLS_INDEX ( ch_markdup ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + + ch_reads_index = ch_markdup + .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) + .join(SAMTOOLS_INDEX.out.crai, by: [0], remainder: true) + .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) + .map{meta, reads, bai, crai, csi -> + if (bai) [ meta, reads, bai ] + else if (crai) [ meta, reads, crai ] + else [ meta, reads, csi ] + } + + BAM_STATS_SAMTOOLS ( ch_reads_index, ch_fasta ) + ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions) + + emit: + bam = PICARD_MARKDUPLICATES.out.bam // channel: [ val(meta), path(bam) ] + cram = PICARD_MARKDUPLICATES.out.cram // channel: [ val(meta), path(cram) ] + metrics = PICARD_MARKDUPLICATES.out.metrics // channel: [ val(meta), path(metrics) ] + bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), path(bai) ] + crai = SAMTOOLS_INDEX.out.crai // channel: [ val(meta), path(crai) ] + csi = SAMTOOLS_INDEX.out.csi // channel: [ val(meta), path(csi) ] + + stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), path(stats) ] + flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), path(flagstat) ] + idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ] + + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/bam_markduplicates_picard/meta.yml b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml new file mode 100644 index 00000000..433d35b2 --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/meta.yml @@ -0,0 +1,71 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "bam_markduplicates_picard" +description: Picard MarkDuplicates, index BAM file and run samtools stats, flagstat and idxstats +keywords: + - markduplicates + - bam + - sam + - cram +components: + - picard/markduplicates + - samtools/index + - samtools/stats + - samtools/idxstats + - samtools/flagstat + - bam_stats_samtools +input: + - ch_reads: + description: | + Sequence reads in BAM/CRAM/SAM format + Structure: [ val(meta), path(reads) ] + - ch_fasta: + description: | + Reference genome fasta file required for CRAM input + Structure: [ path(fasta) ] + - ch_fasta: + description: | + Index of the reference genome fasta file + Structure: [ path(fai) ] +output: + - bam: + description: | + processed BAM/SAM file + Structure: [ val(meta), path(bam) ] + - bai: + description: | + BAM/SAM samtools index + Structure: [ val(meta), path(bai) ] + - cram: + description: | + processed CRAM file + Structure: [ val(meta), path(cram) ] + - crai: + description: | + CRAM samtools index + Structure: [ val(meta), path(crai) ] + - csi: + description: | + CSI samtools index + Structure: [ val(meta), path(csi) ] + - stats: + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] + - flagstat: + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] + - idxstats: + description: | + File containing samtools idxstats output + Structure: [ val(meta), path(idxstats) ] + - versions: + description: | + Files containing software versions + Structure: [ path(versions.yml) ] +authors: + - "@dmarron" + - "@drpatelh" +maintainers: + - "@dmarron" + - "@drpatelh" diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test new file mode 100644 index 00000000..5ef337dc --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -0,0 +1,93 @@ +nextflow_workflow { + + name "Test Workflow BAM_MARKDUPLICATES_PICARD" + script "../main.nf" + workflow "BAM_MARKDUPLICATES_PICARD" + + tag "picard" + tag "picard/markduplicates" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "bam_markduplicates_picard" + tag "subworkflows/bam_markduplicates_picard" + tag "subworkflows/bam_stats_samtools" + tag "bam_stats_samtools" + tag "samtools" + tag "samtools/flagstat" + tag "samtools/idxstats" + tag "samtools/index" + tag "samtools/stats" + + test("sarscov2 - bam") { + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end: false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + path(workflow.out.bam[0][1]), + path(workflow.out.bai[0][1]), + path(workflow.out.flagstat[0][1]), + path(workflow.out.idxstats[0][1]), + path(workflow.out.stats[0][1]), + ).match("sarscov2 - bam") }, + { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("97") } + ) + } + } + + test("homo_sapiens - cram") { + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + file(workflow.out.cram[0][1]).name, + path(workflow.out.crai[0][1]), + path(workflow.out.flagstat[0][1]), + path(workflow.out.idxstats[0][1]), + path(workflow.out.stats[0][1]), + ).match("homo_sapiens - cram") }, + { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("0.999986") } + ) + } + } + +} diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap new file mode 100644 index 00000000..caf4ac8a --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "homo_sapiens - cram": { + "content": [ + "test.cram", + "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e", + "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", + "test.stats:md5,c2f74a4d9b2377bcf4f4f184da3801af" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-20T20:45:38.364189" + }, + "sarscov2 - bam": { + "content": [ + "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b", + "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404", + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", + "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-21T11:38:08.434529" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml new file mode 100644 index 00000000..10b85270 --- /dev/null +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/bam_markduplicates_picard: + - subworkflows/nf-core/bam_markduplicates_picard/** diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index b4c87b9b..bf06bb1c 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -4,19 +4,10 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryMap } from 'plugin/nf-validation' -include { checkSamplesAfterGrouping } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' -include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' -include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' - -include { BAM_MARKDUPLICATES } from '../../subworkflows/local/bam_markduplicates' -include { RECALIBRATE } from '../../subworkflows/local/recalibrate' -include { SPLITNCIGAR } from '../../subworkflows/local/splitncigar' -include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all' -include { FASTQ_ALIGN_STAR } from '../../subworkflows/nf-core/fastq_align_star' - +// local include { GTF2BED } from '../../modules/local/gtf2bed' + +// nf-core include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq' include { FASTQC } from '../../modules/nf-core/fastqc' include { GATK4_BASERECALIBRATOR } from '../../modules/nf-core/gatk4/baserecalibrator' @@ -32,6 +23,26 @@ include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index include { TABIX_TABIX as TABIX } from '../../modules/nf-core/tabix/tabix' include { TABIX_TABIX as TABIXGVCF } from '../../modules/nf-core/tabix/tabix' +// local +include { RECALIBRATE } from '../../subworkflows/local/recalibrate' +include { SPLITNCIGAR } from '../../subworkflows/local/splitncigar' +include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all' + +// nf-core +include { BAM_MARKDUPLICATES_PICARD } from '../../subworkflows/nf-core/bam_markduplicates_picard' +include { FASTQ_ALIGN_STAR } from '../../subworkflows/nf-core/fastq_align_star' + +// local +include { checkSamplesAfterGrouping } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_rnavar_pipeline' + +// nf-core +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' + +// plugin +include { paramsSummaryMap } from 'plugin/nf-validation' + /* ======================================================================================== RUN MAIN WORKFLOW RNAVAR @@ -144,30 +155,37 @@ workflow RNAVAR { // // SUBWORKFLOW: Mark duplicates with GATK4 // - BAM_MARKDUPLICATES( - ch_genome_bam, - ch_fasta.map{ meta, fasta -> [fasta] }, - ch_fasta_fai, - []) - - ch_genome_bam = BAM_MARKDUPLICATES.out.bam + BAM_MARKDUPLICATES_PICARD(ch_genome_bam, + ch_fasta, + ch_fasta_fai.map{ it -> [[id:'genome'], it] }) + + ch_genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam + .join(BAM_MARKDUPLICATES_PICARD.out.bai, remainder: true) + .join(BAM_MARKDUPLICATES_PICARD.out.csi, remainder: true) + .map{meta, bam, bai, csi -> + if (bai) [meta, bam, bai] + else [meta, bam, csi] + } //Gather QC reports - ch_reports = ch_reports.mix(BAM_MARKDUPLICATES.out.reports.collect{it[1]}.ifEmpty([])) - ch_versions = ch_versions.mix(BAM_MARKDUPLICATES.out.versions) + ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.metrics.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.stats.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.flagstat.collect{it[1]}.ifEmpty([])) + ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.idxstats.collect{it[1]}.ifEmpty([])) + ch_versions = ch_versions.mix(BAM_MARKDUPLICATES_PICARD.out.versions) // // SUBWORKFLOW: SplitNCigarReads from GATK4 over the intervals // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). // - ch_splitncigar_bam_bai = Channel.empty() - SPLITNCIGAR( - ch_genome_bam, + + SPLITNCIGAR(ch_genome_bam_bai, ch_fasta, ch_fasta_fai, ch_dict, ch_interval_list_split ) + ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions) @@ -242,7 +260,7 @@ workflow RNAVAR { ch_haplotypecaller_vcf = Channel.empty() ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) .map{ meta, bam, bai, interval_list -> - [meta + [id:meta.id + "_" + interval_list.baseName, variantcaller:'haplotypecaller'], bam, bai, interval_list, []] + [ meta + [ id:meta.id + "_" + interval_list.baseName, sample:meta.id, variantcaller:'haplotypecaller' ], bam, bai, interval_list, [] ] } // @@ -259,11 +277,7 @@ workflow RNAVAR { ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } ) - ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf - .map{ meta, vcf -> - meta.id = meta.sample - [meta, vcf]} - .groupTuple() + ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions) From d95d300798d36581db0ba9686142b698a36b0e9b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 29 May 2024 14:37:16 +0200 Subject: [PATCH 129/275] fix expected test outputs --- tests/test_annotation.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml index 86b5b876..3693a80e 100644 --- a/tests/test_annotation.yml +++ b/tests/test_annotation.yml @@ -4,8 +4,8 @@ - annotation - snpeff files: - - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz - - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz.tbi + - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz + - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz.tbi - path: results/reports/multiqc_report.html - name: Run VEP command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results --download_cache @@ -13,8 +13,8 @@ - annotation - vep files: - - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz - - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz.tbi + - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz + - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz.tbi - name: Run snpEff followed by VEP command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results --download_cache tags: @@ -23,5 +23,5 @@ - snpeff - vep files: - - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz - - path: results/variant_annotation/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz.tbi + - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz + - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz.tbi From a8a5172c90e48b28d45bf3fc904bcbeef859cec2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 11:07:46 +0200 Subject: [PATCH 130/275] fix dbsnp usage --- workflows/rnavar/main.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index bf06bb1c..9fe15fb6 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -253,8 +253,11 @@ workflow RNAVAR { interval_flag = params.no_intervals // Run haplotyper even in the absence of dbSNP files if (!params.dbsnp){ - ch_dbsnp = [] - ch_dbsnp_tbi = [] + ch_dbsnp_for_haplotypecaller = [[id:'null'], []] + ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] + } else { + ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ it -> [[id:it.baseName], it] }, + ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } } ch_haplotypecaller_vcf = Channel.empty() @@ -273,8 +276,8 @@ workflow RNAVAR { ch_fasta, ch_fasta_fai.map{ it -> [[id:it.baseName], it] }, ch_dict, - ch_dbsnp.map{ it -> [[id:it.baseName], it] }, - ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } + ch_dbsnp_for_haplotypecaller, + ch_dbsnp_for_haplotypecaller_tbi ) ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() From 74192bedeb7bd8d03643f8c8a7d814111433d980 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 11:08:55 +0200 Subject: [PATCH 131/275] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a23056fa..576a7389 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir - [#136](https://github.com/nf-core/rnavar/pull/136) - Replaced unzip module with gunzip, removed unzip module - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF +- [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels ### Dependencies From 5be19815d5a6aaacc41deb353c28fe5bbd41ecfa Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 14:13:54 +0200 Subject: [PATCH 132/275] fix dbsnp usage --- workflows/rnavar/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 9fe15fb6..6b0a4256 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -256,8 +256,8 @@ workflow RNAVAR { ch_dbsnp_for_haplotypecaller = [[id:'null'], []] ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] } else { - ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ it -> [[id:it.baseName], it] }, - ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ it -> [[id:it.baseName], it] } + ch_dbsnp_for_haplotypecaller = ch_dbsnp + ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi } ch_haplotypecaller_vcf = Channel.empty() From 358c6ffb3c250674d745fab11b98df3c231fe281 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 31 May 2024 16:08:53 +0200 Subject: [PATCH 133/275] fix dbsnp usage --- workflows/rnavar/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 6b0a4256..ee776519 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -256,8 +256,8 @@ workflow RNAVAR { ch_dbsnp_for_haplotypecaller = [[id:'null'], []] ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] } else { - ch_dbsnp_for_haplotypecaller = ch_dbsnp - ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi + ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ vcf -> [[id:'dbsnp'], vcf] } + ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } } ch_haplotypecaller_vcf = Channel.empty() From a118f1d2a7cc9746cedc91ecebaf1d12c0c39a66 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Jun 2024 11:18:29 +0200 Subject: [PATCH 134/275] add contig ignore to beintervals --- conf/modules.config | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 6890a8ed..87651eb8 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -3,10 +3,10 @@ Config file for defining DSL2 per module options and publishing paths ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. ---------------------------------------------------------------------------------------- */ @@ -150,7 +150,7 @@ process { process { withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { - ext.prefix = {"${meta.id}.aligned"} + ext.prefix = {"${meta.id}.aligned"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, @@ -161,7 +161,7 @@ process { withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' - ext.prefix = {"${meta.id}.aligned"} + ext.prefix = {"${meta.id}.aligned"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, @@ -190,7 +190,7 @@ process { '--VALIDATION_STRINGENCY LENIENT', params.remove_duplicates ? '--REMOVE_DUPLICATES true' : '' ].join(' ').trim() - ext.prefix = {"${meta.id}.md"} + ext.prefix = {"${meta.id}.md"} publishDir = [ [ path: { "${params.outdir}/preprocessing/${meta.id}" }, @@ -255,7 +255,7 @@ if(!params.skip_baserecalibration) { '--use-original-qualities', '--add-output-sam-program-record' ].join(' ').trim() - ext.prefix = {"${meta.id}.recal"} + ext.prefix = {"${meta.id}.recal"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, @@ -266,7 +266,7 @@ if(!params.skip_baserecalibration) { withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' - ext.prefix = {"${meta.id}.recal"} + ext.prefix = {"${meta.id}.recal"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, mode: params.publish_dir_mode, @@ -310,7 +310,7 @@ process { withName: TABIX_TABIX { ext.args = params.bam_csi_index ? '--csi' : '' - ext.prefix = {"${meta.id}.haplotypecaller"} + ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, mode: params.publish_dir_mode, @@ -319,7 +319,7 @@ process { } withName: GATK4_VARIANTFILTRATION { - ext.prefix = {"${meta.id}.haplotypecaller.filtered"} + ext.prefix = {"${meta.id}.haplotypecaller.filtered"} ext.args = [ params.gatk_vf_window_size ? "--window $params.gatk_vf_window_size" : '', params.gatk_vf_cluster_size ? "--cluster $params.gatk_vf_cluster_size" : '', @@ -332,4 +332,8 @@ process { pattern: "*.{vcf.gz,vcf.gz.tbi}" ] } + + withName: 'NFCORE_RNAVAR:RNAVAR:GATK4_BEDTOINTERVALLIST' { + ext.args = '--DROP_MISSING_CONTIGS TRUE' + } } From 14895d283230d306a50e3f7e1f93721d0312709a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 10 Jun 2024 15:29:08 +0200 Subject: [PATCH 135/275] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 576a7389..2bd6b758 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#136](https://github.com/nf-core/rnavar/pull/136) - Replaced unzip module with gunzip, removed unzip module - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels +- [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` ### Dependencies From 08240b5484e2b52b88ef99a82d84e427d9827e45 Mon Sep 17 00:00:00 2001 From: Robert Syme Date: Mon, 17 Jun 2024 15:04:53 +0000 Subject: [PATCH 136/275] Change gatk_vf params from integer to floats --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b3de2e1a..a1b1b1ed 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -505,13 +505,13 @@ }, "gatk_vf_fs_filter": { "type": "number", - "default": 30, + "default": 30.0, "description": "Value to be used for the FisherStrand (FS) filter", "help_text": "This parameter defines the value to use for the FisherStrand (FS) filter in the GATK variant-filtering step. \nThe value should given in a float number format. Default is 30.0" }, "gatk_vf_qd_filter": { "type": "number", - "default": 2, + "default": 2.0, "description": "Value to be used for the QualByDepth (QD) filter", "help_text": "This parameter defines the value to use for the QualByDepth (QD) filter in the GATK variant-filtering step. \nThe value should given in a float number format. Default is 2.0" } From c52ab2630471417dbfd32bfa7c9e4f7ed8bc4697 Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 26 Jun 2024 14:46:21 +0000 Subject: [PATCH 137/275] Updated ch_gtf channel in main.nf --- CHANGELOG.md | 1 + main.nf | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2bd6b758..0a5d8b58 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` +- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf channel emitted by main.nf ### Dependencies diff --git a/main.nf b/main.nf index 6e638a85..ab40a8b9 100644 --- a/main.nf +++ b/main.nf @@ -111,14 +111,13 @@ workflow NFCORE_RNAVAR { ch_fasta = PREPARE_GENOME.out.fasta ch_star_index = PREPARE_GENOME.out.star_index + ch_gtf = PREPARE_GENOME.out.gtf ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect() : PREPARE_GENOME.out.fasta_fai ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed - ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ it -> [ [id:'gtf'], it ] }.collect() - : PREPARE_GENOME.out.gtf ch_dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([]) ch_known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() From ccd9d82c1c29771e37ffb8a83a3d1a67d88f32c9 Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 26 Jun 2024 20:59:46 +0000 Subject: [PATCH 138/275] Updated ch_fasta_fai channel --- CHANGELOG.md | 2 +- main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a5d8b58..32a5a0f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` -- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf channel emitted by main.nf +- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf ### Dependencies diff --git a/main.nf b/main.nf index ab40a8b9..cd9d1005 100644 --- a/main.nf +++ b/main.nf @@ -114,7 +114,7 @@ workflow NFCORE_RNAVAR { ch_gtf = PREPARE_GENOME.out.gtf ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict - ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect() + ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai) : PREPARE_GENOME.out.fasta_fai ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed From 383d4b5b3d95b32ae9343bce36f5fab63573f781 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 8 Oct 2024 12:31:57 +0000 Subject: [PATCH 139/275] Template update for nf-core/tools version 3.0.0 --- .editorconfig | 4 + .github/CONTRIBUTING.md | 10 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 23 +- .github/workflows/ci.yml | 17 +- .github/workflows/download_pipeline.yml | 53 ++- .github/workflows/linting.yml | 23 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 43 ++ .gitpod.yml | 7 +- .nf-core.yml | 16 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + CHANGELOG.md | 2 +- CITATIONS.md | 4 +- README.md | 5 +- assets/schema_input.json | 2 +- conf/base.config | 34 +- conf/igenomes_ignored.config | 9 + conf/modules.config | 1 - conf/test.config | 13 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 11 +- docs/usage.md | 12 +- main.nf | 10 +- modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/fastqc/meta.yml | 57 +-- modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 14 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 20 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 148 ++++--- nextflow_schema.json | 85 +--- .../utils_nfcore_rnavar_pipeline/main.nf | 56 +-- .../nf-core/utils_nextflow_pipeline/main.nf | 24 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 45 ++- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ---------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/rnavar.nf | 23 +- 56 files changed, 1205 insertions(+), 808 deletions(-) create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 conf/igenomes_ignored.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 72dda289..e1058815 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,6 +11,7 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 + # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -25,9 +26,12 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset + + [/assets/email*] indent_size = unset + # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 0f558d4a..f631d51a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/rnavar, the standard workflow is as 1. Check that there isn't already an issue about your idea in the [nf-core/rnavar issues](https://github.com/nf-core/rnavar/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/rnavar repository](https://github.com/nf-core/rnavar) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 866f5cb1..8a1a0b62 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnav - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnavar/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/rnavar _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 46a3767e..0df8b921 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,33 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/rnavar' + if: github.repository == 'nf-core/rnavar' && github.event.review.state == 'approved' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9993584f..dc791d5d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,6 +7,7 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false @@ -24,7 +25,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" steps: - name: Check out pipeline code @@ -38,9 +39,21 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data + - name: Run pipeline with test data (docker) # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + + - name: Run pipeline with test data (singularity) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results + if: "${{ github.base_ref == 'master' }}" + + - name: Run pipeline with test data (conda) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results + if: "${{ github.base_ref == 'master' }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d644..713dc3e7 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -54,33 +56,64 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe88..b882838a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,32 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf7..c6ba35df 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 00000000..9dea41f0 --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,43 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Read template version from .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: pip list --outdated | grep nf-core + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + ## :warning: Newer version of the nf-core template is available. + + Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + Please update your pipeline to the latest version. + + For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitpod.yml b/.gitpod.yml index 105a1821..46118637 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,14 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a77..39f92ecb 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,16 @@ +bump_version: null +lint: null +nf_core_version: 3.0.0 +org_path: null repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: Praveen Raj, Maxime U Garcia + description: GATK4 RNA variant calling pipeline + force: false + is_nfcore: true + name: rnavar + org: nf-core + outdir: . + skip_features: null + version: 2.0.0dev +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dc..9e9f0e1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/.prettierignore b/.prettierignore index 437d763d..610e5069 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,3 +1,4 @@ + email_template.html adaptivecard.json slackreport.json diff --git a/CHANGELOG.md b/CHANGELOG.md index 9eb1e73a..0f35df8c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.1.0dev - [date] +## v2.0.0dev - [date] Initial release of nf-core/rnavar, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 20cd17cf..bda4c349 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index 167ef66b..06ae4283 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -67,8 +67,7 @@ nextflow run nf-core/rnavar \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters). diff --git a/assets/schema_input.json b/assets/schema_input.json index 11fb8e80..bcb2e914 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/rnavar/master/assets/schema_input.json", "title": "nf-core/rnavar pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index 969a3162..01895aef 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,9 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +27,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 00000000..b4034d82 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b6..d266a387 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,7 +21,6 @@ process { withName: FASTQC { ext.args = '--quiet' } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index bd95ea07..ca6300a9 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index 91fb21ba..3d8ad22e 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline + - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -29,16 +30,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
    diff --git a/docs/usage.md b/docs/usage.md index d31e7c03..1bc76211 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/rnavar -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index 5ca33427..ed49309a 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,7 +18,6 @@ nextflow.enable.dsl = 2 include { RNAVAR } from './workflows/rnavar' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnavar_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rnavar_pipeline' - include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_rnavar_pipeline' /* @@ -56,10 +53,8 @@ workflow NFCORE_RNAVAR { RNAVAR ( samplesheet ) - emit: multiqc_report = RNAVAR.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,27 +65,24 @@ workflow NFCORE_RNAVAR { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // NFCORE_RNAVAR ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index aabfbc51..87e3ed71 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c86..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
    Mon 2 Oct 2023
    test.gz
    - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("
    ") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("    ") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert path(process.out.html[0][1][2]).text.contains("") }, - { assert path(process.out.html[0][1][3]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c311..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..f1cd99b0 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..b9ccebdb 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..b779e469 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index 81386593..3ad8f0bb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,6 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -33,48 +32,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true + } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/rnavar custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/rnavar.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/rnavar profiles: ${params.custom_config_base}/pipeline/rnavar.config") -} profiles { debug { dumpHashes = true @@ -89,7 +66,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -178,25 +155,23 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/rnavar custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnavar.config" : "/dev/null" +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -208,8 +183,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -238,43 +220,47 @@ manifest { homePage = 'https://github.com/nf-core/rnavar' description = """GATK4 RNA variant calling pipeline""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '1.1.0dev' + nextflowVersion = '!>=24.04.2' + version = '2.0.0dev' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + diff --git a/nextflow_schema.json b/nextflow_schema.json index 43ca4b36..1c875df1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/rnavar/master/nextflow_schema.json", "title": "nf-core/rnavar pipeline parameters", "description": "GATK4 RNA variant calling pipeline", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -71,6 +71,14 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -122,41 +130,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +137,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -245,27 +212,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -278,19 +224,16 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 009baaff..d529d309 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -8,17 +8,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* ======================================================================================== @@ -30,7 +27,6 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -51,20 +47,16 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) + // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) + // // Check config provided to the pipeline @@ -80,8 +72,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -91,8 +84,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -117,13 +110,13 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -131,11 +124,18 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -165,7 +165,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -197,7 +197,6 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // @@ -239,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +262,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f..28e32b20 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,10 +2,6 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) @@ -102,14 +98,16 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + + required_channels_in_order.eachWithIndex { channel, index -> + if (index < required_channels_in_order.size() - 1) { + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + } } if (channels_missing | channel_priority_violation) { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf..a09572e5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39..cbd8495b 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,9 +2,6 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE { // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + @@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") + def manifest_doi = workflow.manifest.doi.tokenize(",") // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + @@ -84,7 +83,7 @@ def workflowCitation() { // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +101,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -124,7 +123,7 @@ def workflowVersionToYAML() { def softwareVersionsToYAML(ch_versions) { return ch_versions .unique() - .map { processVersionsFromYAML(it) } + .map { version -> processVersionsFromYAML(version) } .unique() .mix(Channel.of(workflowVersionToYAML())) } @@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { + summary_params.keySet().each { group -> def group_params = summary_params.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

    $group

    \n" summary_section += "
    \n" - for (param in group_params.keySet()) { + group_params.keySet().sort().each { param -> summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" } summary_section += "
    \n" } } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" @@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi } def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } @@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" @@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..842dc432 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c9..331e0d2f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65d..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 2de63080..c6f27f17 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -3,10 +3,9 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnavar_pipeline' @@ -21,12 +20,10 @@ workflow RNAVAR { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // // MODULE: Run FastQC // @@ -42,11 +39,12 @@ workflow RNAVAR { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -59,18 +57,19 @@ workflow RNAVAR { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +82,14 @@ workflow RNAVAR { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From accb1094ce72f6c767b23c689d0933dc7e7eba51 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 9 Oct 2024 11:08:34 +0000 Subject: [PATCH 140/275] Template update for nf-core/tools version 3.0.1 --- .editorconfig | 4 - .github/CONTRIBUTING.md | 2 +- .github/workflows/awsfulltest.yml | 6 +- .github/workflows/linting.yml | 4 +- .nf-core.yml | 2 +- .prettierignore | 1 - docs/output.md | 1 - modules.json | 6 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 26 +- nextflow.config | 8 +- .../utils_nfcore_rnavar_pipeline/main.nf | 12 +- .../nf-core/utils_nextflow_pipeline/main.nf | 46 ++- .../nf-core/utils_nfcore_pipeline/main.nf | 279 ++++++++++-------- 15 files changed, 209 insertions(+), 194 deletions(-) diff --git a/.editorconfig b/.editorconfig index e1058815..72dda289 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,7 +11,6 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 - # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -26,12 +25,9 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset - - [/assets/email*] indent_size = unset - # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index f631d51a..36468c9a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 0df8b921..58e6b6c9 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,16 +14,18 @@ on: jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/rnavar' && github.event.review.state == 'approved' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/rnavar' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - uses: octokit/request-action@v2.x id: check_approvals with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables + if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b882838a..a502573c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -42,10 +42,10 @@ jobs: architecture: "x64" - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: pietrobolcato/action-read-yaml@1.1.0 id: read_yml with: - config: ${{ github.workspace }}/.nf-core.yaml + config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies run: | diff --git a/.nf-core.yml b/.nf-core.yml index 39f92ecb..6631173b 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,6 +1,6 @@ bump_version: null lint: null -nf_core_version: 3.0.0 +nf_core_version: 3.0.1 org_path: null repository_type: pipeline template: diff --git a/.prettierignore b/.prettierignore index 610e5069..437d763d 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,4 +1,3 @@ - email_template.html adaptivecard.json slackreport.json diff --git a/docs/output.md b/docs/output.md index 3d8ad22e..40fd2f1f 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,7 +14,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC diff --git a/modules.json b/modules.json index 87e3ed71..b0c1f387 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", + "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", + "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b0..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index b9ccebdb..9724d2f3 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index b779e469..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-10-02T17:52:09.185842" } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 3ad8f0bb..2791abd5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,10 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false + // MultiQC options multiqc_config = null multiqc_title = null @@ -36,6 +38,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + // Config options config_profile_name = null config_profile_description = null @@ -44,9 +47,9 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null + // Schema validation default options validate_params = true - } // Load base.config by default for all pipelines @@ -161,6 +164,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load nf-core/rnavar custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/rnavar.config" : "/dev/null" + // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers @@ -172,6 +176,7 @@ charliecloud.registry = 'quay.io' // Load igenomes.config if required includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -263,4 +268,3 @@ validation { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index d529d309..89bd8bc3 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -18,9 +18,9 @@ include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { @@ -99,9 +99,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -147,9 +147,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 28e32b20..2b0dc67a 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -72,11 +71,11 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() @@ -91,9 +90,14 @@ def checkCondaChannels() { try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present @@ -106,19 +110,13 @@ def checkCondaChannels() { required_channels_in_order.eachWithIndex { channel, index -> if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) } } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn( + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index cbd8495b..b78273ca 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE { def checkConfigProvided() { def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -49,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -70,13 +68,7 @@ def workflowCitation() { manifest_doi.each { doi_ref -> temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // @@ -102,7 +94,7 @@ def getWorkflowVersion() { // def processVersionsFromYAML(yaml_file) { def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -121,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { version -> processVersionsFromYAML(version) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - summary_params.keySet().each { group -> - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - group_params.keySet().sort().each { param -> - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() @@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) { def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } From 0fa9c177c84d3e80436fdd248e1877b910bc19ae Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 26 Jun 2024 14:46:21 +0000 Subject: [PATCH 141/275] Updated ch_gtf channel in main.nf --- CHANGELOG.md | 1 + main.nf | 3 +-- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2bd6b758..0a5d8b58 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` +- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf channel emitted by main.nf ### Dependencies diff --git a/main.nf b/main.nf index 6e638a85..ab40a8b9 100644 --- a/main.nf +++ b/main.nf @@ -111,14 +111,13 @@ workflow NFCORE_RNAVAR { ch_fasta = PREPARE_GENOME.out.fasta ch_star_index = PREPARE_GENOME.out.star_index + ch_gtf = PREPARE_GENOME.out.gtf ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect() : PREPARE_GENOME.out.fasta_fai ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed - ch_gtf = params.gtf ? Channel.fromPath(params.gtf).map{ it -> [ [id:'gtf'], it ] }.collect() - : PREPARE_GENOME.out.gtf ch_dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([]) ch_known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() From b54c8a2b519ac1dcb1f4bb4b5f4d6e6fed13f5a6 Mon Sep 17 00:00:00 2001 From: bioloni Date: Wed, 26 Jun 2024 20:59:46 +0000 Subject: [PATCH 142/275] Updated ch_fasta_fai channel --- CHANGELOG.md | 2 +- main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a5d8b58..32a5a0f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,7 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#138](https://github.com/nf-core/rnavar/pull/138) - Proper usage of GVCF - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` -- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf channel emitted by main.nf +- [#145](https://github.com/nf-core/rnavar/pull/145) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf ### Dependencies diff --git a/main.nf b/main.nf index ab40a8b9..cd9d1005 100644 --- a/main.nf +++ b/main.nf @@ -114,7 +114,7 @@ workflow NFCORE_RNAVAR { ch_gtf = PREPARE_GENOME.out.gtf ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict - ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect() + ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai) : PREPARE_GENOME.out.fasta_fai ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed From 4c580448ae30713409a7d2dfc03488a804779dc1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 11 Oct 2024 13:03:13 +0200 Subject: [PATCH 143/275] fix schema and channels --- nextflow_schema.json | 10 +--------- .../local/utils_nfcore_rnavar_pipeline/main.nf | 10 +++------- workflows/rnavar/main.nf | 16 +++++++++++++--- 3 files changed, 17 insertions(+), 19 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 17557d38..5fc8d5a3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -147,7 +147,7 @@ "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively species listed in Ensembl Genomes caches can be used." }, "vep_cache_version": { - "type": "number", + "type": "string", "fa_icon": "fas fa-tag", "description": "VEP cache version.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively cache version can be use to specify the correct Ensembl Genomes version number as these differ from the concurrent Ensembl/VEP version numbers" @@ -163,14 +163,6 @@ "description": "Download annotation cache.", "help_text": "Set this parameter, if you wish to download annotation cache." }, - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes/", - "fa_icon": "fas fa-cloud-download-alt", - "hidden": true - }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 6fbbe857..a8d7125c 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -93,15 +93,11 @@ workflow PIPELINE_INITIALISATION { // Create channel from input file provided through params.input // - ch_samplesheet = Channel - .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) + ch_samplesheet = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map{ meta, fastq_1, fastq_2 -> if (!fastq_2) return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - else { return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - .groupTuple() - .map{ samplesheet -> validateInputSamplesheet(samplesheet) } - .map{ meta, fastqs -> return [ meta, fastqs.flatten() ] } + else return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + }.groupTuple() emit: samplesheet = ch_samplesheet diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index b402fd4d..09456978 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -80,10 +80,18 @@ workflow RNAVAR { ch_versions = Channel.empty() // MODULE: Concatenate FastQ files from same sample if required + ch_fastq = ch_input.groupTuple().map{ samplesheet -> checkSamplesAfterGrouping(samplesheet) } + .branch{ meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [ meta, fastqs.flatten() ] + } + - CAT_FASTQ(ch_input.multiple) + CAT_FASTQ(ch_fastq.multiple) - ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_input.single) + ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_fastq.single) ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) @@ -418,7 +426,9 @@ workflow RNAVAR { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) From b096e05a6bf4f1a74ce15a63473aa6e866219e8a Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 11 Oct 2024 13:15:45 +0200 Subject: [PATCH 144/275] create tests --- nf-test.config | 19 ++++++ tests/.nftignore | 9 +++ tests/annotation.nf.test | 97 ++++++++++++++++++++++++++++ tests/bam_csi.nf.test | 36 +++++++++++ tests/config/nextflow.config | 35 ---------- tests/config/pytest_software.yml | 4 -- tests/config/test_data.config | 15 ----- tests/default.nf.test | 35 ++++++++++ tests/removeduplicates.nf.test | 36 +++++++++++ tests/skip_baserecalibration.nf.test | 36 +++++++++++ tests/test_annotation.yml | 27 -------- tests/test_bamcsiindex.yml | 10 --- tests/test_default.yml | 13 ---- tests/test_removeduplicates.yml | 13 ---- tests/test_skipbasecalib.yml | 11 ---- 15 files changed, 268 insertions(+), 128 deletions(-) create mode 100644 nf-test.config create mode 100644 tests/.nftignore create mode 100644 tests/annotation.nf.test create mode 100644 tests/bam_csi.nf.test delete mode 100644 tests/config/nextflow.config delete mode 100644 tests/config/pytest_software.yml delete mode 100644 tests/config/test_data.config create mode 100644 tests/default.nf.test create mode 100644 tests/removeduplicates.nf.test create mode 100644 tests/skip_baserecalibration.nf.test delete mode 100644 tests/test_annotation.yml delete mode 100644 tests/test_bamcsiindex.yml delete mode 100644 tests/test_default.yml delete mode 100644 tests/test_removeduplicates.yml delete mode 100644 tests/test_skipbasecalib.yml diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..69ef7315 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,19 @@ +config { + // location for all nf-tests + testsDir "." + + // nf-test directory including temporary files for each test + workDir ".nf-test" + + // location of an optional nextflow.config file specific for executing tests + configFile "conf/test.config" + + // run all test with defined profile(s) from the main nextflow.config + profile "test" + + // Include plugins + plugins { + load "nft-bam@0.4.0" + load "nft-utils@0.0.3" + } +} diff --git a/tests/.nftignore b/tests/.nftignore new file mode 100644 index 00000000..559c1dfb --- /dev/null +++ b/tests/.nftignore @@ -0,0 +1,9 @@ +multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_general_stats.txt +multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/picard_deduplication.txt +multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} +multiqc/multiqc_report.html +pipeline_info/*.{html,json,txt,yml} diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test new file mode 100644 index 00000000..647d1d47 --- /dev/null +++ b/tests/annotation.nf.test @@ -0,0 +1,97 @@ +nextflow_pipeline { + + name "Test pipeline | annotation" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test | annotation with snpeff") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + annotate_tools = 'snpeff' + download_cache = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } + + test("Run with profile test | annotation with vep") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + annotate_tools = 'vep' + download_cache = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } + + test("Run with profile test | annotation with merge") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + annotate_tools = 'merge' + download_cache = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/bam_csi.nf.test b/tests/bam_csi.nf.test new file mode 100644 index 00000000..02d196e8 --- /dev/null +++ b/tests/bam_csi.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline | bam_csi_index" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test | bam_csi_index") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + bam_csi_index = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config deleted file mode 100644 index a28463fd..00000000 --- a/tests/config/nextflow.config +++ /dev/null @@ -1,35 +0,0 @@ -params { - outdir = "results/" - publish_dir_mode = "copy" - enable_conda = false - singularity_pull_docker_container = false - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h -} - -process { - cpus = 2 - memory = 6.GB - time = 48.h -} - -if ("$PROFILE" == "singularity") { - singularity.enabled = true - singularity.autoMounts = true -} else if ("$PROFILE" == "conda") { - params.enable_conda = true -} else { - docker.enabled = true - docker.runOptions = '-u \$(id -u):\$(id -g)' -} - -// Load test_data.config containing paths to test data -// includeConfig 'test_data.config' - -// Load modules.config for default module params -includeConfig '../../conf/modules.config' - -manifest { - nextflowVersion = '!>=21.10.3' -} diff --git a/tests/config/pytest_software.yml b/tests/config/pytest_software.yml deleted file mode 100644 index b215cffc..00000000 --- a/tests/config/pytest_software.yml +++ /dev/null @@ -1,4 +0,0 @@ -markduplicates: - - modules/nf-core/software/gatk4/markduplicates/main.nf - - subworkflow/local/markduplicates.nf - - tests/subworkflow/local/markduplicates/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config deleted file mode 100644 index 665947a5..00000000 --- a/tests/config/test_data.config +++ /dev/null @@ -1,15 +0,0 @@ -def test_data_dir = "${launchDir}/tests/data/" -def nf_core_modules_data = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" - -try { - includeConfig "https://raw.githubusercontent.com/nf-core/modules/master/tests/config/test_data.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/modules test data config") -} - -params { - test_data { - 'external' { - } - } -} diff --git a/tests/default.nf.test b/tests/default.nf.test new file mode 100644 index 00000000..217a63a0 --- /dev/null +++ b/tests/default.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/removeduplicates.nf.test b/tests/removeduplicates.nf.test new file mode 100644 index 00000000..3b324eed --- /dev/null +++ b/tests/removeduplicates.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline | remove_duplicates" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test | remove_duplicates") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + remove_duplicates = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/skip_baserecalibration.nf.test b/tests/skip_baserecalibration.nf.test new file mode 100644 index 00000000..dbafa2b9 --- /dev/null +++ b/tests/skip_baserecalibration.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline | skip_baserecalibration" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test | skip_baserecalibration") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + skip_baserecalibration = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/test_annotation.yml b/tests/test_annotation.yml deleted file mode 100644 index 3693a80e..00000000 --- a/tests/test_annotation.yml +++ /dev/null @@ -1,27 +0,0 @@ -- name: Run snpEff - command: nextflow run main.nf -profile test,docker --annotate_tools snpeff --outdir results --download_cache - tags: - - annotation - - snpeff - files: - - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz - - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff.ann.vcf.gz.tbi - - path: results/reports/multiqc_report.html -- name: Run VEP - command: nextflow run main.nf -profile test,docker --annotate_tools vep --skip_multiqc --outdir results --download_cache - tags: - - annotation - - vep - files: - - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz - - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_VEP.ann.vcf.gz.tbi -- name: Run snpEff followed by VEP - command: nextflow run main.nf -profile test,docker --annotate_tools merge --skip_multiqc --outdir results --download_cache - tags: - - annotation - - merge - - snpeff - - vep - files: - - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz - - path: results/annotation/haplotypecaller/GM12878/GM12878.haplotypecaller.filtered_snpEff_VEP.ann.vcf.gz.tbi diff --git a/tests/test_bamcsiindex.yml b/tests/test_bamcsiindex.yml deleted file mode 100644 index 7235d9f9..00000000 --- a/tests/test_bamcsiindex.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: Run pipeline with bam_csi_index for large genomes - command: nextflow run main.nf -profile test,docker --bam_csi_index --outdir results - tags: - - bamcsiindex - files: - - path: results/reports/multiqc_report.html - - path: results/preprocessing/GM12878/GM12878.md.bam - - path: results/preprocessing/GM12878/GM12878.md.bam.csi - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.csi diff --git a/tests/test_default.yml b/tests/test_default.yml deleted file mode 100644 index 776ec6f3..00000000 --- a/tests/test_default.yml +++ /dev/null @@ -1,13 +0,0 @@ -- name: Run default pipeline - command: nextflow run main.nf -profile test,docker --outdir results - tags: - - default - - preprocessing - files: - - path: results/reports/multiqc_report.html - - path: results/preprocessing/GM12878/GM12878.recal.bam - - path: results/preprocessing/GM12878/GM12878.recal.bam.bai - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi diff --git a/tests/test_removeduplicates.yml b/tests/test_removeduplicates.yml deleted file mode 100644 index d0650728..00000000 --- a/tests/test_removeduplicates.yml +++ /dev/null @@ -1,13 +0,0 @@ -- name: Run pipeline with duplicate reads removed - command: nextflow run main.nf -profile test,docker --remove_duplicates true --outdir results - tags: - - removeduplicates - - preprocessing - files: - - path: results/reports/multiqc_report.html - - path: results/preprocessing/GM12878/GM12878.recal.bam - - path: results/preprocessing/GM12878/GM12878.recal.bam.bai - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi diff --git a/tests/test_skipbasecalib.yml b/tests/test_skipbasecalib.yml deleted file mode 100644 index 67f1c463..00000000 --- a/tests/test_skipbasecalib.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: Run pipeline without base calibration step - command: nextflow run main.nf -profile test,docker --skip_baserecalibration true --outdir results - tags: - - skipbasecalib - - preprocessing - files: - - path: results/reports/multiqc_report.html - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz - - path: results/variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi From c143e9cf40a023ad3a8f2479b7831ec63ed0797c Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 11 Oct 2024 12:40:35 +0000 Subject: [PATCH 145/275] Template update for nf-core/tools version 3.0.2 --- .github/workflows/ci.yml | 60 +++++++++++++------ .../workflows/template_version_comment.yml | 21 ++++--- .gitignore | 1 + .nf-core.yml | 2 +- main.nf | 2 +- modules.json | 6 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 4 +- .../utils_nfcore_rnavar_pipeline/main.nf | 4 +- .../nf-core/utils_nextflow_pipeline/main.nf | 30 +++++----- .../nf-core/utils_nfcore_pipeline/main.nf | 10 ++-- workflows/rnavar.nf | 2 - 12 files changed, 86 insertions(+), 58 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dc791d5d..1155cd32 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,6 +11,8 @@ on: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -18,7 +20,7 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnavar') }}" runs-on: ubuntu-latest @@ -27,33 +29,57 @@ jobs: NXF_VER: - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - - name: Run pipeline with test data (docker) - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: Set up Singularity + if: matrix.profile == 'singularity' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda - - name: Run pipeline with test data (singularity) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: Set up Conda + if: matrix.profile == 'conda' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results - if: "${{ github.base_ref == 'master' }}" + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data (conda) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results - if: "${{ github.base_ref == 'master' }}" + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index 9dea41f0..e8aafe44 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -10,9 +10,11 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: nichmor/minimal-read-yaml@v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -24,20 +26,21 @@ jobs: - name: Check nf-core outdated id: nf_core_outdated - run: pip list --outdated | grep nf-core + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 if: | - ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + contains(env.OUTPUT, 'nf-core') with: repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} allow-repeats: false message: | - ## :warning: Newer version of the nf-core template is available. - - Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - Please update your pipeline to the latest version. - - For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). # diff --git a/.gitignore b/.gitignore index 5124c9ac..a42ce016 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/.nf-core.yml b/.nf-core.yml index 6631173b..6acdc938 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,6 +1,6 @@ bump_version: null lint: null -nf_core_version: 3.0.1 +nf_core_version: 3.0.2 org_path: null repository_type: pipeline template: diff --git a/main.nf b/main.nf index ed49309a..90e7fcb4 100644 --- a/main.nf +++ b/main.nf @@ -76,7 +76,7 @@ workflow { params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // diff --git a/modules.json b/modules.json index b0c1f387..db4ad174 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 9724d2f3..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -52,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/nextflow.config b/nextflow.config index 2791abd5..0758a8f9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -254,10 +254,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """ } summary { diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 89bd8bc3..385cfe0b 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - // // Validate parameters and generate parameter summary to stdout // @@ -56,7 +55,6 @@ workflow PIPELINE_INITIALISATION { validate_params, null ) - // // Check config provided to the pipeline @@ -64,6 +62,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -110,7 +109,6 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML - outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a..0fcbf7b3 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -106,17 +106,19 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca..5cb7bafe 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index c6f27f17..c5dcbe5f 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -57,13 +57,11 @@ workflow RNAVAR { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) From 732ee1b8ac48c9c149c00add09f2a29e2e30dd80 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 11 Oct 2024 15:11:54 +0200 Subject: [PATCH 146/275] create tests --- .gitignore | 1 + .../utils_nfcore_rnavar_pipeline/main.nf | 2 +- tests/annotation.nf.test | 6 +- tests/annotation.nf.test.snap | 445 ++++++++++++++++++ tests/bam_csi.nf.test | 2 +- tests/bam_csi.nf.test.snap | 51 ++ tests/default.nf.test | 2 +- tests/default.nf.test.snap | 53 +++ tests/removeduplicates.nf.test | 2 +- tests/removeduplicates.nf.test.snap | 53 +++ tests/skip_baserecalibration.nf.test | 2 +- tests/skip_baserecalibration.nf.test.snap | 51 ++ workflows/rnavar/main.nf | 1 - 13 files changed, 662 insertions(+), 9 deletions(-) create mode 100644 tests/annotation.nf.test.snap create mode 100644 tests/bam_csi.nf.test.snap create mode 100644 tests/default.nf.test.snap create mode 100644 tests/removeduplicates.nf.test.snap create mode 100644 tests/skip_baserecalibration.nf.test.snap diff --git a/.gitignore b/.gitignore index 5124c9ac..792b37f2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,5 @@ .nextflow* +.nf-test* work/ data/ results/ diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index a8d7125c..d06230ad 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -97,7 +97,7 @@ workflow PIPELINE_INITIALISATION { .map{ meta, fastq_1, fastq_2 -> if (!fastq_2) return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] else return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - }.groupTuple() + } emit: samplesheet = ch_samplesheet diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test index 647d1d47..ca4c0c79 100644 --- a/tests/annotation.nf.test +++ b/tests/annotation.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'snpeff' download_cache = true @@ -39,7 +39,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'vep' download_cache = true @@ -69,7 +69,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'merge' download_cache = true diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap new file mode 100644 index 00000000..a482d28f --- /dev/null +++ b/tests/annotation.nf.test.snap @@ -0,0 +1,445 @@ +{ + "Run with profile test | annotation with merge": { + "content": [ + 46, + null, + [ + "annotation", + "annotation/haplotypecaller", + "annotation/haplotypecaller/GM12878", + 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"reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T14:46:10.437216" + } +} \ No newline at end of file diff --git a/tests/bam_csi.nf.test b/tests/bam_csi.nf.test index 02d196e8..64ea8f58 100644 --- a/tests/bam_csi.nf.test +++ b/tests/bam_csi.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" bam_csi_index = true } diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap new file mode 100644 index 00000000..8958e3dc --- /dev/null +++ b/tests/bam_csi.nf.test.snap @@ -0,0 +1,51 @@ +{ + "Run with profile test | bam_csi_index": { + "content": [ + 39, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.csi", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.csi", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.csi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.csi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.csi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T14:57:45.737274" + } +} \ No newline at end of file diff --git a/tests/default.nf.test b/tests/default.nf.test index 217a63a0..18825af0 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 00000000..b1161f20 --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,53 @@ +{ + "Run with profile test": { + "content": [ + 40, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T15:01:04.962148" + } +} \ No newline at end of file diff --git a/tests/removeduplicates.nf.test b/tests/removeduplicates.nf.test index 3b324eed..bac8205b 100644 --- a/tests/removeduplicates.nf.test +++ b/tests/removeduplicates.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" remove_duplicates = true } diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap new file mode 100644 index 00000000..6011aff2 --- /dev/null +++ b/tests/removeduplicates.nf.test.snap @@ -0,0 +1,53 @@ +{ + "Run with profile test | remove_duplicates": { + "content": [ + 40, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T15:05:33.998547" + } +} \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test b/tests/skip_baserecalibration.nf.test index dbafa2b9..78982da0 100644 --- a/tests/skip_baserecalibration.nf.test +++ b/tests/skip_baserecalibration.nf.test @@ -9,7 +9,7 @@ nextflow_pipeline { when { params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" skip_baserecalibration = true } diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap new file mode 100644 index 00000000..2b3cefbe --- /dev/null +++ b/tests/skip_baserecalibration.nf.test.snap @@ -0,0 +1,51 @@ +{ + "Run with profile test | skip_baserecalibration": { + "content": [ + 36, + null, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-11T15:10:25.387052" + } +} \ No newline at end of file diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 09456978..3deaa578 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -88,7 +88,6 @@ workflow RNAVAR { return [ meta, fastqs.flatten() ] } - CAT_FASTQ(ch_fastq.multiple) ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_fastq.single) From 6e7344d345b6013d299d4a1000b81ce463b1f2ec Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 11 Oct 2024 16:08:37 +0200 Subject: [PATCH 147/275] just pipeline tests --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d0e1f940..41ca525d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: NXF_VER: - "24.04.2" - "latest-everything" - filter: ["workflow", "function", "pipeline"] + filter: ["pipeline"] # filter: ["process", "workflow", "function", "pipeline"] profile: ["conda", "docker", "singularity"] shard: [1, 2, 3, 4] From f1aa3f9ff6a2ece6f1455fd7362e765972d35ca9 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 11 Oct 2024 16:17:08 +0200 Subject: [PATCH 148/275] fix linting with gitignore --- .../workflows/template_version_comment.yml | 22 ++++++++++--------- .gitignore | 2 +- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index 9dea41f0..d67ee08c 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -10,9 +10,11 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: nichmor/minimal-read-yaml@v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -21,23 +23,23 @@ jobs: run: | python -m pip install --upgrade pip pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - - name: Check nf-core outdated id: nf_core_outdated - run: pip list --outdated | grep nf-core + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 if: | - ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + contains(env.OUTPUT, 'nf-core') with: repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} allow-repeats: false message: | - ## :warning: Newer version of the nf-core template is available. - - Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - Please update your pipeline to the latest version. - - For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). # diff --git a/.gitignore b/.gitignore index 792b37f2..2eef655b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,4 @@ .nextflow* -.nf-test* work/ data/ results/ @@ -7,3 +6,4 @@ results/ testing/ testing* *.pyc +.nf-test* From 66dd5b5fb80f7056c947dd1d4b6cca10fdd42462 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 11 Oct 2024 17:04:53 +0200 Subject: [PATCH 149/275] Apply suggestions from code review --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4f10d8ef..cbd58e59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#117](https://github.com/nf-core/rnavar/pull/117) - Template update for nf-core/tools v2.11.1 - [#120](https://github.com/nf-core/rnavar/pull/120) - Template update for nf-core/tools v2.12 - [#140](https://github.com/nf-core/rnavar/pull/140) - Template update for nf-core/tools v2.14.1 -- [#152](https://github.com/nf-core/rnavar/pull/152) - Template update for nf-core/tools v3.0.1 +- [#153](https://github.com/nf-core/rnavar/pull/153) - Template update for nf-core/tools v3.0.2 +- [#153](https://github.com/nf-core/rnavar/pull/153) - Converted pytest tests to nf-test tests ### Fixed From 9915cc7503bbdb92e8f061c18e04e79bb13bee17 Mon Sep 17 00:00:00 2001 From: Felipe Marques de Almeida Date: Fri, 15 Nov 2024 08:25:56 +0000 Subject: [PATCH 150/275] convert reference channels from queue to value channel --- CHANGELOG.md | 1 + subworkflows/local/prepare_genome/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cbd58e59..3256a119 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#142](https://github.com/nf-core/rnavar/pull/142) - Fix dbsnp channels - [#143](https://github.com/nf-core/rnavar/pull/143) - Use `DROP_MISSING_CONTIGS` by default in `GATK4_BEDTOINTERVALLIST` - [#144](https://github.com/nf-core/rnavar/pull/144) - Change gatk_vf params from integer to floats +- [#145](https://github.com/nf-core/rnavar/issues/145) - Converted `star_index` and `gtf` emit channels from queue to value channels in `PREPARE_GENOME` subworkflow - [#149](https://github.com/nf-core/rnavar/pull/149) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf ### Dependencies diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index a568e1a8..e5d9c8ce 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -70,8 +70,8 @@ workflow PREPARE_GENOME { exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed fasta = ch_fasta fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai - gtf = ch_gtf // path: genome.gtf - star_index = STAR_GENOMEGENERATE.out.index // path: star/index/ + gtf = ch_gtf.first() // path: genome.gtf + star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi versions = ch_versions // channel: [ versions.yml ] From 46c8922c0957ca70c9fde904ef9aa36d1f5e4acd Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 12 Dec 2024 11:26:06 +0000 Subject: [PATCH 151/275] Template update for nf-core/tools version 3.1.0 --- .github/CONTRIBUTING.md | 12 +- .github/workflows/awsfulltest.yml | 21 +- .github/workflows/branch.yml | 18 +- .github/workflows/ci.yml | 2 +- .github/workflows/download_pipeline.yml | 8 +- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting.yml | 10 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 2 +- .gitpod.yml | 11 +- .nf-core.yml | 7 +- .vscode/settings.json | 3 + conf/base.config | 2 +- conf/modules.config | 1 + docs/usage.md | 32 +- modules.json | 8 +- modules/nf-core/fastqc/main.nf | 2 +- modules/nf-core/fastqc/meta.yml | 1 + nextflow.config | 53 +++- nextflow_schema.json | 6 + ro-crate-metadata.json | 295 ++++++++++++++++++ .../utils_nfcore_rnavar_pipeline/main.nf | 7 +- .../nf-core/utils_nextflow_pipeline/main.nf | 2 + .../tests/main.workflow.nf.test | 10 +- .../nf-core/utils_nfcore_pipeline/main.nf | 89 ++---- .../tests/main.function.nf.test | 46 ++- .../tests/main.function.nf.test.snap | 30 -- .../utils_nfschema_plugin/tests/main.nf.test | 4 +- workflows/rnavar.nf | 2 +- 30 files changed, 473 insertions(+), 219 deletions(-) create mode 100644 .vscode/settings.json create mode 100644 ro-crate-metadata.json diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 36468c9a..79ea4075 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,4 +1,4 @@ -# nf-core/rnavar: Contributing Guidelines +# `nf-core/rnavar`: Contributing Guidelines Hi there! Many thanks for taking an interest in improving nf-core/rnavar. @@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/master`. +- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. - Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. +- Open a pull-request from `patch` to `main`/`master` with the changes. ## Getting help @@ -65,13 +65,13 @@ For further information/help, please consult the [nf-core/rnavar documentation]( ## Pipeline contribution conventions -To make the nf-core/rnavar code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. +To make the `nf-core/rnavar` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. ### Adding a new step If you wish to contribute a new step, please use the following coding standards: -1. Define the corresponding input channel into your new process from the expected previous process channel +1. Define the corresponding input channel into your new process from the expected previous process channel. 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). @@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards: ### Default values -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. +Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 58e6b6c9..0ee85feb 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,11 +1,12 @@ name: nf-core AWS full size tests -# This workflow is triggered on PRs opened against the master branch. +# This workflow is triggered on PRs opened against the main/master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: pull_request: branches: + - main - master workflow_dispatch: pull_request_review: @@ -18,18 +19,30 @@ jobs: if: github.repository == 'nf-core/rnavar' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - - uses: octokit/request-action@v2.x + - name: Get PR reviews + uses: octokit/request-action@v2.x + if: github.event_name != 'workflow_dispatch' id: check_approvals + continue-on-error: true with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - id: test_variables + + - name: Check for approvals + if: ${{ failure() && github.event_name != 'workflow_dispatch' }} + run: | + echo "No review approvals found. At least 2 approvals are required to run this action automatically." + exit 1 + + - name: Check for enough approvals (>=2) + id: test_variables if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 0d32dfd4..7699cbb6 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,15 +1,17 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to `main`/`master` branch on the repository +# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: + - main + - master jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'nf-core/rnavar' run: | @@ -22,7 +24,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +34,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch. + The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1155cd32..d4714261 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,7 +45,7 @@ jobs: profile: "singularity" steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 713dc3e7..2576cc0c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main/master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: @@ -17,9 +17,11 @@ on: - edited - synchronize branches: + - main - master pull_request_target: branches: + - main - master env: @@ -35,7 +37,7 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -69,7 +71,7 @@ jobs: --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ --download-configuration 'yes' diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 7ca33128..2394380f 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a502573c..dbd52d5a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -31,12 +31,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -74,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 42e519bf..0bed96d3 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 + uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c6ba35df..450b1d5e 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -31,7 +31,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index e8aafe44..537529bc 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.gitpod.yml b/.gitpod.yml index 46118637..83599f63 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -6,12 +6,5 @@ tasks: nextflow self-update vscode: - extensions: # based on nf-core.nf-core-extensionpack - #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - charliermarsh.ruff # Code linter Ruff + extensions: + - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index 6acdc938..17cbd60c 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,4 @@ -bump_version: null -lint: null -nf_core_version: 3.0.2 -org_path: null +nf_core_version: 3.1.0 repository_type: pipeline template: author: Praveen Raj, Maxime U Garcia @@ -11,6 +8,4 @@ template: name: rnavar org: nf-core outdir: . - skip_features: null version: 2.0.0dev -update: null diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..a33b527c --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "markdown.styles": ["public/vscode_markdown.css"] +} diff --git a/conf/base.config b/conf/base.config index 01895aef..66e435c8 100644 --- a/conf/base.config +++ b/conf/base.config @@ -20,7 +20,7 @@ process { maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. diff --git a/conf/modules.config b/conf/modules.config index d266a387..d203d2b6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,6 +21,7 @@ process { withName: FASTQC { ext.args = '--quiet' } + withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/docs/usage.md b/docs/usage.md index 1bc76211..60b7f06e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -75,9 +75,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -106,23 +105,21 @@ nextflow pull nf-core/rnavar ### Reproducibility -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the [nf-core/rnavar releases page](https://github.com/nf-core/rnavar/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -130,16 +127,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -175,13 +171,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. diff --git a/modules.json b/modules.json index db4ad174..ce2c1e82 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164", "installed_by": ["modules"] }, "multiqc": { @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d8989f48..752c3a10 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -24,7 +24,7 @@ process FASTQC { // Make list of old name and new name pairs to use for renaming in the bash while loop def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4827da7a..2b2e62b8 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -11,6 +11,7 @@ tools: FastQC gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other overrepresented sequences. homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ diff --git a/nextflow.config b/nextflow.config index 0758a8f9..64f18cd2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -38,8 +38,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - - // Config options + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options config_profile_name = null config_profile_description = null @@ -153,6 +152,13 @@ profiles { executor.name = 'local' executor.cpus = 4 executor.memory = 8.GB + process { + resourceLimits = [ + memory: 8.GB, + cpus : 4, + time : 1.h + ] + } } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } @@ -201,30 +207,49 @@ set -C # No clobber - prevent output redirection from overwriting files. // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'nf-core/rnavar' - author = """Praveen Raj, Maxime U Garcia""" + author = """Praveen Raj, Maxime U Garcia""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead + contributors = [ + // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 + [ + name: 'Praveen Raj', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: ' Maxime U Garcia', + affiliation: '', + email: '', + github: '', + contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + ] homePage = 'https://github.com/nf-core/rnavar' description = """GATK4 RNA variant calling pipeline""" mainScript = 'main.nf' + defaultBranch = 'master' nextflowVersion = '!>=24.04.2' version = '2.0.0dev' doi = '' @@ -237,9 +262,10 @@ plugins { validation { defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs help { enabled = true - command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + command = "nextflow run nf-core/rnavar -profile --input samplesheet.csv --outdir " fullParameter = "help_full" showHiddenParameter = "show_hidden" beforeText = """ @@ -249,15 +275,15 @@ validation { \033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m \033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m \033[0;32m`._,._,\'\033[0m -\033[0;35m ${manifest.name} ${manifest.version}\033[0m +\033[0;35m nf-core/rnavar ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/nf-core/rnavar/blob/master/CITATIONS.md """ } summary { @@ -265,6 +291,3 @@ validation { afterText = validation.help.afterText } } - -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 1c875df1..a90dc2b5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -218,6 +218,12 @@ "description": "Base URL or local path to location of pipeline test dataset files", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", "hidden": true + }, + "trace_report_suffix": { + "type": "string", + "fa_icon": "far calendar", + "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", + "hidden": true } } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 00000000..59b145f2 --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,295 @@ +{ + "@context": [ + "https://w3id.org/ro/crate/1.1/context", + { + "GithubService": "https://w3id.org/ro/terms/test#GithubService", + "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService", + "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine", + "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition", + "TestInstance": "https://w3id.org/ro/terms/test#TestInstance", + "TestService": "https://w3id.org/ro/terms/test#TestService", + "TestSuite": "https://w3id.org/ro/terms/test#TestSuite", + "TravisService": "https://w3id.org/ro/terms/test#TravisService", + "definition": "https://w3id.org/ro/terms/test#definition", + "engineVersion": "https://w3id.org/ro/terms/test#engineVersion", + "instance": "https://w3id.org/ro/terms/test#instance", + "resource": "https://w3id.org/ro/terms/test#resource", + "runsOn": "https://w3id.org/ro/terms/test#runsOn" + } + ], + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "InProgress", + "datePublished": "2024-12-12T11:25:52+00:00", + "description": "

    \n \n \n \"nf-core/rnavar\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnavar** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/rnavar \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnavar/output).\n\n## Credits\n\nnf-core/rnavar was originally written by Praveen Raj, Maxime U Garcia.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnavar` channel](https://nfcore.slack.com/channels/rnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "docs/images/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CODE_OF_CONDUCT.md" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/nf-core/rnavar", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "mentions": [ + { + "@id": "#b35294a0-a0fd-4665-a18e-9b000bc53a56" + } + ], + "name": "nf-core/rnavar" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "dateCreated": "", + "dateModified": "2024-12-12T11:25:52Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": ["nf-core", "nextflow", "gatk4", "rna", "rnaseq", "variant-calling", "worflow"], + "license": ["MIT"], + "name": ["nf-core/rnavar"], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": ["https://github.com/nf-core/rnavar", "https://nf-co.re/rnavar/dev/"], + "version": ["2.0.0dev"] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=24.04.2" + }, + { + "@id": "#b35294a0-a0fd-4665-a18e-9b000bc53a56", + "@type": "TestSuite", + "instance": [ + { + "@id": "#66d20ede-45cf-4db2-8323-6cbe720b35ab" + } + ], + "mainEntity": { + "@id": "main.nf" + }, + "name": "Test suite for nf-core/rnavar" + }, + { + "@id": "#66d20ede-45cf-4db2-8323-6cbe720b35ab", + "@type": "TestInstance", + "name": "GitHub Actions workflow for testing nf-core/rnavar", + "resource": "repos/nf-core/rnavar/actions/workflows/ci.yml", + "runsOn": { + "@id": "https://w3id.org/ro/terms/test#GithubService" + }, + "url": "https://api.github.com" + }, + { + "@id": "https://w3id.org/ro/terms/test#GithubService", + "@type": "TestService", + "name": "Github Actions", + "url": { + "@id": "https://github.com" + } + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "docs/images/", + "@type": "Dataset", + "description": "Images for the documentation files" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@type": "File", + "description": "The license - should be MIT" + }, + { + "@id": "CODE_OF_CONDUCT.md", + "@type": "File", + "description": "The nf-core code of conduct" + }, + { + "@id": "CITATIONS.md", + "@type": "File", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + } + ] +} diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 385cfe0b..c4ff7fc0 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -116,7 +116,8 @@ workflow PIPELINE_COMPLETION { main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - + def multiqc_reports = multiqc_report.toList() + // // Completion email and summary // @@ -129,7 +130,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_report.toList() + multiqc_reports.getVal(), ) } @@ -225,7 +226,7 @@ def toolBibliographyText() { } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = workflow.toMap() meta["manifest_map"] = workflow.manifest.toMap() diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 0fcbf7b3..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -92,10 +92,12 @@ def checkCondaChannels() { channels = config.channels } catch (NullPointerException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } catch (IOException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..bfd25876 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) { } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // @@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // @@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) { return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] - } +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - catch (Exception all) { - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } - } - return mqc_report } // @@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) @@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi if (email_address) { try { if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } ['sendmail', '-t'].execute() << sendmail_html log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f8..f117040c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232c..02c67014 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index c5dcbe5f..81af239d 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -39,7 +39,7 @@ workflow RNAVAR { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', + name: 'nf_core_' + 'rnavar_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From 25295ff6f693bf8bbe8dffd95eef2e148df8e513 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 20 Dec 2024 13:10:36 +0000 Subject: [PATCH 152/275] Template update for nf-core/tools version 3.1.1 --- .editorconfig | 4 ++ .github/ISSUE_TEMPLATE/bug_report.yml | 1 - .github/workflows/download_pipeline.yml | 41 ++++++++++------ .nf-core.yml | 2 +- .prettierignore | 1 + CITATIONS.md | 4 +- LICENSE | 2 +- README.md | 15 ++---- docs/output.md | 11 ++--- docs/usage.md | 2 +- nextflow.config | 3 ++ ro-crate-metadata.json | 49 +++++++++++++------ .../utils_nfcore_rnavar_pipeline/main.nf | 2 +- 13 files changed, 80 insertions(+), 57 deletions(-) diff --git a/.editorconfig b/.editorconfig index 72dda289..6d9b74cc 100644 --- a/.editorconfig +++ b/.editorconfig @@ -31,3 +31,7 @@ indent_size = unset # ignore python and markdown [*.{py,md}] indent_style = unset + +# ignore ro-crate metadata files +[**/ro-crate-metadata.json] +insert_final_newline = unset diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index b70618d8..d6f0d51f 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,7 +9,6 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [nf-core/rnavar pipeline documentation](https://nf-co.re/rnavar/usage) - - type: textarea id: description attributes: diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2576cc0c..13b51e2c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,8 +28,12 @@ env: NXF_ANSI_LOG: false jobs: - download: + configure: runs-on: ubuntu-latest + outputs: + REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} + REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} + REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -53,22 +57,27 @@ jobs: pip install git+https://github.com/nf-core/tools.git@dev - name: Get the repository name and current branch set as environment variable + id: get_repo_properties run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Make a cache directory for the container images run: | mkdir -p ./singularity_container_images + download: + runs-on: ubuntu-latest + needs: configure + steps: - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ @@ -76,14 +85,14 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} - name: Count the downloaded number of container images id: count_initial run: | image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Initial container image count: $image_count" - echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" - name: Run the downloaded pipeline (stub) id: stub_run_pipeline @@ -91,27 +100,27 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results - name: Count the downloaded number of container images id: count_afterwards run: | image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Post-pipeline run container image count: $image_count" - echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts run: | - if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - initial_count=${{ env.IMAGE_COUNT_INITIAL }} - final_count=${{ env.IMAGE_COUNT_AFTER }} + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} difference=$((final_count - initial_count)) echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" tree ./singularity_container_images diff --git a/.nf-core.yml b/.nf-core.yml index 17cbd60c..3c023ae2 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,4 @@ -nf_core_version: 3.1.0 +nf_core_version: 3.1.1 repository_type: pipeline template: author: Praveen Raj, Maxime U Garcia diff --git a/.prettierignore b/.prettierignore index 437d763d..edd29f01 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,3 +10,4 @@ testing/ testing* *.pyc bin/ +ro-crate-metadata.json diff --git a/CITATIONS.md b/CITATIONS.md index bda4c349..a471b8ee 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,9 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. diff --git a/LICENSE b/LICENSE index 747ad37f..b0c7da48 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Praveen Raj, Maxime U Garcia +Copyright (c) The nf-core/rnavar team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 06ae4283..b1fbaf59 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,7 @@ nf-core/rnavar - - -[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) @@ -29,15 +27,12 @@ - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - - - + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/docs/output.md b/docs/output.md index 40fd2f1f..3d490a5f 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,8 +12,7 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline +- [FastQC](#fastqc) - Raw read QC- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -27,9 +26,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - -### MultiQC +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).### MultiQC
    Output files @@ -43,9 +40,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . - -### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information
    Output files diff --git a/docs/usage.md b/docs/usage.md index 60b7f06e..91015fc2 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -130,7 +130,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli > [!IMPORTANT] > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. diff --git a/nextflow.config b/nextflow.config index 64f18cd2..fd3e09f8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -291,3 +291,6 @@ validation { afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 59b145f2..eea1f876 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-12T11:25:52+00:00", - "description": "

    \n \n \n \"nf-core/rnavar\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnavar** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/rnavar \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnavar/output).\n\n## Credits\n\nnf-core/rnavar was originally written by Praveen Raj, Maxime U Garcia.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnavar` channel](https://nfcore.slack.com/channels/rnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2024-12-20T13:10:35+00:00", + "description": "

    \n \n \n \"nf-core/rnavar\"\n \n

    [![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnavar** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/rnavar \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnavar/output).\n\n## Credits\n\nnf-core/rnavar was originally written by Praveen Raj, Maxime U Garcia.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnavar` channel](https://nfcore.slack.com/channels/rnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#b35294a0-a0fd-4665-a18e-9b000bc53a56" + "@id": "#cb58e61f-4cc9-4fab-962d-1a7c1ac1c329" } ], "name": "nf-core/rnavar" @@ -121,21 +121,42 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "dateCreated": "", - "dateModified": "2024-12-12T11:25:52Z", + "dateModified": "2024-12-20T13:10:35Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", - "keywords": ["nf-core", "nextflow", "gatk4", "rna", "rnaseq", "variant-calling", "worflow"], - "license": ["MIT"], - "name": ["nf-core/rnavar"], + "keywords": [ + "nf-core", + "nextflow", + "gatk4", + "rna", + "rnaseq", + "variant-calling", + "worflow" + ], + "license": [ + "MIT" + ], + "name": [ + "nf-core/rnavar" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/rnavar", "https://nf-co.re/rnavar/dev/"], - "version": ["2.0.0dev"] + "url": [ + "https://github.com/nf-core/rnavar", + "https://nf-co.re/rnavar/dev/" + ], + "version": [ + "2.0.0dev" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -150,11 +171,11 @@ "version": "!>=24.04.2" }, { - "@id": "#b35294a0-a0fd-4665-a18e-9b000bc53a56", + "@id": "#cb58e61f-4cc9-4fab-962d-1a7c1ac1c329", "@type": "TestSuite", "instance": [ { - "@id": "#66d20ede-45cf-4db2-8323-6cbe720b35ab" + "@id": "#bbcc4db9-1638-4fd6-9f87-7d2acff32057" } ], "mainEntity": { @@ -163,7 +184,7 @@ "name": "Test suite for nf-core/rnavar" }, { - "@id": "#66d20ede-45cf-4db2-8323-6cbe720b35ab", + "@id": "#bbcc4db9-1638-4fd6-9f87-7d2acff32057", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rnavar", "resource": "repos/nf-core/rnavar/actions/workflows/ci.yml", @@ -292,4 +313,4 @@ "url": "https://nf-co.re/" } ] -} +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index c4ff7fc0..6416fcfc 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -117,7 +117,7 @@ workflow PIPELINE_COMPLETION { main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") def multiqc_reports = multiqc_report.toList() - + // // Completion email and summary // From cebbe92f9a48511c3e181c60e6255af8cf9481aa Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 15:58:05 +0100 Subject: [PATCH 153/275] update samplesheet schema --- assets/schema_input.json | 34 ++++++++++++++++++- .../utils_nfcore_rnavar_pipeline/main.nf | 27 ++++++++++++--- 2 files changed, 55 insertions(+), 6 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index b21e53d8..97382d08 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -32,8 +32,40 @@ "errorMessage": "Strandedness must be provided and be one of 'forward', 'reverse' or 'unstranded'", "enum": ["forward", "reverse", "unstranded"], "meta": ["strandedness"] + }, + "bam": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.bam$", + "errorMessage": "BAM file should end with `.bam`, should not contains spaces and should exist." + }, + "bai": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.bai$", + "errorMessage": "BAI file should end with `.bai`, should not contains spaces and should exist." + }, + "cram": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.cram$", + "errorMessage": "CRAM file should end with `.cram`, should not contains spaces and should exist." + }, + "crai": { + "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.crai$", + "errorMessage": "CRAI file should end with `.crai`, should not contains spaces and should exist." } }, - "required": ["sample", "fastq_1", "strandedness"] + "oneOf": [ + { "required": ["sample", "fastq_1", "strandedness"] }, + { "required": ["sample", "bam"] }, + { "required": ["sample", "cram"] } + ] } } diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 431e7286..de6dfe78 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -92,9 +92,9 @@ workflow PIPELINE_INITIALISATION { // ch_samplesheet = Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) - .map{ meta, fastq_1, fastq_2 -> - if (!fastq_2) return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - else return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + .map{ meta, fastq_1, fastq_2, bam, bai, cram, crai -> + def new_meta = meta + [ single_end: !fastq_2 ] + [ meta.id, new_meta, fastq_1, fastq_2, bam, bai, cram, crai ] } emit: @@ -180,7 +180,24 @@ def validateInputSamplesheet(input) { // Function to check samples are internally consistent after being grouped // def checkSamplesAfterGrouping(input) { - def (metas, fastqs) = input[1..2] + def (_ids, metas, fastqs_1, fastqs_2, bams, bais, crams, crais) = input + + def fastqs_1_list = fastqs_1.findAll { it -> it != [] } + def fastqs_2_list = fastqs_2.findAll { it -> it != [] } + def bam_list = bams.findAll { it -> it != [] } + def bai_list = bais.findAll { it -> it != [] } + def cram_list = crams.findAll { it -> it != [] } + def crai_list = crais.findAll { it -> it != [] } + + def alignment_file_list = bam_list + cram_list + if(alignment_file_list.size() > 1) { + error("Please check input samplesheet -> Multiple BAM/CRAM files per sample are not supported: ${metas[0].id}") + } + + def fastqs = fastqs_1_list + fastqs_2_list + if(alignment_file_list.size() == 1 && fastqs.size() > 0) { + error("Please check input samplesheet -> Detected FASTQ and BAM/CRAM files for the same sample. Please provide only one file type per sample: ${metas[0].id}") + } // Check that multiple runs of the same sample are of the same strandedness def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1 @@ -194,7 +211,7 @@ def checkSamplesAfterGrouping(input) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } - return [ metas[0], fastqs ] + return [ metas[0], fastqs, bam_list[0] ?: [], bai_list[0] ?: [], cram_list[0] ?: [], crai_list[0] ?: [] ] } // From eed191f004dd57d9f926f3ee8d5f5d3cef29fe68 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 15:58:14 +0100 Subject: [PATCH 154/275] add bam and cram samplesheet --- tests/csv/1.0/bam.csv | 2 ++ tests/csv/1.0/cram.csv | 2 ++ 2 files changed, 4 insertions(+) create mode 100644 tests/csv/1.0/bam.csv create mode 100644 tests/csv/1.0/cram.csv diff --git a/tests/csv/1.0/bam.csv b/tests/csv/1.0/bam.csv new file mode 100644 index 00000000..706a4baa --- /dev/null +++ b/tests/csv/1.0/bam.csv @@ -0,0 +1,2 @@ +sample,bam,bai,strandedness +GM12878,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai,reverse diff --git a/tests/csv/1.0/cram.csv b/tests/csv/1.0/cram.csv new file mode 100644 index 00000000..28ca3dc4 --- /dev/null +++ b/tests/csv/1.0/cram.csv @@ -0,0 +1,2 @@ +sample,cram,crai,strandedness +GM12878,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai,reverse From 7f27a52b70092078f4449adf5690ed0574e6a565 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 15:58:41 +0100 Subject: [PATCH 155/275] add new subwf prepare_alignment --- modules.json | 5 + .../nf-core/samtools/convert/environment.yml | 8 ++ modules/nf-core/samtools/convert/main.nf | 60 ++++++++ modules/nf-core/samtools/convert/meta.yml | 103 ++++++++++++++ .../samtools/convert/tests/main.nf.test | 107 ++++++++++++++ .../samtools/convert/tests/main.nf.test.snap | 131 ++++++++++++++++++ .../nf-core/samtools/convert/tests/tags.yml | 2 + subworkflows/local/prepare_alignment/main.nf | 46 ++++++ 8 files changed, 462 insertions(+) create mode 100644 modules/nf-core/samtools/convert/environment.yml create mode 100644 modules/nf-core/samtools/convert/main.nf create mode 100644 modules/nf-core/samtools/convert/meta.yml create mode 100644 modules/nf-core/samtools/convert/tests/main.nf.test create mode 100644 modules/nf-core/samtools/convert/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/convert/tests/tags.yml create mode 100755 subworkflows/local/prepare_alignment/main.nf diff --git a/modules.json b/modules.json index c3395b67..d42aada0 100755 --- a/modules.json +++ b/modules.json @@ -135,6 +135,11 @@ "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087", "installed_by": ["bam_markduplicates_picard"] }, + "samtools/convert": { + "branch": "master", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "installed_by": ["modules"] + }, "samtools/faidx": { "branch": "master", "git_sha": "f153f1f10e1083c49935565844cccb7453021682", diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml new file mode 100644 index 00000000..62054fc9 --- /dev/null +++ b/modules/nf-core/samtools/convert/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf new file mode 100644 index 00000000..cf9253d1 --- /dev/null +++ b/modules/nf-core/samtools/convert/main.nf @@ -0,0 +1,60 @@ +process SAMTOOLS_CONVERT { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" + + input: + tuple val(meta), path(input), path(index) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + + output: + tuple val(meta), path("*.bam") , emit: bam , optional: true + tuple val(meta), path("*.cram") , emit: cram, optional: true + tuple val(meta), path("*.bai") , emit: bai , optional: true + tuple val(meta), path("*.crai") , emit: crai, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def output_extension = input.getExtension() == "bam" ? "cram" : "bam" + + """ + samtools view \\ + --threads ${task.cpus} \\ + --reference ${fasta} \\ + $args \\ + $input \\ + -o ${prefix}.${output_extension} + + samtools index -@${task.cpus} ${prefix}.${output_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def output_extension = input.getExtension() == "bam" ? "cram" : "bam" + def index_extension = output_extension == "bam" ? "bai" : "crai" + + """ + touch ${prefix}.${output_extension} + touch ${prefix}.${index_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml new file mode 100644 index 00000000..d5bfa161 --- /dev/null +++ b/modules/nf-core/samtools/convert/meta.yml @@ -0,0 +1,103 @@ +name: samtools_convert +description: convert and then index CRAM -> BAM or BAM -> CRAM file +keywords: + - view + - index + - bam + - cram +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: biotools:samtools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file to create the CRAM file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference index file to create the CRAM file + pattern: "*.{fai}" +output: + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: filtered/converted BAM file + pattern: "*{.bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: filtered/converted CRAM file + pattern: "*{cram}" + - bai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: filtered/converted BAM index + pattern: "*{.bai}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: filtered/converted CRAM index + pattern: "*{.crai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@FriederikeHanssen" + - "@maxulysse" +maintainers: + - "@FriederikeHanssen" + - "@maxulysse" + - "@matthdsm" diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test b/modules/nf-core/samtools/convert/tests/main.nf.test new file mode 100644 index 00000000..91a0c69e --- /dev/null +++ b/modules/nf-core/samtools/convert/tests/main.nf.test @@ -0,0 +1,107 @@ +nextflow_process { + + name "Test Process SAMTOOLS_CONVERT" + script "../main.nf" + process "SAMTOOLS_CONVERT" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/convert" + + test("sarscov2 - [bam, bai], fasta, fai") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'fai' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.cram[0][1]).name).match("bam_to_cram_alignment") }, + { assert snapshot(file(process.out.crai[0][1]).name).match("bam_to_cram_index") }, + { assert snapshot(process.out.versions).match("bam_to_cram_versions") } + ) + } + } + + test("homo_sapiens - [cram, crai], fasta, fai") { + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'fai' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_alignment") }, + { assert snapshot(file(process.out.bai[0][1]).name).match("cram_to_bam_alignment_index") }, + { assert snapshot(process.out.versions).match("cram_to_bam_versions") } + ) + } + } + + test("sarscov2 - [bam, bai], fasta, fai - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'fai' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("stub") } + ) + } + } +} diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap new file mode 100644 index 00000000..a021254e --- /dev/null +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -0,0 +1,131 @@ +{ + "cram_to_bam_alignment": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-06T11:14:51.300147176" + }, + "bam_to_cram_alignment": { + "content": [ + "test.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-06T11:14:36.625470184" + }, + "cram_to_bam_versions": { + "content": [ + [ + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:52:35.516411351" + }, + "bam_to_cram_versions": { + "content": [ + [ + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:52:24.694454205" + }, + "stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" + ], + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:52:45.799885099" + }, + "bam_to_cram_index": { + "content": [ + "test.cram.crai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-06T11:14:36.640009334" + }, + "cram_to_bam_alignment_index": { + "content": [ + "test.bam.bai" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-06T11:14:51.304477426" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/convert/tests/tags.yml b/modules/nf-core/samtools/convert/tests/tags.yml new file mode 100644 index 00000000..030d5eb5 --- /dev/null +++ b/modules/nf-core/samtools/convert/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/convert: + - "modules/nf-core/samtools/convert/**" diff --git a/subworkflows/local/prepare_alignment/main.nf b/subworkflows/local/prepare_alignment/main.nf new file mode 100755 index 00000000..84b728e5 --- /dev/null +++ b/subworkflows/local/prepare_alignment/main.nf @@ -0,0 +1,46 @@ +// +// Prepare input alignment files +// + +include { SAMTOOLS_CONVERT } from '../../../modules/nf-core/samtools/convert' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index' + +workflow PREPARE_ALIGNMENT { + take: + ch_cram // [ val(meta), path(cram), path(crai) ] + ch_bam // [ val(meta), path(bam), path(bai) ] + ch_fasta // [ val(meta), path(fasta) ] + ch_fai // [ val(meta), path(fai) ] + + main: + ch_versions = Channel.empty() + + SAMTOOLS_CONVERT( + ch_cram, + ch_fasta, + ch_fai + ) + ch_versions = ch_versions.mix(SAMTOOLS_CONVERT.out.versions.first()) + + def ch_bam_branch = ch_bam.branch { meta, bam, bai -> + indexed: bai + return [ meta, bam, bai ] + not_indexed: !bai + return [ meta, bam ] + } + + def ch_bam_no_index = ch_bam_branch.not_indexed.mix(SAMTOOLS_CONVERT.out.cram) + + SAMTOOLS_INDEX( + ch_bam_no_index + ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + + def ch_bam_out = ch_bam_no_index + .join(SAMTOOLS_INDEX.out.bai, failOnMismatch: true, failOnDuplicate: true) + .mix(ch_bam_branch.indexed) + + emit: + bam = ch_bam_out // [ val(meta), path(bam), path(bai) ] + versions = ch_versions +} From c52c360ee0fbe135c88d1c7f63a35a8c923c1e06 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 16:24:40 +0100 Subject: [PATCH 156/275] finish up the implementation --- conf/modules.config | 1 + main.nf | 2 +- subworkflows/local/prepare_alignment/main.nf | 39 +++++++++++--------- subworkflows/local/prepare_genome/main.nf | 2 +- workflows/rnavar/main.nf | 36 +++++++++++++----- 5 files changed, 50 insertions(+), 30 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 87651eb8..84e7d625 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -220,6 +220,7 @@ process { withName: '.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { ext.args = '--create-output-bam-index false' + ext.prefix = { "${meta.id}.splitncigarreads" } } withName: '.*:SPLITNCIGAR:SAMTOOLS_INDEX' { diff --git a/main.nf b/main.nf index 4d823ad6..79ba8c9d 100644 --- a/main.nf +++ b/main.nf @@ -112,7 +112,7 @@ workflow NFCORE_RNAVAR { ch_gtf = PREPARE_GENOME.out.gtf ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() : PREPARE_GENOME.out.dict - ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai) + ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fasta_fai'], it ] }.collect() : PREPARE_GENOME.out.fasta_fai ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed diff --git a/subworkflows/local/prepare_alignment/main.nf b/subworkflows/local/prepare_alignment/main.nf index 84b728e5..9df331c9 100755 --- a/subworkflows/local/prepare_alignment/main.nf +++ b/subworkflows/local/prepare_alignment/main.nf @@ -15,32 +15,35 @@ workflow PREPARE_ALIGNMENT { main: ch_versions = Channel.empty() - SAMTOOLS_CONVERT( - ch_cram, - ch_fasta, - ch_fai - ) - ch_versions = ch_versions.mix(SAMTOOLS_CONVERT.out.versions.first()) - - def ch_bam_branch = ch_bam.branch { meta, bam, bai -> - indexed: bai - return [ meta, bam, bai ] - not_indexed: !bai - return [ meta, bam ] - } - - def ch_bam_no_index = ch_bam_branch.not_indexed.mix(SAMTOOLS_CONVERT.out.cram) + def ch_alignment_branch = ch_bam + .mix(ch_cram) + .branch { meta, bam, bai -> + indexed: bai + return [ meta, bam, bai ] + not_indexed_bam: !bai && bam.extension == "bam" + return [ meta, bam ] + not_indexed_cram: !bai && bam.extension == "cram" + return [ meta, bam ] + } + + def ch_bam_no_index = ch_alignment_branch.not_indexed_bam.mix(ch_alignment_branch.not_indexed_cram) SAMTOOLS_INDEX( ch_bam_no_index ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - def ch_bam_out = ch_bam_no_index + def ch_bam_indexed = ch_alignment_branch.not_indexed_bam .join(SAMTOOLS_INDEX.out.bai, failOnMismatch: true, failOnDuplicate: true) - .mix(ch_bam_branch.indexed) + + def ch_cram_indexed = ch_alignment_branch.not_indexed_cram + .join(SAMTOOLS_INDEX.out.crai, failOnMismatch: true, failOnDuplicate: true) + + def ch_alignment_out = ch_bam_indexed + .mix(ch_cram_indexed) + .mix(ch_alignment_branch.indexed) emit: - bam = ch_bam_out // [ val(meta), path(bam), path(bai) ] + bam = ch_alignment_out // [ val(meta), path(bam), path(bai) ] versions = ch_versions } diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index e5d9c8ce..c36767fa 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -69,7 +69,7 @@ workflow PREPARE_GENOME { dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed fasta = ch_fasta - fasta_fai = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] } // path: genome.fasta.fai + fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai gtf = ch_gtf.first() // path: genome.gtf star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 3deaa578..e4f3ce4c 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -27,6 +27,7 @@ include { TABIX_TABIX as TABIXGVCF } from '../../modules/nf-core/tabix/tabix' include { RECALIBRATE } from '../../subworkflows/local/recalibrate' include { SPLITNCIGAR } from '../../subworkflows/local/splitncigar' include { VCF_ANNOTATE_ALL } from '../../subworkflows/local/vcf_annotate_all' +include { PREPARE_ALIGNMENT } from '../../subworkflows/local/prepare_alignment' // nf-core include { BAM_MARKDUPLICATES_PICARD } from '../../subworkflows/nf-core/bam_markduplicates_picard' @@ -79,18 +80,32 @@ workflow RNAVAR { // To gather used softwares versions for MultiQC ch_versions = Channel.empty() - // MODULE: Concatenate FastQ files from same sample if required - ch_fastq = ch_input.groupTuple().map{ samplesheet -> checkSamplesAfterGrouping(samplesheet) } - .branch{ meta, fastqs -> + // Parse the input data + ch_parsed_input = ch_input.groupTuple().map{ samplesheet -> checkSamplesAfterGrouping(samplesheet) } + .branch{ meta, fastqs, bam, bai, cram, crai -> single : fastqs.size() == 1 return [ meta, fastqs.flatten() ] multiple: fastqs.size() > 1 return [ meta, fastqs.flatten() ] + bam : bam + return [ meta, bam, bai ] + cram : cram + return [ meta, cram, crai ] } - CAT_FASTQ(ch_fastq.multiple) + // MODULE: Prepare the alignment files (convert CRAM -> BAM and index) + PREPARE_ALIGNMENT( + ch_parsed_input.cram, + ch_parsed_input.bam, + ch_fasta, + ch_fasta_fai + ) + ch_versions = ch_versions.mix(PREPARE_ALIGNMENT.out.versions) + + // MODULE: Concatenate FastQ files from same sample if required + CAT_FASTQ(ch_parsed_input.multiple) - ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_fastq.single) + ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_parsed_input.single) ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) @@ -162,6 +177,7 @@ workflow RNAVAR { if (bai) [meta, bam, bai] else [meta, bam, csi] } + .mix(PREPARE_ALIGNMENT.out.bam) //Gather QC reports ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.metrics.collect{it[1]}.ifEmpty([])) @@ -177,7 +193,7 @@ workflow RNAVAR { SPLITNCIGAR(ch_genome_bam_bai, ch_fasta, - ch_fasta_fai, + ch_fasta_fai.map { _meta, fai -> fai }, ch_dict, ch_interval_list_split ) @@ -205,7 +221,7 @@ workflow RNAVAR { GATK4_BASERECALIBRATOR( ch_splitncigar_bam_bai_interval, ch_fasta.map{ meta, fasta -> [fasta] }, - ch_fasta_fai, + ch_fasta_fai.map { _meta, fai -> fai }, ch_dict.map{ meta, dict -> [dict] }, ch_known_sites, ch_known_sites_tbi @@ -232,7 +248,7 @@ workflow RNAVAR { params.skip_multiqc, ch_applybqsr_bam_bai_interval, ch_dict.map{ meta, dict -> [dict] }, - ch_fasta_fai, + ch_fasta_fai.map { _meta, fai -> fai }, ch_fasta.map{ meta, fasta -> [fasta] } ) @@ -270,7 +286,7 @@ workflow RNAVAR { GATK4_HAPLOTYPECALLER( ch_haplotypecaller_interval_bam, ch_fasta, - ch_fasta_fai.map{ it -> [[id:it.baseName], it] }, + ch_fasta_fai, ch_dict, ch_dbsnp_for_haplotypecaller, ch_dbsnp_for_haplotypecaller_tbi @@ -319,7 +335,7 @@ workflow RNAVAR { GATK4_VARIANTFILTRATION( ch_haplotypecaller_vcf_tbi, ch_fasta, - ch_fasta_fai.map{ fasta_fai -> [[id:'genome'], fasta_fai]}, + ch_fasta_fai, ch_dict ) From a9ec02d1b70377ca5da8195a7d770e1303bb4cf9 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 16:35:06 +0100 Subject: [PATCH 157/275] fix wrong fai input in markduplicates --- workflows/rnavar/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index e4f3ce4c..fa410948 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -168,7 +168,7 @@ workflow RNAVAR { // BAM_MARKDUPLICATES_PICARD(ch_genome_bam, ch_fasta, - ch_fasta_fai.map{ it -> [[id:'genome'], it] }) + ch_fasta_fai) ch_genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam .join(BAM_MARKDUPLICATES_PICARD.out.bai, remainder: true) From aff0de8ef578278e4ddbc153b94341c9dd77ec7b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 17:14:10 +0100 Subject: [PATCH 158/275] fix and add tests --- tests/all_inputs.nf.test | 36 ++++++++ tests/all_inputs.nf.test.snap | 133 +++++++++++++++++++++++++++ tests/annotation.nf.test | 6 +- tests/bam_csi.nf.test | 2 +- tests/bam_input.nf.test | 36 ++++++++ tests/bam_input.nf.test.snap | 79 ++++++++++++++++ tests/cram_input.nf.test | 36 ++++++++ tests/cram_input.nf.test.snap | 79 ++++++++++++++++ tests/csv/1.0/all.csv | 4 + tests/default.nf.test | 2 +- tests/removeduplicates.nf.test | 2 +- tests/skip_baserecalibration.nf.test | 2 +- 12 files changed, 410 insertions(+), 7 deletions(-) create mode 100644 tests/all_inputs.nf.test create mode 100644 tests/all_inputs.nf.test.snap create mode 100644 tests/bam_input.nf.test create mode 100644 tests/bam_input.nf.test.snap create mode 100644 tests/cram_input.nf.test create mode 100644 tests/cram_input.nf.test.snap create mode 100644 tests/csv/1.0/all.csv diff --git a/tests/all_inputs.nf.test b/tests/all_inputs.nf.test new file mode 100644 index 00000000..ee55eb6e --- /dev/null +++ b/tests/all_inputs.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline | all inputs" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test") { + + when { + params { + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/1.0/all.csv" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap new file mode 100644 index 00000000..41f88fd4 --- /dev/null +++ b/tests/all_inputs.nf.test.snap @@ -0,0 +1,133 @@ +{ + "Run with profile test": { + "content": [ + 79, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878_bam", + "preprocessing/GM12878_bam/GM12878_bam.recal.bam", + "preprocessing/GM12878_bam/GM12878_bam.recal.bam.bai", + "preprocessing/GM12878_cram", + "preprocessing/GM12878_cram/GM12878_cram.recal.bam", + "preprocessing/GM12878_cram/GM12878_cram.recal.bam.bai", + "preprocessing/GM12878_fastq", + "preprocessing/GM12878_fastq/GM12878_fastq.md.bam", + "preprocessing/GM12878_fastq/GM12878_fastq.md.bam.bai", + "preprocessing/GM12878_fastq/GM12878_fastq.recal.bam", + "preprocessing/GM12878_fastq/GM12878_fastq.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878_bam", + "reports/stats/GM12878_bam/GM12878_bam.stats", + "reports/stats/GM12878_cram", + "reports/stats/GM12878_cram/GM12878_cram.stats", + "reports/stats/GM12878_fastq", + "reports/stats/GM12878_fastq/GM12878_fastq.flagstat", + "reports/stats/GM12878_fastq/GM12878_fastq.stats", + "reports/stats/GM12878_fastq/STAR_log", + "reports/stats/GM12878_fastq/STAR_log/GM12878_fastq.Log.final.out", + "reports/stats/GM12878_fastq/STAR_log/GM12878_fastq.Log.out", + "reports/stats/GM12878_fastq/STAR_log/GM12878_fastq.Log.progress.out", + "reports/stats/GM12878_fastq/STAR_log/GM12878_fastq.SJ.out.tab", + "samtools", + "samtools/GM12878_fastq.bam", + "samtools/GM12878_fastq.bam.bai", + "variant_calling", + "variant_calling/GM12878_bam", + "variant_calling/GM12878_bam/GM12878_bam.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878_bam/GM12878_bam.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878_bam/GM12878_bam.haplotypecaller.vcf.gz", + "variant_calling/GM12878_bam/GM12878_bam.haplotypecaller.vcf.gz.tbi", + "variant_calling/GM12878_cram", + "variant_calling/GM12878_cram/GM12878_cram.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878_cram/GM12878_cram.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878_cram/GM12878_cram.haplotypecaller.vcf.gz", + "variant_calling/GM12878_cram/GM12878_cram.haplotypecaller.vcf.gz.tbi", + "variant_calling/GM12878_fastq", + "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.vcf.gz", + "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.1" + }, + "timestamp": "2025-01-07T17:13:49.548731154" + } +} \ No newline at end of file diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test index ca4c0c79..c2677c9e 100644 --- a/tests/annotation.nf.test +++ b/tests/annotation.nf.test @@ -27,7 +27,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } @@ -57,7 +57,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } @@ -87,7 +87,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } diff --git a/tests/bam_csi.nf.test b/tests/bam_csi.nf.test index 64ea8f58..7e3fd41f 100644 --- a/tests/bam_csi.nf.test +++ b/tests/bam_csi.nf.test @@ -26,7 +26,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } diff --git a/tests/bam_input.nf.test b/tests/bam_input.nf.test new file mode 100644 index 00000000..7e78259c --- /dev/null +++ b/tests/bam_input.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline | bam input" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test") { + + when { + params { + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/1.0/bam.csv" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap new file mode 100644 index 00000000..a646d392 --- /dev/null +++ b/tests/bam_input.nf.test.snap @@ -0,0 +1,79 @@ +{ + "Run with profile test": { + "content": [ + 28, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.stats", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.1" + }, + "timestamp": "2025-01-07T17:03:13.667134079" + } +} \ No newline at end of file diff --git a/tests/cram_input.nf.test b/tests/cram_input.nf.test new file mode 100644 index 00000000..315a7041 --- /dev/null +++ b/tests/cram_input.nf.test @@ -0,0 +1,36 @@ +nextflow_pipeline { + + name "Test pipeline | cram input" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test") { + + when { + params { + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/1.0/cram.csv" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap new file mode 100644 index 00000000..fab0606f --- /dev/null +++ b/tests/cram_input.nf.test.snap @@ -0,0 +1,79 @@ +{ + "Run with profile test": { + "content": [ + 28, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.stats", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/dbsnp_146.hg38.vcf", + "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", + "variant_calling/mills_and_1000G.indels.vcf", + "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.1" + }, + "timestamp": "2025-01-07T17:05:36.02051331" + } +} \ No newline at end of file diff --git a/tests/csv/1.0/all.csv b/tests/csv/1.0/all.csv new file mode 100644 index 00000000..09829568 --- /dev/null +++ b/tests/csv/1.0/all.csv @@ -0,0 +1,4 @@ +sample,fastq_1,fastq_2,bam,bai,cram,crai,strandedness +GM12878_fastq,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,,,,,reverse +GM12878_bam,,,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai,,,reverse +GM12878_cram,,,,,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai,reverse diff --git a/tests/default.nf.test b/tests/default.nf.test index 18825af0..e0904024 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -25,7 +25,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } diff --git a/tests/removeduplicates.nf.test b/tests/removeduplicates.nf.test index bac8205b..8d3d6116 100644 --- a/tests/removeduplicates.nf.test +++ b/tests/removeduplicates.nf.test @@ -26,7 +26,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } diff --git a/tests/skip_baserecalibration.nf.test b/tests/skip_baserecalibration.nf.test index 78982da0..4599ba8f 100644 --- a/tests/skip_baserecalibration.nf.test +++ b/tests/skip_baserecalibration.nf.test @@ -26,7 +26,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnavar_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name ).match() } From d9534bff3a3fa01e628569e848de63e991959065 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 7 Jan 2025 17:20:54 +0100 Subject: [PATCH 159/275] update docs & changelog --- CHANGELOG.md | 1 + docs/usage.md | 9 +++++++++ 2 files changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3256a119..83c8d2a7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - [#116](https://github.com/nf-core/rnavar/pull/116) - Added `unzip` from nf-core modules for working with unzipped fasta and gtf files +- [#157](https://github.com/nf-core/rnavar/pull/157) - Added support for `bam` and `cram` input files ### Changed diff --git a/docs/usage.md b/docs/usage.md index 8e2f2abf..af76cf85 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -111,8 +111,17 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,reverse | `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | | `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | | `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `bam` | Full path to BAM file created with STAR and duplicate marked. File has to have the extension ".bam". | +| `bai` | Full path to index file of the BAM file. File has to have the extension ".bai". | +| `cram` | Full path to CRAM file created with STAR and duplicate marked. File has to have the extension ".cram". | +| `crai` | Full path to index file of the CRAM file. File has to have the extension ".crai". | | `strandedness` | Sample strand-specificity. Must be one of `unstranded`, `forward` or `reverse`. | +:::note +Only one file type per sample is allowed. Supplying FASTQ files and a BAM/CRAM file for the same sample will cause an error in the pipeline. +The pipeline also has no support for multiple BAM/CRAM file per sample. +::: + An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. ## PIPELINE PARAMETERS AND DESCRIPTION From c7885440b858e038b6e074666a251c735ed21c78 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 8 Jan 2025 14:27:36 +0100 Subject: [PATCH 160/275] fix snapshots --- tests/all_inputs.nf.test.snap | 4 +- tests/annotation.nf.test.snap | 234 ++++++++++++++++++++-- tests/bam_csi.nf.test.snap | 67 ++++++- tests/default.nf.test.snap | 70 ++++++- tests/removeduplicates.nf.test.snap | 70 ++++++- tests/skip_baserecalibration.nf.test.snap | 64 +++++- 6 files changed, 472 insertions(+), 37 deletions(-) diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 41f88fd4..23afadb6 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -126,8 +126,8 @@ ], "meta": { "nf-test": "0.9.1", - "nextflow": "24.10.1" + "nextflow": "24.10.3" }, - "timestamp": "2025-01-07T17:13:49.548731154" + "timestamp": "2025-01-08T13:56:22.79954652" } } \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index a482d28f..afadab8f 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,8 +1,80 @@ { "Run with profile test | annotation with merge": { "content": [ - 46, - null, + 47, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "ENSEMBLVEP_VEP": { + "ensemblvep": 111.0 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "SNPEFF_SNPEFF": { + "snpeff": "5.1d" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "TABIX_BGZIPTABIX": { + "tabix": "1.19.1" + }, + "TABIX_TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "annotation", "annotation/haplotypecaller", @@ -185,15 +257,81 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T14:54:33.842224" + "timestamp": "2025-01-08T13:44:12.561904068" }, "Run with profile test | annotation with vep": { "content": [ - 43, - null, + 44, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "ENSEMBLVEP_VEP": { + "ensemblvep": 111.0 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "TABIX_TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "annotation", "annotation/haplotypecaller", @@ -363,15 +501,81 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T14:49:38.621181" + "timestamp": "2025-01-08T13:37:37.774766173" }, "Run with profile test | annotation with snpeff": { "content": [ - 43, - null, + 44, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "SNPEFF_SNPEFF": { + "snpeff": "5.1d" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "TABIX_BGZIPTABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "annotation", "annotation/haplotypecaller", @@ -437,9 +641,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T14:46:10.437216" + "timestamp": "2025-01-08T13:31:39.422563362" } } \ No newline at end of file diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index 8958e3dc..f984dd6a 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -1,8 +1,65 @@ { "Run with profile test | bam_csi_index": { "content": [ - 39, - null, + 40, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", @@ -43,9 +100,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T14:57:45.737274" + "timestamp": "2025-01-08T14:02:00.162034514" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index b1161f20..a7c2b652 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,8 +1,68 @@ { "Run with profile test": { "content": [ - 40, - null, + 41, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", @@ -45,9 +105,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T15:01:04.962148" + "timestamp": "2025-01-08T14:15:23.218615886" } } \ No newline at end of file diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 6011aff2..25ee58b7 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,8 +1,68 @@ { "Run with profile test | remove_duplicates": { "content": [ - 40, - null, + 41, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "CAT_FASTQ": { + "cat": 8.3 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", @@ -45,9 +105,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T15:05:33.998547" + "timestamp": "2025-01-08T14:21:28.482683082" } } \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index 2b3cefbe..eb925e0f 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -1,8 +1,62 @@ { "Run with profile test | skip_baserecalibration": { "content": [ - 36, - null, + 37, + { + "CAT_FASTQ": { + "cat": 8.3 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.1.1" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_IDXSTATS": { + "samtools": "1.19.2" + }, + "SAMTOOLS_INDEX": { + "samtools": "1.19.2" + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": "1.19.2" + }, + "SAMTOOLS_STATS": { + "samtools": "1.19.2" + }, + "STAR_ALIGN": { + "star": "2.7.10a", + "samtools": 1.18, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, [ "pipeline_info", "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", @@ -43,9 +97,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-10-11T15:10:25.387052" + "timestamp": "2025-01-08T14:26:44.327045503" } } \ No newline at end of file From ecdf0a085b53cbb1121f07519e340d46aa8eeede Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 8 Jan 2025 15:26:36 +0100 Subject: [PATCH 161/275] fix conf and main workflows --- main.nf | 2 +- nextflow.config | 9 ++- workflows/rnavar/main.nf | 149 +++++++++++++++++---------------------- 3 files changed, 71 insertions(+), 89 deletions(-) diff --git a/main.nf b/main.nf index 79ba8c9d..4cd8513f 100644 --- a/main.nf +++ b/main.nf @@ -128,7 +128,7 @@ workflow NFCORE_RNAVAR { snpeff_info = Channel.of([ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], params.snpeff_genome, params.snpeff_db ]) DOWNLOAD_CACHE_SNPEFF_VEP(ensemblvep_info, snpeff_info) snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache - vep_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ meta, cache -> [ cache ] } + vep_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ _meta, cache -> [ cache ] } ch_versions = ch_versions.mix(DOWNLOAD_CACHE_SNPEFF_VEP.out.versions) } else { diff --git a/nextflow.config b/nextflow.config index 03a582ed..e8958404 100644 --- a/nextflow.config +++ b/nextflow.config @@ -269,22 +269,21 @@ set -C # No clobber - prevent output redirection from overwriting files. // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = timeline.file.replace("timeline", "report") } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = timeline.file.replace("timeline", "trace") } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = timeline.file.replace("execution_timeline", "pipeline_dag") } manifest { diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index fa410948..592f58b6 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -75,10 +75,10 @@ workflow RNAVAR { main: // To gather all QC reports for MultiQC - ch_reports = Channel.empty() + def ch_reports = Channel.empty() // To gather used softwares versions for MultiQC - ch_versions = Channel.empty() + def ch_versions = Channel.empty() // Parse the input data ch_parsed_input = ch_input.groupTuple().map{ samplesheet -> checkSamplesAfterGrouping(samplesheet) } @@ -105,13 +105,13 @@ workflow RNAVAR { // MODULE: Concatenate FastQ files from same sample if required CAT_FASTQ(ch_parsed_input.multiple) - ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_parsed_input.single) + def ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_parsed_input.single) ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) // MODULE: Generate QC summary using FastQC FASTQC(ch_cat_fastq) - ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ meta, logs -> logs }) + ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ _meta, logs -> logs }) ch_versions = ch_versions.mix(FASTQC.out.versions) // @@ -119,30 +119,24 @@ workflow RNAVAR { // GATK4_BEDTOINTERVALLIST(ch_exon_bed, ch_dict) - ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list + def ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions) // // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools // - ch_interval_list_split = Channel.empty() + def ch_interval_list_split = Channel.empty() if (!params.skip_intervallisttools) { GATK4_INTERVALLISTTOOLS(ch_interval_list) - ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ meta, bed -> [bed] }.flatten() + ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.flatten() + } + else { + ch_interval_list_split = ch_interval_list } - else ch_interval_list_split = ch_interval_list // // SUBWORKFLOW: Perform read alignment using STAR aligner // - ch_genome_bam = Channel.empty() - ch_genome_bam_index = Channel.empty() - ch_samtools_stats = Channel.empty() - ch_samtools_flagstat = Channel.empty() - ch_samtools_idxstats = Channel.empty() - ch_star_multiqc = Channel.empty() - ch_aligner_pca_multiqc = Channel.empty() - ch_aligner_clustering_multiqc = Channel.empty() if (params.aligner == 'star') { FASTQ_ALIGN_STAR(ch_cat_fastq, @@ -154,9 +148,7 @@ workflow RNAVAR { ch_fasta, [[:],[]]) //ch_transcripts_fasta) - ch_genome_bam = FASTQ_ALIGN_STAR.out.bam - ch_genome_bam_index = FASTQ_ALIGN_STAR.out.bai - ch_transcriptome_bam = FASTQ_ALIGN_STAR.out.bam_transcript + def ch_genome_bam = FASTQ_ALIGN_STAR.out.bam // Gather QC reports ch_reports = ch_reports.mix(FASTQ_ALIGN_STAR.out.log_out) @@ -170,9 +162,9 @@ workflow RNAVAR { ch_fasta, ch_fasta_fai) - ch_genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam + def ch_genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam .join(BAM_MARKDUPLICATES_PICARD.out.bai, remainder: true) - .join(BAM_MARKDUPLICATES_PICARD.out.csi, remainder: true) + .join(BAM_MARKDUPLICATES_PICARD.out.csi, remainder: true) // TODO fix this bottleneck .map{meta, bam, bai, csi -> if (bai) [meta, bam, bai] else [meta, bam, csi] @@ -198,47 +190,44 @@ workflow RNAVAR { ch_interval_list_split ) - ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai - ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions) + def ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai + ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions) // // MODULE: BaseRecalibrator from GATK4 // Generates a recalibration table based on various co-variates // - ch_bam_variant_calling = Channel.empty() + def ch_bam_variant_calling = Channel.empty() if (!params.skip_baserecalibration) { - ch_bqsr_table = Channel.empty() // known_sites is made by grouping both the dbsnp and the known indels ressources // they can either or both be optional - ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() - ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() + def ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() + def ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() - ch_interval_list_recalib = ch_interval_list.map{ meta, bed -> [bed] }.flatten() - ch_splitncigar_bam_bai_interval = ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) + def ch_interval_list_recalib = ch_interval_list.map{ _meta, bed -> [bed] }.flatten() + def ch_splitncigar_bam_bai_interval = ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] } GATK4_BASERECALIBRATOR( ch_splitncigar_bam_bai_interval, - ch_fasta.map{ meta, fasta -> [fasta] }, + ch_fasta.map{ _meta, fasta -> [fasta] }, ch_fasta_fai.map { _meta, fai -> fai }, - ch_dict.map{ meta, dict -> [dict] }, + ch_dict.map{ _meta, dict -> [dict] }, ch_known_sites, ch_known_sites_tbi ) - ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table + def ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table // Gather QC reports - ch_reports = ch_reports.mix(ch_bqsr_table.map{ meta, table -> table}) + ch_reports = ch_reports.mix(ch_bqsr_table.map{ _meta, table -> table}) ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions) - ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table) - ch_bam_recalibrated_qc = Channel.empty() + def ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table) - ch_interval_list_applybqsr = ch_interval_list.map{ meta, bed -> [bed] }.flatten() - ch_bam_applybqsr.combine(ch_interval_list_applybqsr) + def ch_interval_list_applybqsr = ch_interval_list.map{ _meta, bed -> [bed] }.flatten() + def ch_applybqsr_bam_bai_interval = ch_bam_applybqsr.combine(ch_interval_list_applybqsr) .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} - .set{ch_applybqsr_bam_bai_interval} // // MODULE: ApplyBaseRecalibrator from GATK4 @@ -247,13 +236,12 @@ workflow RNAVAR { RECALIBRATE( params.skip_multiqc, ch_applybqsr_bam_bai_interval, - ch_dict.map{ meta, dict -> [dict] }, + ch_dict.map{ _meta, dict -> [dict] }, ch_fasta_fai.map { _meta, fai -> fai }, - ch_fasta.map{ meta, fasta -> [fasta] } + ch_fasta.map{ _meta, fasta -> [fasta] } ) ch_bam_variant_calling = RECALIBRATE.out.bam - ch_bam_recalibrated_qc = RECALIBRATE.out.qc // Gather QC reports ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) @@ -262,8 +250,9 @@ workflow RNAVAR { ch_bam_variant_calling = ch_splitncigar_bam_bai } - interval_flag = params.no_intervals // Run haplotyper even in the absence of dbSNP files + def ch_dbsnp_for_haplotypecaller = Channel.empty() + def ch_dbsnp_for_haplotypecaller_tbi = Channel.empty() if (!params.dbsnp){ ch_dbsnp_for_haplotypecaller = [[id:'null'], []] ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] @@ -272,7 +261,6 @@ workflow RNAVAR { ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } } - ch_haplotypecaller_vcf = Channel.empty() ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) .map{ meta, bam, bai, interval_list -> [ meta + [ id:meta.id + "_" + interval_list.baseName, sample:meta.id, variantcaller:'haplotypecaller' ], bam, bai, interval_list, [] ] @@ -292,10 +280,11 @@ workflow RNAVAR { ch_dbsnp_for_haplotypecaller_tbi ) - ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() + def ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() // TODO fix this bottleneck ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions) + def ch_haplotypecaller_vcf = Channel.empty() if (!params.generate_gvcf){ // // MODULE: MergeVCFS from GATK4 @@ -315,16 +304,16 @@ workflow RNAVAR { ch_haplotypecaller_vcf ) - ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf + def ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf .join(TABIX.out.tbi, by: [0], remainder: true) - .join(TABIX.out.csi, by: [0], remainder: true) + .join(TABIX.out.csi, by: [0], remainder: true) // TODO fix this bottleneck .map{meta, vcf, tbi, csi -> if (tbi) [meta, vcf, tbi] else [meta, vcf, csi] } - ch_versions = ch_versions.mix(TABIX.out.versions) - ch_final_vcf = ch_haplotypecaller_vcf + ch_versions = ch_versions.mix(TABIX.out.versions) + def ch_final_vcf = Channel.empty() // // MODULE: VariantFiltration from GATK4 @@ -339,9 +328,11 @@ workflow RNAVAR { ch_dict ) - ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf + def ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf ch_final_vcf = ch_filtered_vcf ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions) + } else { + ch_final_vcf = ch_haplotypecaller_vcf } // @@ -349,11 +340,11 @@ workflow RNAVAR { // if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { - vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []] + def ch_vep_fasta = (params.vep_include_fasta) ? ch_fasta: [[id: 'null'], []] VCF_ANNOTATE_ALL( ch_final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, - vep_fasta, + ch_vep_fasta, params.annotate_tools, params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}", snpeff_cache, @@ -371,26 +362,26 @@ workflow RNAVAR { ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions) } - } - else{ - ch_haplotypecaller_raw_index = GATK4_HAPLOTYPECALLER.out.tbi - .map{ meta, idx -> - meta.id = meta.sample - [meta, idx]} - .groupTuple() + } else { + def ch_combinegvcfs_input = GATK4_HAPLOTYPECALLER.out.vcf + .join(GATK4_HAPLOTYPECALLER.out.tbi, failOnMismatch:true, failOnDuplicate:true) + .map{ meta, vcf, tbi -> + def new_meta = meta + [id:meta.sample] + [new_meta, vcf, tbi] + } + .groupTuple() // TODO fix this bottleneck // // MODULE: CombineGVCFS from GATK4 // Merge multiple GVCF files into one GVCF // GATK4_COMBINEGVCFS( - ch_haplotypecaller_raw, - ch_haplotypecaller_raw_index, - ch_fasta, - ch_fai, - ch_dict + ch_combinegvcfs_input, + ch_fasta.map { _meta, fasta -> fasta }, + ch_fasta_fai.map { _meta, fai -> fai }, + ch_dict.map { _meta, dict -> dict } ) - ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf + def ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions) // @@ -398,14 +389,6 @@ workflow RNAVAR { // TABIXGVCF(ch_haplotypecaller_gvcf) - ch_haplotypecaller_gvcf_tbi = ch_haplotypecaller_gvcf - .join(TABIXGVCF.out.tbi, by: [0], remainder: true) - .join(TABIXGVCF.out.csi, by: [0], remainder: true) - .map{meta, vcf, tbi, csi -> - if (tbi) [meta, vcf, tbi] - else [meta, vcf, csi] - } - ch_versions = ch_versions.mix(TABIXGVCF.out.versions) } @@ -414,24 +397,24 @@ workflow RNAVAR { // // Collate and save software versions // - ch_collated_versions = softwareVersionsToYAML(ch_versions).collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + def ch_collated_versions = softwareVersionsToYAML(ch_versions).collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) // // MODULE: MultiQC // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report // - multiqc_report = Channel.empty() + def multiqc_report = Channel.empty() if (!params.skip_multiqc){ - ch_multiqc_files = Channel.empty() - - ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + def ch_multiqc_files = Channel.empty() + + def ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + def ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + def ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + def summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + def ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + def ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) From 43eda7dfcdf4a762a6d439f0be1e480b911c0bdf Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 8 Jan 2025 15:39:47 +0100 Subject: [PATCH 162/275] fix local subwfs --- main.nf | 2 - .../local/cram_qc_mosdepth_samtools/main.nf | 2 +- subworkflows/local/prepare_alignment/main.nf | 2 - subworkflows/local/prepare_genome/main.nf | 4 +- subworkflows/local/recalibrate/main.nf | 39 ++++++++----------- subworkflows/local/splitncigar/main.nf | 8 ++-- .../utils_nfcore_rnavar_pipeline/main.nf | 2 - subworkflows/local/vcf_annotate_all/main.nf | 37 ++++++++---------- .../local/vcf_annotate_bcftools/main.nf | 7 +--- workflows/rnavar/main.nf | 6 +-- 10 files changed, 44 insertions(+), 65 deletions(-) diff --git a/main.nf b/main.nf index 4cd8513f..7a4f7f4f 100644 --- a/main.nf +++ b/main.nf @@ -190,10 +190,8 @@ workflow { PIPELINE_INITIALISATION ( params.version, params.validate_params, - params.monochrome_logs, args, params.outdir, - params.input ) // diff --git a/subworkflows/local/cram_qc_mosdepth_samtools/main.nf b/subworkflows/local/cram_qc_mosdepth_samtools/main.nf index e2b51418..d44ff623 100644 --- a/subworkflows/local/cram_qc_mosdepth_samtools/main.nf +++ b/subworkflows/local/cram_qc_mosdepth_samtools/main.nf @@ -20,7 +20,7 @@ workflow CRAM_QC_MOSDEPTH_SAMTOOLS { // Reports run on cram SAMTOOLS_STATS(cram, fasta) - MOSDEPTH(cram.combine(intervals.map{ meta, bed -> [ bed ?: [] ] }), fasta) + MOSDEPTH(cram.combine(intervals.map{ _meta, bed -> [ bed ?: [] ] }), fasta) // Gather all reports generated reports = reports.mix(SAMTOOLS_STATS.out.stats) diff --git a/subworkflows/local/prepare_alignment/main.nf b/subworkflows/local/prepare_alignment/main.nf index 9df331c9..a9c3d85d 100755 --- a/subworkflows/local/prepare_alignment/main.nf +++ b/subworkflows/local/prepare_alignment/main.nf @@ -9,8 +9,6 @@ workflow PREPARE_ALIGNMENT { take: ch_cram // [ val(meta), path(cram), path(crai) ] ch_bam // [ val(meta), path(bam), path(bai) ] - ch_fasta // [ val(meta), path(fasta) ] - ch_fai // [ val(meta), path(fai) ] main: ch_versions = Channel.empty() diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index c36767fa..69a1a7f8 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -72,8 +72,8 @@ workflow PREPARE_GENOME { fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai gtf = ch_gtf.first() // path: genome.gtf star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ - dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi - known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi + dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi + known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi versions = ch_versions // channel: [ versions.yml ] // bedtools_sort = ch_bedtools_sort // path: sort.bed // bedtools_merge = ch_bedtools_merge // path: merge.bed diff --git a/subworkflows/local/recalibrate/main.nf b/subworkflows/local/recalibrate/main.nf index bbf80e1b..5d41143e 100644 --- a/subworkflows/local/recalibrate/main.nf +++ b/subworkflows/local/recalibrate/main.nf @@ -11,33 +11,29 @@ include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools workflow RECALIBRATE { take: skip_samtools // boolean: true/false - bam // channel: [mandatory] bam - dict // channel: [mandatory] dict - fai // channel: [mandatory] fai - fasta // channel: [mandatory] fasta + ch_bam // channel: [mandatory] bam + ch_dict // channel: [mandatory] dict + ch_fai // channel: [mandatory] fai + ch_fasta // channel: [mandatory] fasta main: - ch_versions = Channel.empty() - - bam_recalibrated_index = Channel.empty() - bam_recalibrated = Channel.empty() - bam_reports = Channel.empty() + def ch_versions = Channel.empty() APPLYBQSR ( - bam, - fasta, - fai, - dict + ch_bam, + ch_fasta, + ch_fai, + ch_dict ) - bam_recalibrated = APPLYBQSR.out.bam + def bam_recalibrated = APPLYBQSR.out.bam ch_versions = ch_versions.mix(APPLYBQSR.out.versions.first()) SAMTOOLS_INDEX(bam_recalibrated) - bam_recalibrated_index = bam_recalibrated + def bam_recalibrated_index = bam_recalibrated .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) - .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) + .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) // TODO fix this bottleneck .map{meta, bam, bai, csi -> if (bai) [meta, bam, bai] else [meta, bam, csi] @@ -45,20 +41,19 @@ workflow RECALIBRATE { ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - samtools_stats = Channel.empty() + def bam_reports = Channel.empty() if (!skip_samtools) { SAMTOOLS_STATS(bam_recalibrated_index, [[], []]) - samtools_stats = SAMTOOLS_STATS.out.stats + bam_reports = SAMTOOLS_STATS.out.stats ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first()) } - bam_reports = samtools_stats emit: - bam = bam_recalibrated_index - qc = bam_reports + bam = bam_recalibrated_index + qc = bam_reports - versions = ch_versions + versions = ch_versions } diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 91524e64..d6f3e044 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -8,16 +8,16 @@ include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index workflow SPLITNCIGAR { take: - bam // channel: [ val(meta), [ bam ], [bai] ] + ch_bam // channel: [ val(meta), [ bam ], [bai] ] ch_fasta // channel: [ fasta ] ch_fai // channel: [ fai ] ch_dict // channel: [ dict ] - intervals // channel: [ interval_list] + ch_intervals // channel: [ interval_list] main: ch_versions = Channel.empty() - bam_interval = bam.combine(intervals).map{ meta, bam, bai, intervals -> [ meta + [sample:meta.id], bam, bai, intervals ] } + def bam_interval = ch_bam.combine(ch_intervals).map{ meta, bam, bai, intervals -> [ meta + [sample:meta.id], bam, bai, intervals ] } GATK4_SPLITNCIGARREADS(bam_interval, ch_fasta, @@ -40,7 +40,7 @@ workflow SPLITNCIGAR { splitncigar_bam_bai = splitncigar_bam .join(SAMTOOLS_INDEX.out.bai, remainder: true) - .join(SAMTOOLS_INDEX.out.csi, remainder: true) + .join(SAMTOOLS_INDEX.out.csi, remainder: true) // TODO fix this bottleneck .map{meta, bam, bai, csi -> if (bai) [meta, bam, bai] else [meta, bam, csi] diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index de6dfe78..e4f83075 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -28,10 +28,8 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit validate_params // boolean: Boolean whether to validate parameters against the schema at runtime - monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved - input // string: Path to input samplesheet main: diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf index 20cab4be..d25801a3 100644 --- a/subworkflows/local/vcf_annotate_all/main.nf +++ b/subworkflows/local/vcf_annotate_all/main.nf @@ -9,8 +9,8 @@ include { VCF_ANNOTATE_SNPEFF } from '../../nf-core/vc workflow VCF_ANNOTATE_ALL { take: - vcf // channel: [ val(meta), vcf ] - fasta + ch_vcf // channel: [ val(meta), vcf ] + ch_fasta tools // Mandatory, list of tools to apply snpeff_db snpeff_cache @@ -19,19 +19,16 @@ workflow VCF_ANNOTATE_ALL { vep_cache_version vep_cache vep_extra_files - bcftools_annotations - bcftools_annotations_index - bcftools_header_lines main: - reports = Channel.empty() - vcf_ann = Channel.empty() - tab_ann = Channel.empty() - json_ann = Channel.empty() - versions = Channel.empty() + def ch_reports = Channel.empty() + def vcf_ann = Channel.empty() + def tab_ann = Channel.empty() + def json_ann = Channel.empty() + def versions = Channel.empty() if (tools.split(',').contains('bcfann')) { - VCF_ANNOTATE_BCFTOOLS(vcf, bcftools_annotations, bcftools_annotations_index, bcftools_header_lines) + VCF_ANNOTATE_BCFTOOLS(ch_vcf) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) versions = versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions) @@ -39,27 +36,27 @@ workflow VCF_ANNOTATE_ALL { if (tools.split(',').contains('merge') || tools.split(',').contains('snpeff')) { - VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache) + VCF_ANNOTATE_SNPEFF(ch_vcf, snpeff_db, snpeff_cache) - reports = reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ meta, reports -> [ reports ] }) + ch_reports = ch_reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ _meta, reports -> [ reports ] }) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi) versions = versions.mix(VCF_ANNOTATE_SNPEFF.out.versions) } if (tools.split(',').contains('merge')) { - vcf_ann_for_merge = VCF_ANNOTATE_SNPEFF.out.vcf_tbi.map{ meta, vcf, tbi -> [ meta, vcf, [] ] } - VCF_ANNOTATE_MERGE(vcf_ann_for_merge, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) + vcf_ann_for_merge = VCF_ANNOTATE_SNPEFF.out.vcf_tbi.map{ meta, vcf, _tbi -> [ meta, vcf, [] ] } + VCF_ANNOTATE_MERGE(vcf_ann_for_merge, ch_fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) - reports = reports.mix(VCF_ANNOTATE_MERGE.out.reports) + ch_reports = ch_reports.mix(VCF_ANNOTATE_MERGE.out.reports) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi) versions = versions.mix(VCF_ANNOTATE_MERGE.out.versions) } if (tools.split(',').contains('vep')) { - vcf_for_vep = vcf.map{ meta, vcf -> [ meta, vcf, [] ] } - VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) + vcf_for_vep = ch_vcf.map{ meta, vcf -> [ meta, vcf, [] ] } + VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, ch_fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) - reports = reports.mix(VCF_ANNOTATE_ENSEMBLVEP.out.reports) + ch_reports = ch_reports.mix(VCF_ANNOTATE_ENSEMBLVEP.out.reports) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi) tab_ann = tab_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab) json_ann = json_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json) @@ -70,6 +67,6 @@ workflow VCF_ANNOTATE_ALL { vcf_ann // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] tab_ann json_ann - reports // path: *.html + reports = ch_reports // path: *.html versions // path: versions.yml } diff --git a/subworkflows/local/vcf_annotate_bcftools/main.nf b/subworkflows/local/vcf_annotate_bcftools/main.nf index f616af8c..fb506f2d 100644 --- a/subworkflows/local/vcf_annotate_bcftools/main.nf +++ b/subworkflows/local/vcf_annotate_bcftools/main.nf @@ -8,15 +8,12 @@ include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow VCF_ANNOTATE_BCFTOOLS { take: - vcf // channel: [ val(meta), vcf ] - annotations // - annotations_index // - header_lines // + ch_vcf // channel: [ val(meta), vcf ] main: ch_versions = Channel.empty() - BCFTOOLS_ANNOTATE(vcf, annotations, annotations_index, header_lines) + BCFTOOLS_ANNOTATE(ch_vcf.map { meta, vcf -> [ meta, vcf, [], [], [], []]}) TABIX_TABIX(BCFTOOLS_ANNOTATE.out.vcf) ch_vcf_tbi = BCFTOOLS_ANNOTATE.out.vcf.join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 592f58b6..c19d0223 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -97,8 +97,6 @@ workflow RNAVAR { PREPARE_ALIGNMENT( ch_parsed_input.cram, ch_parsed_input.bam, - ch_fasta, - ch_fasta_fai ) ch_versions = ch_versions.mix(PREPARE_ALIGNMENT.out.versions) @@ -353,9 +351,7 @@ workflow RNAVAR { vep_cache_version, vep_cache, vep_extra_files, - [], // bcftools_annotations, - [], //bcftools_annotations_tbi, - []) //bcftools_header_lines) + ) // Gather QC reports ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports) From 77dc247477e0fd56c9d8d999ca902f060a6d4fe3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 09:30:10 +0100 Subject: [PATCH 163/275] fix subwfs --- modules.json | 246 +- .../picard/markduplicates/environment.yml | 4 +- modules/nf-core/picard/markduplicates/main.nf | 4 +- .../nf-core/picard/markduplicates/meta.yml | 116 +- .../picard/markduplicates/tests/main.nf.test | 99 +- .../markduplicates/tests/main.nf.test.snap | 271 +- .../nf-core/samtools/flagstat/environment.yml | 8 +- modules/nf-core/samtools/flagstat/main.nf | 5 +- modules/nf-core/samtools/flagstat/meta.yml | 54 +- .../samtools/flagstat/tests/main.nf.test | 28 +- .../samtools/flagstat/tests/main.nf.test.snap | 78 +- .../nf-core/samtools/idxstats/environment.yml | 8 +- modules/nf-core/samtools/idxstats/main.nf | 5 +- modules/nf-core/samtools/idxstats/meta.yml | 51 +- .../samtools/idxstats/tests/main.nf.test | 29 +- .../samtools/idxstats/tests/main.nf.test.snap | 78 +- .../nf-core/samtools/index/environment.yml | 8 +- modules/nf-core/samtools/index/main.nf | 11 +- modules/nf-core/samtools/index/meta.yml | 68 +- .../nf-core/samtools/index/tests/main.nf.test | 87 +- .../samtools/index/tests/main.nf.test.snap | 264 +- modules/nf-core/samtools/sort/environment.yml | 8 +- modules/nf-core/samtools/sort/main.nf | 29 +- modules/nf-core/samtools/sort/meta.yml | 99 +- .../nf-core/samtools/sort/tests/main.nf.test | 114 +- .../samtools/sort/tests/main.nf.test.snap | 191 +- .../samtools/sort/tests/nextflow_cram.config | 8 + .../nf-core/samtools/stats/environment.yml | 8 +- modules/nf-core/samtools/stats/main.nf | 5 +- modules/nf-core/samtools/stats/meta.yml | 69 +- .../nf-core/samtools/stats/tests/main.nf.test | 60 +- .../samtools/stats/tests/main.nf.test.snap | 98 +- modules/nf-core/star/align/environment.yml | 9 +- modules/nf-core/star/align/main.nf | 48 +- modules/nf-core/star/align/meta.yml | 269 +- modules/nf-core/star/align/tests/main.nf.test | 509 +++- .../star/align/tests/main.nf.test.snap | 2344 ++++++++++++----- .../star/align/tests/nextflow.arriba.config | 3 - .../nf-core/star/align/tests/nextflow.config | 3 - .../align/tests/nextflow.starfusion.config | 3 - .../tests/main.nf.test | 71 +- .../tests/main.nf.test.snap | 326 ++- .../tests/main.nf.test | 76 +- .../tests/main.nf.test.snap | 328 ++- .../bam_stats_samtools/tests/main.nf.test | 116 +- .../tests/main.nf.test.snap | 352 ++- .../fastq_align_star/tests/main.nf.test | 114 +- .../fastq_align_star/tests/main.nf.test.snap | 944 +------ .../nf-core/utils_nextflow_pipeline/main.nf | 2 + .../tests/main.workflow.nf.test | 10 +- .../nf-core/utils_nfcore_pipeline/main.nf | 89 +- .../tests/main.function.nf.test | 46 +- .../tests/main.function.nf.test.snap | 30 - .../utils_nfschema_plugin/tests/main.nf.test | 4 +- 54 files changed, 5341 insertions(+), 2566 deletions(-) create mode 100644 modules/nf-core/samtools/sort/tests/nextflow_cram.config diff --git a/modules.json b/modules.json index d42aada0..c2c6a5be 100755 --- a/modules.json +++ b/modules.json @@ -8,207 +8,303 @@ "bcftools/annotate": { "branch": "master", "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/concat": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep", + "vcf_annotate_snpeff" + ] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep", + "vcf_annotate_snpeff" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep", + "vcf_annotate_snpeff" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "a5377837fe9013bde89de8689829e83e84086536", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/download": { "branch": "master", "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": ["modules", "vcf_annotate_ensemblvep"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep" + ] }, "fastqc": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/applybqsr": { "branch": "master", "git_sha": "af273ea6618c50e82c372abe18b0a225e84fe6f7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/baserecalibrator": { "branch": "master", "git_sha": "8a223e11d4e6deb36484e01891eae9c1cacb5f5d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "d3f215802f696f7993f25c759781d2db91232015", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/combinegvcfs": { "branch": "master", "git_sha": "fe3d7aac1b62efe4fd05cc9629d192e9cdfc3ccb", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/indexfeaturefile": { "branch": "master", "git_sha": "108e1f5bafc045ac19890852a41e8d95ae12aa67", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/splitncigarreads": { "branch": "master", "git_sha": "1e15ad71d9022293985dd02e24186e5e496a0b3c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "00409369b2aff69bded4f0a9e7a80e17d933b426", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gffread": { "branch": "master", "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "picard/markduplicates": { "branch": "master", - "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087", - "installed_by": ["bam_markduplicates_picard"] + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "installed_by": [ + "bam_markduplicates_picard" + ] }, "samtools/convert": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "f153f1f10e1083c49935565844cccb7453021682", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_stats_samtools", "modules"] + "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", + "installed_by": [ + "bam_stats_samtools", + "modules" + ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_stats_samtools", "modules"] + "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", + "installed_by": [ + "bam_stats_samtools", + "modules" + ] }, "samtools/index": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"] + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", + "installed_by": [ + "bam_markduplicates_picard", + "bam_sort_stats_samtools", + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", - "installed_by": ["bam_sort_stats_samtools", "modules"] + "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", + "installed_by": [ + "bam_sort_stats_samtools", + "modules" + ] }, "samtools/stats": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_stats_samtools", "modules"] + "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", + "installed_by": [ + "bam_stats_samtools", + "modules" + ] }, "snpeff/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/snpeff": { "branch": "master", "git_sha": "2f3db6f45147ebbb56b371536e31bdf622b5bfee", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_snpeff" + ] }, "star/align": { "branch": "master", - "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["fastq_align_star", "modules"] + "git_sha": "59f52afcd8eabf15e8713095207272624171c65a", + "installed_by": [ + "fastq_align_star", + "modules" + ] }, "star/genomegenerate": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_snpeff" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", - "installed_by": ["modules", "vcf_annotate_ensemblvep"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep" + ] }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -216,51 +312,71 @@ "nf-core": { "bam_markduplicates_picard": { "branch": "master", - "git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087", - "installed_by": ["subworkflows"] + "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "installed_by": [ + "subworkflows" + ] }, "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", - "installed_by": ["fastq_align_star", "subworkflows"] + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", + "installed_by": [ + "fastq_align_star", + "subworkflows" + ] }, "bam_stats_samtools": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"] + "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", + "installed_by": [ + "bam_markduplicates_picard", + "bam_sort_stats_samtools" + ] }, "fastq_align_star": { "branch": "master", - "git_sha": "1d1d7df613ff53223259c14185858cd742cd4743", - "installed_by": ["subworkflows"] + "git_sha": "6a367612c2c27aa659293c656afa764361223db4", + "installed_by": [ + "subworkflows" + ] }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", - "installed_by": ["subworkflows"] + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", - "installed_by": ["subworkflows"] + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": ["subworkflows"] + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 58b795f5..1d715d56 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -1,7 +1,5 @@ -name: picard_markduplicates channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::picard=3.1.1 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index ad0b2963..8a2ed64e 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : - 'biocontainers/picard:3.1.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 1f0ffe16..bcaf9160 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -15,60 +15,82 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Sequence reads file, can be SAM/BAM/CRAM format - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file, required for CRAM input - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference genome fasta index - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file, required for CRAM input + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference genome fasta index + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be + passed as a flag + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" - metrics: - type: file - description: Duplicate metrics file generated by picard - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by picard + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test b/modules/nf-core/picard/markduplicates/tests/main.nf.test index e3e97f6c..9ed90965 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test @@ -27,9 +27,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("unsorted_bam_name") }, - { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("unsorted_bam_metrics") }, - { assert snapshot(process.out.versions).match("unsorted_bam_versions") } + { assert snapshot( + file(process.out.bam[0][1]).name, + path(process.out.metrics.get(0).get(1)).readLines()[0..2], + process.out.versions) + .match() } ) } } @@ -52,9 +54,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("sorted_bam_name") }, - { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("sorted_bam_metrics") }, - { assert snapshot(process.out.versions).match("sorted_bam_versions") } + { assert snapshot( + file(process.out.bam[0][1]).name, + path(process.out.metrics.get(0).get(1)).readLines()[0..2], + process.out.versions) + .match() } ) } } @@ -83,9 +87,86 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.cram[0][1]).name).match("cram_name") }, - { assert snapshot(path(process.out.metrics.get(0).get(1)).readLines()[0..2]).match("cram_metrics") }, - { assert snapshot(process.out.versions).match("cram_versions") } + { assert snapshot( + file(process.out.cram[0][1]).name, + path(process.out.metrics.get(0).get(1)).readLines()[0..2], + process.out.versions) + .match() } + ) + } + } + + test("sarscov2 [unsorted bam] - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 [sorted bam] - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = [ [:], [] ] + input[2] = [ [:], [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens [cram] - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index eb17111e..13770a8e 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -1,110 +1,251 @@ { - "sorted_bam_versions": { + "sarscov2 [sorted bam] - stub": { "content": [ - [ - "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ], + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-20T15:31:50.928021" + "timestamp": "2024-10-18T10:58:50.046420643" }, - "unsorted_bam_name": { + "sarscov2 [unsorted bam] - stub": { "content": [ - "test.marked.bam" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ], + "bai": [ + + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-19T10:26:28.100755" + "timestamp": "2024-10-18T10:58:36.738907079" }, - "cram_metrics": { + "sarscov2 [unsorted bam]": { "content": [ + "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" + ], + [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-20T15:25:47.518152" + "timestamp": "2024-10-18T10:57:16.683233382" }, - "sorted_bam_metrics": { + "sarscov2 [sorted bam]": { "content": [ + "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-21T11:39:10.318331" - }, - "cram_name": { - "content": [ - "test.marked.cram" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-20T15:25:47.459663" - }, - "cram_versions": { - "content": [ + ], [ - "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-19T10:27:03.26989" + "timestamp": "2024-10-18T10:57:47.416956759" }, - "unsorted_bam_versions": { - "content": [ - [ - "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-03-20T15:31:24.040403" - }, - "unsorted_bam_metrics": { + "homo_sapiens [cram]": { "content": [ + "test.marked.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" + ], + [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-21T10:51:12.831787" + "timestamp": "2024-10-18T10:58:15.143314223" }, - "sorted_bam_name": { + "homo_sapiens [cram] - stub": { "content": [ - "test.marked.bam" + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ], + "bai": [ + + ], + "bam": [ + + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.marked.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-19T10:26:45.080116" + "timestamp": "2024-10-18T10:59:03.402916523" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index bd57cb54..62054fc9 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,8 +1,8 @@ -name: samtools_flagstat +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index eb5f5252..c23f3a5c 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) @@ -18,7 +18,6 @@ process SAMTOOLS_FLAGSTAT { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ samtools \\ diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 97991358..cdc4c254 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,5 +1,6 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG + type keywords: - stats - mapping @@ -17,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flagstat": + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test index 24c3c04b..3b648a37 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test @@ -11,9 +11,30 @@ nextflow_process { test("BAM") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("BAM - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ @@ -28,8 +49,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.flagstat).match("flagstat") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index a76fc27e..04c3852b 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -1,32 +1,72 @@ { - "flagstat": { + "BAM - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-12T18:31:37.783927" + "timestamp": "2024-09-16T08:02:58.866491759" }, - "versions": { + "BAM": { "content": [ - [ - "versions.yml:md5,fd0030ce49ab3a92091ad80260226452" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "1": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], + "versions": [ + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:11:44.299617452" + "timestamp": "2024-09-16T08:02:47.383332837" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 174973b8..62054fc9 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,8 +1,8 @@ -name: samtools_idxstats +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index a544026f..e2bb6b20 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) @@ -18,7 +18,6 @@ process SAMTOOLS_IDXSTATS { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 344e92a3..f0a6bcb2 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -18,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idxstats": + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test index a2dcb27c..5fd1fc78 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test @@ -11,9 +11,6 @@ nextflow_process { test("bam") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -28,9 +25,29 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.idxstats).match("idxstats") }, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot(process.out).match() } ) } } -} + + test("bam - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + }} diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a7050bdc..2cc89a3b 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -1,32 +1,72 @@ { - "versions": { + "bam - stub": { "content": [ - [ - "versions.yml:md5,613dde56f108418039ffcdeeddba397a" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:16:50.147462763" + "timestamp": "2024-09-16T08:11:56.466856235" }, - "idxstats": { + "bam": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ], + "1": [ + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + ] + ], + "versions": [ + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-12T18:36:41.561026" + "timestamp": "2024-09-16T08:11:46.311550359" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index a5e50649..62054fc9 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,8 @@ -name: samtools_index +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index dc14f98d..31175610 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -35,10 +35,11 @@ process SAMTOOLS_INDEX { """ stub: + def args = task.ext.args ?: '' + def extension = file(input).getExtension() == 'cram' ? + "crai" : args.contains("-c") ? "csi" : "bai" """ - touch ${input}.bai - touch ${input}.crai - touch ${input}.csi + touch ${input}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03..db8df0d5 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,38 +15,52 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test index bb7756d1..ca34fb5c 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -9,11 +9,7 @@ nextflow_process { tag "samtools/index" test("bai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -27,18 +23,13 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.bai).match("bai") }, - { assert snapshot(process.out.versions).match("bai_versions") } + { assert snapshot(process.out).match() } ) } } test("crai") { - when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -52,20 +43,83 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.crai).match("crai") }, - { assert snapshot(process.out.versions).match("crai_versions") } + { assert snapshot(process.out).match() } ) } } test("csi") { - config "./csi.nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.csi[0][1]).name, + process.out.versions + ).match() } + ) + } + } + + test("bai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("crai - stub") { + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("csi - stub") { + options "-stub" + config "./csi.nextflow.config" + + when { process { """ input[0] = Channel.of([ @@ -79,8 +133,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.csi.get(0).get(1)).exists() }, - { assert snapshot(process.out.versions).match("csi_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 3dc8e7de..72d65e81 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -1,74 +1,250 @@ { - "crai_versions": { + "csi - stub": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + + ], + "crai": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:12:00.324667957" + "timestamp": "2024-09-16T08:21:25.261127166" }, - "csi_versions": { + "crai - stub": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:12:07.885103162" + "timestamp": "2024-09-16T08:21:12.653194876" }, - "crai": { + "bai - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-12T18:41:38.446424" + "timestamp": "2024-09-16T08:21:01.854932651" }, - "bai": { + "csi": { "content": [ + "test.paired_end.sorted.bam.csi", [ - [ - { - "id": "test", - "single_end": false - }, - "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" - ] + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-12T18:40:46.579747" + "timestamp": "2024-09-16T08:20:51.485364222" }, - "bai_versions": { + "crai": { "content": [ - [ - "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e" - ] + { + "0": [ + + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:20:40.518873972" + }, + "bai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ], + "crai": [ + + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:11:51.641425452" + "timestamp": "2024-09-16T08:20:21.184050361" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 4d898e48..62054fc9 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,8 +1,8 @@ -name: samtools_sort +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index fc374f98..caf3c61a 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,19 +4,19 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta) , path(bam) tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ @@ -50,10 +49,20 @@ process SAMTOOLS_SORT { """ stub: + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" """ - touch ${prefix}.bam - touch ${prefix}.bam.csi + touch ${prefix}.${extension} + if [ "${extension}" == "bam" ]; + then + touch ${prefix}.${extension}.csi + elif [ "${extension}" == "cram" ]; + then + touch ${prefix}.${extension}.crai + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0e..a9dbec5a 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,52 +15,73 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file(s) - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta,fna}" - optional: true + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 8360e2b1..b05e6691 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -30,13 +30,83 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("multiple bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} ) } } test("cram") { + config "./nextflow_cram.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.cram.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.crai.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + + test("bam - stub") { + + options "-stub" config "./nextflow.config" when { @@ -62,24 +132,51 @@ nextflow_process { } } - test("bam_stub") { + test("multiple bam - stub") { config "./nextflow.config" - options "-stub" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("cram - stub") { + + options "-stub" + config "./nextflow_cram.config" + + when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) ]) input[1] = Channel.of([ [ id:'fasta' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]) """ } @@ -88,8 +185,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, - { assert snapshot(process.out.versions).match("bam_stub_versions") } + { assert snapshot(process.out).match() } ) } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 38477656..469891fe 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -1,5 +1,35 @@ { "cram": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:49:58.207549273" + }, + "bam - stub": { "content": [ { "0": [ @@ -8,7 +38,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -23,11 +53,11 @@ "id": "test", "single_end": false }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "4": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -35,7 +65,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + "test.sorted.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "crai": [ @@ -50,43 +80,116 @@ "id": "test", "single_end": false }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + "test.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-04T15:08:00.830294" + "timestamp": "2024-09-16T08:50:08.630951018" }, - "bam_stub_bam": { + "cram - stub": { "content": [ - "test.sorted.bam" + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-12T19:21:04.364044" + "timestamp": "2024-09-16T08:50:19.061912443" }, - "bam_stub_versions": { + "multiple bam": { "content": [ [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.09.0" }, - "timestamp": "2024-02-13T16:15:00.20800281" + "timestamp": "2024-10-08T11:59:55.479443" }, - "bam": { + "multiple bam - stub": { "content": [ { "0": [ @@ -95,7 +198,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" ] ], "1": [ @@ -110,11 +213,11 @@ "id": "test", "single_end": false }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" ] ], "4": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -122,7 +225,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" ] ], "crai": [ @@ -137,18 +240,48 @@ "id": "test", "single_end": false }, - "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" ] ], "versions": [ - "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:36:13.781404" + }, + "bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" }, - "timestamp": "2024-03-04T15:07:48.773803" + "timestamp": "2024-10-08T11:59:46.372244" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow_cram.config b/modules/nf-core/samtools/sort/tests/nextflow_cram.config new file mode 100644 index 00000000..3a8c0188 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/nextflow_cram.config @@ -0,0 +1,8 @@ +process { + + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index --output-fmt cram" + } + +} diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 67bb0ca4..62054fc9 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,8 +1,8 @@ -name: samtools_stats +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 52b00f4b..4443948b 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) @@ -19,7 +19,6 @@ process SAMTOOLS_STATS { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" """ diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 735ff812..77b020f7 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -16,43 +16,46 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing samtools stats output + pattern: "*.{stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test index e3d5cb14..5bc89309 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test +++ b/modules/nf-core/samtools/stats/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process SAMTOOLS_STATS" script "../main.nf" process "SAMTOOLS_STATS" + tag "modules" tag "modules_nfcore" tag "samtools" @@ -11,9 +12,6 @@ nextflow_process { test("bam") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -37,9 +35,59 @@ nextflow_process { test("cram") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ]) + """ } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = [[],[]] + """ + } + } + + then { + assertAll( + {assert process.success}, + {assert snapshot(process.out).match()} + ) + } + } + + test("cram - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ @@ -49,7 +97,7 @@ nextflow_process { ]) input[1] = Channel.of([ [ id:'genome' ], // meta map - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) ]) """ } diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 1b7c9ba4..df507be7 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,01812900aa4027532906c5d431114233" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "1": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -20,19 +20,89 @@ "id": "test", "single_end": false }, - "test.stats:md5,01812900aa4027532906c5d431114233" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "versions": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:15:25.562429714" + "timestamp": "2024-09-16T09:29:16.767396182" + }, + "bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:29:29.721580274" + }, + "cram - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:29:53.567964304" }, "bam": { "content": [ @@ -43,11 +113,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,5d8681bf541199898c042bf400391d59" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "1": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -55,18 +125,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,5d8681bf541199898c042bf400391d59" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "versions": [ - "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:15:07.857611509" + "timestamp": "2024-09-16T09:28:50.73610604" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 8bd58cff..9ed1940f 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,10 +1,9 @@ -name: star_align channels: - conda-forge - bioconda - - defaults + dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 + - bioconda::star=2.7.11b - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 8e9c48b1..b435f60c 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,8 +4,8 @@ process STAR_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data' : + 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' }" input: tuple val(meta), path(reads, stageAs: "input*/*") @@ -21,33 +21,35 @@ process STAR_ALIGN { tuple val(meta), path('*Log.progress.out'), emit: log_progress path "versions.yml" , emit: versions - tuple val(meta), path('*d.out.bam') , optional:true, emit: bam - tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted - tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript - tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted - tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq - tuple val(meta), path('*.tab') , optional:true, emit: tab - tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab - tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab - tuple val(meta), path('*.out.junction') , optional:true, emit: junction - tuple val(meta), path('*.out.sam') , optional:true, emit: sam - tuple val(meta), path('*.wig') , optional:true, emit: wig - tuple val(meta), path('*.bg') , optional:true, emit: bedgraph + tuple val(meta), path('*d.out.bam') , optional:true, emit: bam + tuple val(meta), path("${prefix}.sortedByCoord.out.bam") , optional:true, emit: bam_sorted + tuple val(meta), path("${prefix}.Aligned.sortedByCoord.out.bam") , optional:true, emit: bam_sorted_aligned + tuple val(meta), path('*toTranscriptome.out.bam') , optional:true, emit: bam_transcript + tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted + tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq + tuple val(meta), path('*.tab') , optional:true, emit: tab + tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab + tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab + tuple val(meta), path('*.out.junction') , optional:true, emit: junction + tuple val(meta), path('*.out.sam') , optional:true, emit: sam + tuple val(meta), path('*.wig') , optional:true, emit: wig + tuple val(meta), path('*.bg') , optional:true, emit: bedgraph when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def reads1 = [], reads2 = [] + prefix = task.ext.prefix ?: "${meta.id}" + def reads1 = [] + def reads2 = [] meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" - def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" - def seq_center = seq_center ? "'CN:$seq_center'" : "" - def attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" + def seq_platform_arg = seq_platform ? "'PL:$seq_platform'" : "" + def seq_center_arg = seq_center ? "'CN:$seq_center'" : "" + attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center_arg 'SM:$prefix' $seq_platform_arg" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' - def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' + mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ STAR \\ --genomeDir $index \\ @@ -79,8 +81,10 @@ process STAR_ALIGN { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ + echo "" | gzip > ${prefix}.unmapped_1.fastq.gz + echo "" | gzip > ${prefix}.unmapped_2.fastq.gz touch ${prefix}Xd.out.bam touch ${prefix}.Log.final.out touch ${prefix}.Log.out @@ -89,8 +93,6 @@ process STAR_ALIGN { touch ${prefix}.toTranscriptome.out.bam touch ${prefix}.Aligned.unsort.out.bam touch ${prefix}.Aligned.sortedByCoord.out.bam - touch ${prefix}.unmapped_1.fastq.gz - touch ${prefix}.unmapped_2.fastq.gz touch ${prefix}.tab touch ${prefix}.SJ.out.tab touch ${prefix}.ReadsPerGene.out.tab diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index e80dbb7d..5cfe763e 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -14,97 +14,212 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: - type: directory - description: STAR genome index - pattern: "star" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - star_ignore_sjdbgtf: - type: boolean - description: Ignore annotation GTF file - - seq_platform: - type: string - description: Sequencing platform - - seq_center: - type: string - description: Sequencing center + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - index: + type: directory + description: STAR genome index + pattern: "star" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - - seq_platform: + type: string + description: Sequencing platform + - - seq_center: + type: string + description: Sequencing center output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*d.out.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bam_sorted: - type: file - description: Sorted BAM file of read alignments (optional) - pattern: "*sortedByCoord.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sortedByCoord.out.bam: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" + - bam_sorted_aligned: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.Aligned.sortedByCoord.out.bam: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*.Aligned.sortedByCoord.out.bam" - bam_transcript: - type: file - description: Output BAM file of transcriptome alignment (optional) - pattern: "*toTranscriptome.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*toTranscriptome.out.bam": + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" - bam_unsorted: - type: file - description: Unsorted BAM file of read alignments (optional) - pattern: "*Aligned.unsort.out.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*Aligned.unsort.out.bam": + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" - fastq: - type: file - description: Unmapped FastQ files (optional) - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" - tab: - type: file - description: STAR output tab file(s) (optional) - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - spl_junc_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.SJ.out.tab": + type: file + description: STAR output splice junction tab file + pattern: "*.SJ.out.tab" + - read_per_gene_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ReadsPerGene.out.tab": + type: file + description: STAR output read per gene tab file + pattern: "*.ReadsPerGene.out.tab" - junction: - type: file - description: STAR chimeric junction output file (optional) - pattern: "*.out.junction" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out.junction": + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.out.sam" + - "*.out.sam": + type: file + description: STAR output SAM file(s) (optional) + pattern: "*.out.sam" - wig: - type: file - description: STAR output wiggle format file(s) (optional) - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" - bedgraph: - type: file - description: STAR output bedGraph format file(s) (optional) - pattern: "*.bg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bg": + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test index 6ecd7786..a62c17db 100644 --- a/modules/nf-core/star/align/tests/main.nf.test +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -9,27 +9,351 @@ nextflow_process { tag "star/align" tag "star/genomegenerate" - setup { - run("STAR_GENOMEGENERATE") { - script "../../../star/genomegenerate/main.nf" + test("homo_sapiens - single_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { process { """ input[0] = Channel.of([ - [ id:'test_fasta' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ]) - input[1] = Channel.of([ + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ [ id:'test_gtf' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] ]) + input[3] = false + input[4] = 'illumina' + input[5] = false """ } } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), + process.out.bedgraph, + process.out.fastq, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } } - test("homo_sapiens - single_end") { + test("homo_sapiens - paired_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), + process.out.bedgraph, + process.out.fastq, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - paired_end - arriba") { + config "./nextflow.arriba.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.bedgraph, + process.out.fastq, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - paired_end - starfusion") { + config "./nextflow.starfusion.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + file(process.out.junction[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.bedgraph, + process.out.fastq, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - paired_end - multiple") { config "./nextflow.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.log_final[0][1]).name, + file(process.out.log_out[0][1]).name, + file(process.out.log_progress[0][1]).name, + bam(process.out.bam[0][1]).getReadsMD5(), + bam(process.out.bam_sorted_aligned[0][1]).getReadsMD5(), + process.out.bedgraph, + process.out.fastq, + process.out.read_per_gene_tab, + process.out.sam, + process.out.spl_junc_tab, + process.out.tab, + process.out.wig, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens - single_end - stub") { + options "-stub" + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -52,29 +376,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") }, - { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") }, - { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end") { + test("homo_sapiens - paired_end - stub") { + options "-stub" config "./nextflow.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -100,29 +428,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") }, - { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end - arriba") { + test("homo_sapiens - paired_end - arriba - stub") { + options "-stub" config "./nextflow.arriba.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -148,29 +480,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") }, - { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end - starfusion") { + test("homo_sapiens - paired_end - starfusion - stub") { + options "-stub" config "./nextflow.starfusion.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -196,29 +532,33 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") }, - { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") } + { assert snapshot(process.out).match() } ) } } - test("homo_sapiens - paired_end - multiple") { + test("homo_sapiens - paired_end - multiple - stub") { + options "-stub" config "./nextflow.config" + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + when { process { """ @@ -246,23 +586,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") }, - { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") }, - { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") }, - { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") }, - { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") }, - { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") }, - { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") }, - { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") }, - { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") }, - { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") }, - { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") }, - { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") }, - { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") }, - { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") }, - { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") }, - { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") } + { assert snapshot(process.out).match() } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index 08edb914..a1ec3a3d 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -1,231 +1,665 @@ { - "homo_sapiens - paired_end - multiple - bam_sorted": { + "homo_sapiens - single_end - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" - ] - ] - ], - "timestamp": "2023-12-04T18:01:19.968225733" - }, - "homo_sapiens - paired_end - multiple - wig": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:29:01.857804" - }, - "homo_sapiens - paired_end - arriba - tab": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c" - ] - ] - ], - "timestamp": "2023-12-04T17:56:12.347549723" - }, - "homo_sapiens - single_end - wig": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:22:55.24701" - }, - "homo_sapiens - paired_end - sam": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:23:33.383818" - }, - "homo_sapiens - paired_end - arriba - versions": { - "content": [ - [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" - ] - ], - "timestamp": "2023-12-04T17:56:12.431212643" - }, - "homo_sapiens - paired_end - multiple - bedgraph": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, + { + "0": [ [ - "test.Signal.Unique.str1.out.bg:md5,d7bf8b70b436ca048a62513e1d0ece3a", - "test.Signal.UniqueMultiple.str1.out.bg:md5,686d58493b9eb445b56ace4d67f76ef6" + { + "id": "test", + "single_end": true + }, + "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "11": [ + [ + { + "id": "test", + "single_end": true + }, + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + [ + { + "id": "test", + "single_end": true + }, + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "13": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "14": [ + [ + { + "id": "test", + "single_end": true + }, + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "15": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,b416145d7b5b8a080e832a7f7cde4c44" + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": true + }, + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", + "testXd.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "bam_sorted": [ + [ + { + "id": "test", + "single_end": true + }, + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_transcript": [ + [ + { + "id": "test", + "single_end": true + }, + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_unsorted": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bedgraph": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "junction": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_final": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_progress": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "read_per_gene_tab": [ + [ + { + "id": "test", + "single_end": true + }, + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "spl_junc_tab": [ + [ + { + "id": "test", + "single_end": true + }, + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tab": [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,b416145d7b5b8a080e832a7f7cde4c44" + ], + "wig": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] - ] - ], - "timestamp": "2023-12-04T18:01:20.07119229" - }, - "homo_sapiens - paired_end - read_per_gene_tab": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:23:33.368841" - }, - "homo_sapiens - paired_end - arriba - bedgraph": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:25:07.102537" - }, - "homo_sapiens - single_end - junction": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:22:55.185369" - }, - "homo_sapiens - paired_end - arriba - spl_junc_tab": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.SJ.out.tab:md5,5155c9fd1f787ad6d7d80987fb06219c" - ] - ] - ], - "timestamp": "2023-12-04T17:56:12.268388251" - }, - "homo_sapiens - single_end - sam": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:22:55.216183" - }, - "homo_sapiens - paired_end - fastq": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:23:33.327236" - }, - "homo_sapiens - single_end - versions": { - "content": [ - [ - "versions.yml:md5,2e6b6d8809f5a17f38f4d27c45dcb22f" - ] - ], - "timestamp": "2023-12-04T17:53:26.664210196" - }, - "homo_sapiens - paired_end - multiple - log_out": { - "content": [ - "test.Log.out" - ], - "timestamp": "2023-11-23T13:29:01.022176" - }, - "homo_sapiens - paired_end - arriba - fastq": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:25:07.15277" - }, - "homo_sapiens - paired_end - multiple - junction": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:29:01.52923" - }, - "homo_sapiens - paired_end - multiple - spl_junc_tab": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.SJ.out.tab:md5,069877e053714e23010fe4e1c003b4a2" - ] - ] + } ], - "timestamp": "2023-12-04T18:01:20.189486201" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-11T16:28:39.242074494" }, - "homo_sapiens - paired_end - starfusion - log_final": { + "homo_sapiens - paired_end - arriba - stub": { "content": [ - "test.Log.final.out" - ], - "timestamp": "2023-11-23T13:27:55.905883" - }, - "homo_sapiens - paired_end - starfusion - fastq": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:27:56.192302" - }, - "homo_sapiens - paired_end - multiple - sam": { - "content": [ - [ - - ] - ], - "timestamp": "2023-11-23T13:29:01.661837" - }, - "homo_sapiens - paired_end - multiple - log_final": { - "content": [ - "test.Log.final.out" - ], - "timestamp": "2023-11-23T13:29:00.966417" - }, - "homo_sapiens - paired_end - starfusion - bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.out.bam:md5,bcad07b838f6762fc01eea52b5cd3f84" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "11": [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + [ + { + "id": "test", + "single_end": false + }, + 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"test.Signal.UniqueMultiple.str1.out.bg:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fastq": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "junction": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_final": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.final.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_out": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log_progress": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Log.progress.out:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "read_per_gene_tab": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "spl_junc_tab": [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tab": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,b416145d7b5b8a080e832a7f7cde4c44" + ], + "wig": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], - "timestamp": "2023-11-23T13:27:55.93945" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-11T16:29:20.015372487" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config index 2324b9e5..cf09323f 100644 --- a/modules/nf-core/star/align/tests/nextflow.arriba.config +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config index c4ac5808..18bc2ee8 100644 --- a/modules/nf-core/star/align/tests/nextflow.config +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config index 467b6497..7880bfcf 100644 --- a/modules/nf-core/star/align/tests/nextflow.starfusion.config +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test index 5ef337dc..420cc702 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test @@ -42,14 +42,15 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, + { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("97") }, { assert snapshot( path(workflow.out.bam[0][1]), path(workflow.out.bai[0][1]), path(workflow.out.flagstat[0][1]), path(workflow.out.idxstats[0][1]), path(workflow.out.stats[0][1]), - ).match("sarscov2 - bam") }, - { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("97") } + workflow.out.versions + ).match() } ) } } @@ -78,16 +79,78 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, + { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("0.999986") }, { assert snapshot( file(workflow.out.cram[0][1]).name, path(workflow.out.crai[0][1]), path(workflow.out.flagstat[0][1]), path(workflow.out.idxstats[0][1]), path(workflow.out.stats[0][1]), - ).match("homo_sapiens - cram") }, - { assert path(workflow.out.metrics.get(0).get(1)).getText().contains("0.999986") } + workflow.out.versions + ).match() } ) } } + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end: false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("homo_sapiens - cram - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index caf4ac8a..50ecf675 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -2,29 +2,333 @@ "homo_sapiens - cram": { "content": [ "test.cram", - "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e", + "test.cram.crai:md5,9a74bf028b7146d8ef285442a14bbc8f", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", - "test.stats:md5,c2f74a4d9b2377bcf4f4f184da3801af" + "test.stats:md5,1a4569080c6f73546a863b0c3bc72c49", + [ + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-20T20:45:38.364189" + "timestamp": "2024-10-18T10:59:53.440891602" + }, + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T11:00:20.860494683" + }, + "homo_sapiens - cram - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + + ], + "4": [ + [ + { + "id": "test" + }, + "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + + ], + "6": [ + [ + { + "id": "test" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" + ], + "bai": [ + + ], + "bam": [ + + ], + "crai": [ + [ + { + "id": "test" + }, + "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + [ + { + "id": "test" + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "flagstat": [ + [ + { + "id": "test" + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test" + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "metrics": [ + [ + { + "id": "test" + }, + "test.MarkDuplicates.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test" + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T11:00:42.042387118" }, "sarscov2 - bam": { "content": [ - "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b", - "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404", + "test.bam:md5,c8a3a56d56bf2c87f09e143ed2f78a7d", + "test.bam.bai:md5,7d205e4e0b3d98887b1eafb5c50a3363", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", - "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" + "test.stats:md5,ba007b13981dad548358c7c957d41e12", + [ + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-21T11:38:08.434529" + "timestamp": "2024-10-18T10:59:22.840531827" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index 75b5b934..821a3cf5 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -19,9 +19,6 @@ nextflow_workflow { test("test_bam_sort_stats_samtools_single_end") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -41,9 +38,11 @@ nextflow_workflow { { assert workflow.success}, { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, - { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_single_end_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_single_end_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_single_end_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } ) } } @@ -51,9 +50,6 @@ nextflow_workflow { test("test_bam_sort_stats_samtools_paired_end") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -73,9 +69,65 @@ nextflow_workflow { { assert workflow.success}, { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, - { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_paired_end_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_paired_end_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_paired_end_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } + ) + } + } + + test("test_bam_sort_stats_samtools_single_end - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("test_bam_sort_stats_samtools_paired_end - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } ) } } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 6645a092..c3c9a049 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_bam_sort_stats_samtools_paired_end_flagstats": { + "test_bam_sort_stats_samtools_single_end": { "content": [ [ [ @@ -7,53 +7,42 @@ "id": "test", "single_end": false }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2023-10-22T20:25:03.687121177" - }, - "test_bam_sort_stats_samtools_paired_end_idxstats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2023-10-22T20:25:03.709648916" - }, - "test_bam_sort_stats_samtools_single_end_stats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.stats:md5,cb0bf2b79de52fdf0c61e80efcdb0bb4" + "test.stats:md5,2fe0f3a7a1f07906061c1dadb62e0d05" ] + ], + [ + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:44:38.553256801" + "timestamp": "2024-09-16T08:26:24.36986488" }, - "test_bam_sort_stats_samtools_paired_end_stats": { + "test_bam_sort_stats_samtools_paired_end": { "content": [ [ [ @@ -61,50 +50,281 @@ "id": "test", "single_end": false }, - "test.stats:md5,d7796222a087b9bb97f631f1c21b9c95" + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-02-13T16:44:48.355870518" - }, - "test_bam_sort_stats_samtools_single_end_idxstats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-01-18T17:10:02.84631" - }, - "test_bam_sort_stats_samtools_single_end_flagstats": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + "test.stats:md5,ba007b13981dad548358c7c957d41e12" ] + ], + [ + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:26:38.683996037" + }, + "test_bam_sort_stats_samtools_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T08:07:18.896460047" + }, + "test_bam_sort_stats_samtools_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csi": [ + + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-18T17:10:02.829756" + "timestamp": "2024-09-16T08:07:39.028688324" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test index c8b21f28..76e7a40a 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test @@ -15,9 +15,6 @@ nextflow_workflow { test("test_bam_stats_samtools_single_end") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -36,9 +33,11 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_single_end_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_single_end_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_single_end_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } ) } } @@ -46,9 +45,6 @@ nextflow_workflow { test("test_bam_stats_samtools_paired_end") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -67,9 +63,11 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } ) } } @@ -77,9 +75,6 @@ nextflow_workflow { test("test_bam_stats_samtools_paired_end_cram") { when { - params { - outdir = "$outputDir" - } workflow { """ input[0] = Channel.of([ @@ -98,11 +93,96 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out.stats).match("test_bam_stats_samtools_paired_end_cram_stats") }, - { assert snapshot(workflow.out.flagstat).match("test_bam_stats_samtools_paired_end_cram_flagstats") }, - { assert snapshot(workflow.out.idxstats).match("test_bam_stats_samtools_paired_end_cram_idxstats") } + { assert snapshot( + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats, + workflow.out.versions).match() } ) } } + test ("test_bam_stats_samtools_single_end - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("test_bam_stats_samtools_paired_end - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("test_bam_stats_samtools_paired_end_cram - stub") { + + options "-stub" + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } } diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap index bf0b0c69..8ca22526 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -1,59 +1,230 @@ { - "test_bam_stats_samtools_paired_end_cram_flagstats": { + "test_bam_stats_samtools_paired_end - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-06T09:31:26.194017574" + "timestamp": "2024-09-16T08:08:35.660286921" }, - "test_bam_stats_samtools_paired_end_stats": { + "test_bam_stats_samtools_single_end - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.stats:md5,ddaf8f33fe9c1ebe9b06933213aec8ed" + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": true + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:45:06.230091746" + "timestamp": "2024-09-16T08:08:24.220305512" }, - "test_bam_stats_samtools_paired_end_flagstats": { + "test_bam_stats_samtools_paired_end_cram - stub": { "content": [ - [ - [ - { - "id": "test", - "single_end": true - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" + ], + "flagstat": [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "idxstats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "stats": [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] - ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-01-18T17:17:27.717482" + "timestamp": "2024-09-16T08:08:54.206770141" }, - "test_bam_stats_samtools_single_end_flagstats": { + "test_bam_stats_samtools_single_end": { "content": [ [ [ @@ -63,52 +234,48 @@ }, "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2023-11-06T09:26:10.340046381" - }, - "test_bam_stats_samtools_paired_end_cram_idxstats": { - "content": [ + ], [ [ { "id": "test", - "single_end": false + "single_end": true }, - "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15" + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2023-11-06T09:31:26.207052003" - }, - "test_bam_stats_samtools_single_end_stats": { - "content": [ + ], [ [ { "id": "test", "single_end": true }, - "test.stats:md5,dc178e1a4956043aba8abc83e203521b" + "test.stats:md5,291bb2393ec947140d12d42c2795b222" ] + ], + [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:44:57.442208382" + "timestamp": "2024-09-16T08:07:49.731645858" }, - "test_bam_stats_samtools_paired_end_idxstats": { + "test_bam_stats_samtools_paired_end": { "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" + ] + ], [ [ { @@ -117,33 +284,29 @@ }, "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-01-18T17:17:27.726719" - }, - "test_bam_stats_samtools_single_end_idxstats": { - "content": [ + ], [ [ { "id": "test", "single_end": true }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + "test.stats:md5,8140d69cdedd77570ca1d7618a744e16" ] + ], + [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-06T09:26:10.349439801" + "timestamp": "2024-09-16T08:08:01.421996172" }, - "test_bam_stats_samtools_paired_end_cram_stats": { + "test_bam_stats_samtools_paired_end_cram": { "content": [ [ [ @@ -151,14 +314,37 @@ "id": "test", "single_end": false }, - "test.stats:md5,d3345c4887f4a9ea4f7f56405b495db0" + "test.flagstat:md5,a53f3d26e2e9851f7d528442bbfe9781" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,1622856127bafd6cdbadee9cd64ec9b7" + ] + ], + [ + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:45:14.997164209" + "timestamp": "2024-09-16T08:08:12.640915756" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test index 2c512c96..c1ad73a9 100644 --- a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test @@ -59,21 +59,17 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out.orig_bam).match('orig_bam_single_end')}, - { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_single_end')}, - { assert snapshot(workflow.out.fastq).match('fastq_single_end')}, - { assert snapshot(workflow.out.tab).match('tab_single_end')}, - { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_single_end')}, - { assert snapshot(workflow.out.bam).match('bam_single_end')}, - { assert snapshot(workflow.out.bai).match('bai_single_end')}, - { assert snapshot(workflow.out.stats).match('stats_single_end')}, - { assert snapshot(workflow.out.flagstat).match('flagstat_single_end')}, - { assert snapshot(workflow.out.idxstats).match('idxstats_single_end')}, - { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_single_end')}, - { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_single_end')}, - { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_single_end')}, - { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_single_end')}, - { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_single_end')}, + { assert snapshot( + bam(workflow.out.bam[0][1]).getReadsMD5(), + bam(workflow.out.orig_bam[0][1]).getReadsMD5(), + workflow.out.fastq, + workflow.out.tab, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions + ).match() }, + { assert path(workflow.out.bai.get(0).get(1)).exists() }, { assert path(workflow.out.log_out.get(0).get(1)).exists() }, { assert path(workflow.out.log_final.get(0).get(1)).exists() }, { assert path(workflow.out.log_progress.get(0).get(1)).exists() } @@ -114,22 +110,17 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out.orig_bam).match('orig_bam_paired_end')}, - { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_paired_end')}, - { assert snapshot(workflow.out.fastq).match('fastq_paired_end')}, - { assert snapshot(workflow.out.tab).match('tab_paired_end')}, - { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_paired_end')}, - { assert snapshot(workflow.out.bam).match('bam_paired_end')}, - { assert snapshot(workflow.out.bai).match('bai_paired_end')}, - { assert snapshot(workflow.out.stats).match('stats_paired_end')}, - { assert snapshot(workflow.out.flagstat).match('flagstat_paired_end')}, - { assert snapshot(workflow.out.idxstats).match('idxstats_paired_end')}, - { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_paired_end')}, - { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_paired_end')}, - { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_paired_end')}, - { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_paired_end')}, - { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_paired_end')}, - { assert snapshot(workflow.out.idxstats_transcript).match('versions_paired_end')}, + { assert snapshot( + bam(workflow.out.bam[0][1]).getReadsMD5(), + bam(workflow.out.orig_bam[0][1]).getReadsMD5(), + workflow.out.fastq, + workflow.out.tab, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.versions + ).match() }, + { assert path(workflow.out.bai.get(0).get(1)).exists() }, { assert path(workflow.out.log_out.get(0).get(1)).exists() }, { assert path(workflow.out.log_final.get(0).get(1)).exists() }, { assert path(workflow.out.log_progress.get(0).get(1)).exists() } @@ -181,22 +172,23 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out.orig_bam).match('orig_bam_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.fastq).match('fastq_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.tab).match('tab_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.bam).match('bam_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.bai).match('bai_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.stats).match('stats_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.flagstat).match('flagstat_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.idxstats).match('idxstats_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_paired_end_with_transcriptome')}, - { assert snapshot(workflow.out.idxstats_transcript).match('versions_paired_end_with_transcriptome')}, + { assert snapshot( + bam(workflow.out.bam[0][1]).getReadsMD5(), + bam(workflow.out.orig_bam[0][1]).getReadsMD5(), + bam(workflow.out.bam_transcript[0][1]).getReadsMD5(), + bam(workflow.out.orig_bam_transcript[0][1]).getReadsMD5(), + workflow.out.fastq, + workflow.out.tab, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats_transcript, + workflow.out.flagstat_transcript, + workflow.out.idxstats_transcript, + workflow.out.versions + ).match() }, + { assert path(workflow.out.bai.get(0).get(1)).exists() }, + { assert path(workflow.out.bai_transcript.get(0).get(1)).exists() }, { assert path(workflow.out.log_out.get(0).get(1)).exists() }, { assert path(workflow.out.log_final.get(0).get(1)).exists() }, { assert path(workflow.out.log_progress.get(0).get(1)).exists() } @@ -237,22 +229,18 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out.orig_bam).match('orig_bam_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.bam_sorted).match('bam_sorted_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.fastq).match('fastq_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.tab).match('tab_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.orig_bam_transcript).match('orig_bam_transcript_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.bam).match('bam_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.bai).match('bai_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.stats).match('stats_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.flagstat).match('flagstat_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.idxstats).match('idxstats_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.bam_transcript).match('bam_transcript_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.bai_transcript).match('bai_transcript_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.stats_transcript).match('stats_transcript_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.flagstat_transcript).match('flagstat_transcript_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.idxstats_transcript).match('idxstats_transcript_paired_end_transcripts_no_transcriptome')}, - { assert snapshot(workflow.out.idxstats_transcript).match('versions_paired_end_transcripts_no_transcriptome')}, + { assert snapshot( + bam(workflow.out.bam[0][1]).getReadsMD5(), + bam(workflow.out.orig_bam[0][1]).getReadsMD5(), + workflow.out.fastq, + workflow.out.tab, + workflow.out.stats, + workflow.out.flagstat, + workflow.out.idxstats, + workflow.out.stats_transcript, + workflow.out.versions + ).match() }, + { assert path(workflow.out.bai.get(0).get(1)).exists() }, { assert path(workflow.out.log_out.get(0).get(1)).exists() }, { assert path(workflow.out.log_final.get(0).get(1)).exists() }, { assert path(workflow.out.log_progress.get(0).get(1)).exists() } diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap index 989d38a6..c21ec0cc 100644 --- a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap @@ -1,210 +1,112 @@ { - "flagstat_transcript_paired_end_with_transcriptome": { + "homo_sapiens - fastq - paired_end - transcripts - no_transcriptome": { "content": [ + "1e02b8e6b4a02ab58bfe4ee795aba815", + "47a5da42b696886e2ed36af199a9042e", + [ + + ], [ [ { "id": "test", "single_end": false }, - "test.sorted.bam.flagstat:md5,a204dee59ef8b7cd0f7d952a80119b77" + "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-16T11:04:06.836115665" - }, - "orig_bam_paired_end": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.Aligned.out.bam:md5,51d2ef198d5725978a4b6da6fbec17dd" + "test.sorted.bam.stats:md5,d7509941ffbfb221115faa2481115f23" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-15T19:37:37.493635239" - }, - "tab_paired_end": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" + "test.sorted.bam.flagstat:md5,db0e25cd0b37d3030e807846c022199e" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-15T19:37:37.62565966" - }, - "stats_single_end": { - "content": [ + ], [ [ { "id": "test", - "single_end": true + "single_end": false }, - "test.sorted.bam.stats:md5,2b8eb6967b68f03584cc242499658e92" + "test.sorted.bam.idxstats:md5,107ca94dd426cc44db316f0d402307c5" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-16T11:01:51.011841774" - }, - "bam_sorted_single_end": { - "content": [ - [ - - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-15T19:36:01.366823434" - }, - "idxstats_paired_end": { - "content": [ + ], [ [ { "id": "test", "single_end": false }, - "test.sorted.bam.idxstats:md5,107ca94dd426cc44db316f0d402307c5" + "test.sorted.bam.stats:md5,10c63f09ff2b849443bafad71a824b0e" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-15T19:37:37.799888732" - }, - "fastq_paired_end_with_transcriptome": { - "content": [ + ], [ - + "versions.yml:md5,167faaf660e4936645b0ad5a9d3bf620", + "versions.yml:md5,24b681997fbdd563910240af500d965e", + "versions.yml:md5,2bdea75e8dad77676c54b806ceecb68b", + "versions.yml:md5,2e0fd05eea17eb1f5cdf079c12a30b88", + "versions.yml:md5,421308f325b1038feafdb6862cebc28a", + "versions.yml:md5,63c683e2834a8968f4d626dbe9b7a07f", + "versions.yml:md5,6a96fec10a72e1da236e6e1d7519590e", + "versions.yml:md5,9dd7217e54100569bf9f87f7a1cca54a", + "versions.yml:md5,a305cb08e7cb3194be54d0bb8a257722", + "versions.yml:md5,ade8e9901ff456f43bc0f93f5f7af793", + "versions.yml:md5,ec328c7ea462702388fa15204aeb6689" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": 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"2024-02-15T19:36:01.971850654" - }, - "fastq_paired_end_transcripts_no_transcriptome": { - "content": [ - [ - + "versions.yml:md5,167faaf660e4936645b0ad5a9d3bf620", + "versions.yml:md5,24b681997fbdd563910240af500d965e", + "versions.yml:md5,2e0fd05eea17eb1f5cdf079c12a30b88", + "versions.yml:md5,421308f325b1038feafdb6862cebc28a", + "versions.yml:md5,6a96fec10a72e1da236e6e1d7519590e", + "versions.yml:md5,9dd7217e54100569bf9f87f7a1cca54a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-15T19:39:50.410098606" + "timestamp": "2024-12-11T17:08:08.904146433" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 0fcbf7b3..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -92,10 +92,12 @@ def checkCondaChannels() { channels = config.channels } catch (NullPointerException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } catch (IOException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..bfd25876 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) { } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // @@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // @@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) { return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] - } +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - catch (Exception all) { - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } - } - return mqc_report } // @@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) @@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi if (email_address) { try { if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } ['sendmail', '-t'].execute() << sendmail_html log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f8..f117040c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232c..02c67014 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { From bcaaee9dd4d945663093c9178e9155e070442f15 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 09:32:15 +0100 Subject: [PATCH 164/275] fix configs --- conf/modules.config | 61 +++++++------- conf/modules/annotate.config | 150 ++++++++++++++++------------------- 2 files changed, 99 insertions(+), 112 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 84e7d625..70acd95b 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -243,41 +243,40 @@ process { } // BASE RECALIBRATION PROCESS -if(!params.skip_baserecalibration) { - process { - - withName: GATK4_BASERECALIBRATOR { - ext.args = '--use-original-qualities' - publishDir = [ enabled: false ] - } - - withName: '.*:RECALIBRATE:APPLYBQSR' { - ext.args = [ - '--use-original-qualities', - '--add-output-sam-program-record' - ].join(' ').trim() - ext.prefix = {"${meta.id}.recal"} - publishDir = [ - path: { "${params.outdir}/preprocessing/${meta.id}" }, - mode: params.publish_dir_mode, - enabled: true, - pattern: "*.{bam}" - ] - } +process { - withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' { - ext.args = params.bam_csi_index ? '-c' : '' - ext.prefix = {"${meta.id}.recal"} - publishDir = [ - path: { "${params.outdir}/preprocessing/${meta.id}" }, - mode: params.publish_dir_mode, - enabled: true, - pattern: "*.{bai,csi}" - ] - } + withName: GATK4_BASERECALIBRATOR { + ext.args = '--use-original-qualities' + publishDir = [ enabled: false ] + } + + withName: '.*:RECALIBRATE:APPLYBQSR' { + ext.args = [ + '--use-original-qualities', + '--add-output-sam-program-record' + ].join(' ').trim() + ext.prefix = {"${meta.id}.recal"} + publishDir = [ + path: { "${params.outdir}/preprocessing/${meta.id}" }, + mode: params.publish_dir_mode, + enabled: true, + pattern: "*.{bam}" + ] + } + + withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' { + ext.args = params.bam_csi_index ? '-c' : '' + ext.prefix = {"${meta.id}.recal"} + publishDir = [ + path: { "${params.outdir}/preprocessing/${meta.id}" }, + mode: params.publish_dir_mode, + enabled: true, + pattern: "*.{bai,csi}" + ] } } + // VARIANT CALLING AND FILTERING process { diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index ea4f921e..0704a6ca 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -16,102 +16,90 @@ process { // SNPEFF - if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) { - withName: 'SNPEFF_SNPEFF' { - ext.args = { '-nodownload -canon -v' } - ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' } - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{csv,html,genes.txt}", - saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null } - ] + withName: 'SNPEFF_SNPEFF' { + ext.args = { '-nodownload -canon -v' } + ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' } + publishDir = [ + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{csv,html,genes.txt}", + saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null } ] - } + ] } // VEP - if (params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge'))) { - withName: 'ENSEMBLVEP_VEP' { - ext.args = { [ - "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html", - (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', - (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', - (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', - (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', - (params.vep_custom_args) ?: '' - ].join(' ').trim() } - // If just VEP: _VEP.ann.vcf - ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' } - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" }, - pattern: "*html" - ], - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{gz}" - ] + withName: 'ENSEMBLVEP_VEP' { + ext.args = { [ + "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html", + (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', + (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', + (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', + (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', + (params.vep_custom_args) ?: '' + ].join(' ').trim() } + // If just VEP: _VEP.ann.vcf + ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' } + publishDir = [ + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" }, + pattern: "*html" + ], + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{gz}" ] - } + ] } // BCFTOOLS ANNOTATE - if (params.annotate_tools && params.annotate_tools.split(',').contains('bcfann')) { - withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' { - ext.args = { '--output-type z' } - ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{gz}" - ] - } + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' { + ext.args = { '--output-type z' } + ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{gz}" + ] } // SNPEFF THEN VEP - if (params.annotate_tools && params.annotate_tools.split(',').contains('merge')) { - withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' { - ext.args = { [ - "--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html", - (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', - (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', - (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', - (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', - (params.vep_custom_args) ?: '' - ].join(' ').trim() } - // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab - ext.prefix = { vcf.baseName - '.ann.vcf' + '_VEP.ann' } - } + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' { + ext.args = { [ + "--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html", + (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '', + (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', + (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', + (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', + (params.vep_custom_args) ?: '' + ].join(' ').trim() } + // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab + ext.prefix = { vcf.baseName - '.ann.vcf' + '_VEP.ann' } } // ALL ANNOTATION TOOLS - if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge') || params.annotate_tools.split(',').contains('bcfann'))) { - withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' { - ext.prefix = { input.name - '.vcf' } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{gz.tbi}" - ] - } - } - - if (params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge'))) { - withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' { - publishDir = [ + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' { + ext.prefix = { input.name - '.vcf' } + publishDir = [ mode: params.publish_dir_mode, path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{gz,gz.tbi}", - saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null } - ] - } + pattern: "*{gz.tbi}" + ] + } + + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{gz,gz.tbi}", + saveAs: { params.annotate_tools.split(',').contains('snpeff') ? it : null } + ] } } From a0813deb77c417032c24487bf81bf661a2909db4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 09:32:44 +0100 Subject: [PATCH 165/275] prettier --- modules.json | 218 ++++++++++++--------------------------------------- 1 file changed, 51 insertions(+), 167 deletions(-) diff --git a/modules.json b/modules.json index c2c6a5be..d73b11a1 100755 --- a/modules.json +++ b/modules.json @@ -8,303 +8,207 @@ "bcftools/annotate": { "branch": "master", "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", - "installed_by": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bcftools/sort": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": [ - "vcf_annotate_ensemblvep", - "vcf_annotate_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bedtools/merge": { "branch": "master", "git_sha": "a5377837fe9013bde89de8689829e83e84086536", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "fastqc": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/applybqsr": { "branch": "master", "git_sha": "af273ea6618c50e82c372abe18b0a225e84fe6f7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", "git_sha": "8a223e11d4e6deb36484e01891eae9c1cacb5f5d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", "git_sha": "d3f215802f696f7993f25c759781d2db91232015", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/combinegvcfs": { "branch": "master", "git_sha": "fe3d7aac1b62efe4fd05cc9629d192e9cdfc3ccb", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", "git_sha": "108e1f5bafc045ac19890852a41e8d95ae12aa67", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/splitncigarreads": { "branch": "master", "git_sha": "1e15ad71d9022293985dd02e24186e5e496a0b3c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", "git_sha": "00409369b2aff69bded4f0a9e7a80e17d933b426", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gffread": { "branch": "master", "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "bam_markduplicates_picard" - ] + "installed_by": ["bam_markduplicates_picard"] }, "samtools/convert": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "f153f1f10e1083c49935565844cccb7453021682", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", - "installed_by": [ - "bam_stats_samtools", - "modules" - ] + "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/idxstats": { "branch": "master", "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", - "installed_by": [ - "bam_stats_samtools", - "modules" - ] + "installed_by": ["bam_stats_samtools", "modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "bam_markduplicates_picard", - "bam_sort_stats_samtools", - "modules" - ] + "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"] }, "samtools/merge": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", - "installed_by": [ - "bam_sort_stats_samtools", - "modules" - ] + "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { "branch": "master", "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", - "installed_by": [ - "bam_stats_samtools", - "modules" - ] + "installed_by": ["bam_stats_samtools", "modules"] }, "snpeff/download": { "branch": "master", "git_sha": "214d575774c172062924ad3564b4f66655600730", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", "git_sha": "2f3db6f45147ebbb56b371536e31bdf622b5bfee", - "installed_by": [ - "modules", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "star/align": { "branch": "master", "git_sha": "59f52afcd8eabf15e8713095207272624171c65a", - "installed_by": [ - "fastq_align_star", - "modules" - ] + "installed_by": ["fastq_align_star", "modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", - "installed_by": [ - "modules", - "vcf_annotate_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -313,70 +217,50 @@ "bam_markduplicates_picard": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_sort_stats_samtools": { "branch": "master", "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", - "installed_by": [ - "fastq_align_star", - "subworkflows" - ] + "installed_by": ["fastq_align_star", "subworkflows"] }, "bam_stats_samtools": { "branch": "master", "git_sha": "763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d", - "installed_by": [ - "bam_markduplicates_picard", - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"] }, "fastq_align_star": { "branch": "master", "git_sha": "6a367612c2c27aa659293c656afa764361223db4", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 7b157746192e073597037ea8c3b6e767b4540822 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 15:08:47 +0100 Subject: [PATCH 166/275] let everything run again --- workflows/rnavar/main.nf | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index c19d0223..43faed3c 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -129,7 +129,7 @@ workflow RNAVAR { ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.flatten() } else { - ch_interval_list_split = ch_interval_list + ch_interval_list_split = ch_interval_list.map { _meta, bed -> bed } } // @@ -338,7 +338,11 @@ workflow RNAVAR { // if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { - def ch_vep_fasta = (params.vep_include_fasta) ? ch_fasta: [[id: 'null'], []] + def ch_vep_fasta = [[id: 'null'], []] + + if (params.vep_include_fasta) { + ch_vep_fasta = ch_fasta + } VCF_ANNOTATE_ALL( ch_final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, @@ -399,7 +403,7 @@ workflow RNAVAR { // MODULE: MultiQC // Present summary of reads, alignment, duplicates, BSQR stats for all samples as well as workflow summary/parameters as single report // - def multiqc_report = Channel.empty() + def val_multiqc_report = Channel.empty() if (!params.skip_multiqc){ def ch_multiqc_files = Channel.empty() @@ -424,13 +428,13 @@ workflow RNAVAR { [], [] ) - multiqc_report = MULTIQC.out.report.toList() + val_multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions) } emit: - multiqc_report // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [ path(versions.yml) ] + multiqc_report = val_multiqc_report // channel: /path/to/multiqc_report.html + versions = ch_versions // channel: [ path(versions.yml) ] } /* From 5c095bea566f02dba02fcabfa2169cddc5c46cbf Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 9 Jan 2025 15:17:16 +0100 Subject: [PATCH 167/275] Update workflows/rnavar/main.nf Co-authored-by: Maxime U Garcia --- workflows/rnavar/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 43faed3c..728511f7 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -342,7 +342,7 @@ workflow RNAVAR { if (params.vep_include_fasta) { ch_vep_fasta = ch_fasta - } + } VCF_ANNOTATE_ALL( ch_final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, From d1b409d341f426dbf5324579f0ade315bb634cbc Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 15:36:00 +0100 Subject: [PATCH 168/275] remove verbose and debug from nf-test ci (real errors were being cropped) --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 36ddf598..2f2be0c0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -105,8 +105,6 @@ jobs: run: | nf-test test \ --ci \ - --debug \ - --verbose \ --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ --shard ${{ matrix.shard }}/5 \ --changed-since HEAD^ \ From 717ca2a6aad04c6d7d11c8754b8d7919de8e8450 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 15:56:48 +0100 Subject: [PATCH 169/275] remove ch_ prefix --- subworkflows/local/prepare_alignment/main.nf | 36 +-- subworkflows/local/prepare_genome/main.nf | 48 ++-- subworkflows/local/recalibrate/main.nf | 22 +- subworkflows/local/splitncigar/main.nf | 36 +-- subworkflows/local/vcf_annotate_all/main.nf | 30 +-- .../local/vcf_annotate_bcftools/main.nf | 10 +- workflows/rnavar/main.nf | 248 +++++++++--------- 7 files changed, 215 insertions(+), 215 deletions(-) diff --git a/subworkflows/local/prepare_alignment/main.nf b/subworkflows/local/prepare_alignment/main.nf index a9c3d85d..81520f7a 100755 --- a/subworkflows/local/prepare_alignment/main.nf +++ b/subworkflows/local/prepare_alignment/main.nf @@ -7,41 +7,41 @@ include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index' workflow PREPARE_ALIGNMENT { take: - ch_cram // [ val(meta), path(cram), path(crai) ] - ch_bam // [ val(meta), path(bam), path(bai) ] + cram // [ val(meta), path(cram), path(crai) ] + bam // [ val(meta), path(bam), path(bai) ] main: ch_versions = Channel.empty() - def ch_alignment_branch = ch_bam - .mix(ch_cram) - .branch { meta, bam, bai -> + def alignment_branch = bam + .mix(cram) + .branch { meta, bam_, bai -> indexed: bai - return [ meta, bam, bai ] - not_indexed_bam: !bai && bam.extension == "bam" - return [ meta, bam ] - not_indexed_cram: !bai && bam.extension == "cram" - return [ meta, bam ] + return [ meta, bam_, bai ] + not_indexed_bam: !bai && bam_.extension == "bam" + return [ meta, bam_ ] + not_indexed_cram: !bai && bam_.extension == "cram" + return [ meta, bam_ ] } - def ch_bam_no_index = ch_alignment_branch.not_indexed_bam.mix(ch_alignment_branch.not_indexed_cram) + def bam_no_index = alignment_branch.not_indexed_bam.mix(alignment_branch.not_indexed_cram) SAMTOOLS_INDEX( - ch_bam_no_index + bam_no_index ) ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - def ch_bam_indexed = ch_alignment_branch.not_indexed_bam + def bam_indexed = alignment_branch.not_indexed_bam .join(SAMTOOLS_INDEX.out.bai, failOnMismatch: true, failOnDuplicate: true) - def ch_cram_indexed = ch_alignment_branch.not_indexed_cram + def cram_indexed = alignment_branch.not_indexed_cram .join(SAMTOOLS_INDEX.out.crai, failOnMismatch: true, failOnDuplicate: true) - def ch_alignment_out = ch_bam_indexed - .mix(ch_cram_indexed) - .mix(ch_alignment_branch.indexed) + def alignment_out = bam_indexed + .mix(cram_indexed) + .mix(alignment_branch.indexed) emit: - bam = ch_alignment_out // [ val(meta), path(bam), path(bai) ] + bam = alignment_out // [ val(meta), path(bam), path(bai) ] versions = ch_versions } diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 69a1a7f8..f3c5f486 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -16,11 +16,11 @@ include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tab workflow PREPARE_GENOME { take: - ch_fasta_raw // file: /path/to/genome.fasta - ch_gff // file: /path/to/genome.gff - ch_gtf_raw // file: /path/to/genome.gtf - ch_dbsnp - ch_known_indels + fasta_raw // file: /path/to/genome.fasta + gff // file: /path/to/genome.gff + gtf_raw // file: /path/to/genome.gtf + dbsnp + known_indels feature_type main: @@ -29,33 +29,33 @@ workflow PREPARE_GENOME { //Unzip reference genome files if needed if (params.fasta.endsWith('.gz')) { - GUNZIP_FASTA(ch_fasta_raw) + GUNZIP_FASTA(fasta_raw) - ch_fasta = GUNZIP_FASTA.out.gunzip + fasta = GUNZIP_FASTA.out.gunzip } else { - ch_fasta = ch_fasta_raw + fasta = fasta_raw } if (params.gtf.endsWith('.gz')) { - GUNZIP_GTF(ch_gtf_raw) + GUNZIP_GTF(gtf_raw) - ch_gtf = GUNZIP_GTF.out.gunzip + gtf = GUNZIP_GTF.out.gunzip } else { - ch_gtf = ch_gtf_raw + gtf = gtf_raw } - GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) - GFFREAD(ch_gff, ch_fasta) - SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) - TABIX_DBSNP(ch_dbsnp.flatten().map{ it -> [ [ id:it.baseName ], it ] }) - TABIX_KNOWN_INDELS(ch_known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) + GATK4_CREATESEQUENCEDICTIONARY(fasta) + GFFREAD(gff, fasta) + SAMTOOLS_FAIDX(fasta, [['id':'genome'], []]) + TABIX_DBSNP(dbsnp.flatten().map{ it -> [ [ id:it.baseName ], it ] }) + TABIX_KNOWN_INDELS(known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) - ch_gtf = ch_gtf.mix(GFFREAD.out.gtf) + gtf = gtf.mix(GFFREAD.out.gtf) - GTF2BED(ch_gtf, feature_type) - STAR_GENOMEGENERATE(ch_fasta, ch_gtf) + GTF2BED(gtf, feature_type) + STAR_GENOMEGENERATE(fasta, gtf) ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) ch_versions = ch_versions.mix(GFFREAD.out.versions) @@ -68,13 +68,13 @@ workflow PREPARE_GENOME { emit: dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed - fasta = ch_fasta + fasta = fasta fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai - gtf = ch_gtf.first() // path: genome.gtf + gtf = gtf.first() // path: genome.gtf star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi - versions = ch_versions // channel: [ versions.yml ] - // bedtools_sort = ch_bedtools_sort // path: sort.bed - // bedtools_merge = ch_bedtools_merge // path: merge.bed + versions = ch_versions // channel: [ ch_versions.yml ] + // bedtools_sort = bedtools_sort // path: sort.bed + // bedtools_merge = bedtools_merge // path: merge.bed } diff --git a/subworkflows/local/recalibrate/main.nf b/subworkflows/local/recalibrate/main.nf index 5d41143e..5a03c308 100644 --- a/subworkflows/local/recalibrate/main.nf +++ b/subworkflows/local/recalibrate/main.nf @@ -11,20 +11,20 @@ include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools workflow RECALIBRATE { take: skip_samtools // boolean: true/false - ch_bam // channel: [mandatory] bam - ch_dict // channel: [mandatory] dict - ch_fai // channel: [mandatory] fai - ch_fasta // channel: [mandatory] fasta + bam // channel: [mandatory] bam + dict // channel: [mandatory] dict + fai // channel: [mandatory] fai + fasta // channel: [mandatory] fasta main: def ch_versions = Channel.empty() APPLYBQSR ( - ch_bam, - ch_fasta, - ch_fai, - ch_dict + bam, + fasta, + fai, + dict ) def bam_recalibrated = APPLYBQSR.out.bam ch_versions = ch_versions.mix(APPLYBQSR.out.versions.first()) @@ -34,9 +34,9 @@ workflow RECALIBRATE { def bam_recalibrated_index = bam_recalibrated .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) // TODO fix this bottleneck - .map{meta, bam, bai, csi -> - if (bai) [meta, bam, bai] - else [meta, bam, csi] + .map{meta, bam_, bai, csi -> + if (bai) [meta, bam_, bai] + else [meta, bam_, csi] } ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index d6f3e044..ee5575bd 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -8,30 +8,30 @@ include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index workflow SPLITNCIGAR { take: - ch_bam // channel: [ val(meta), [ bam ], [bai] ] - ch_fasta // channel: [ fasta ] - ch_fai // channel: [ fai ] - ch_dict // channel: [ dict ] - ch_intervals // channel: [ interval_list] + bam // channel: [ val(meta), [ bam ], [bai] ] + fasta // channel: [ fasta ] + fai // channel: [ fai ] + dict // channel: [ dict ] + intervals // channel: [ interval_list] main: - ch_versions = Channel.empty() + def ch_versions = Channel.empty() - def bam_interval = ch_bam.combine(ch_intervals).map{ meta, bam, bai, intervals -> [ meta + [sample:meta.id], bam, bai, intervals ] } + def bam_interval = bam.combine(intervals).map{ meta, bam_, bai, intervals_ -> [ meta + [sample:meta.id], bam_, bai, intervals_ ] } GATK4_SPLITNCIGARREADS(bam_interval, - ch_fasta, - ch_fai.map{ fai -> [[id:'genome'], fai] }, - ch_dict) + fasta, + fai.map{ fai_ -> [[id:'genome'], fai_] }, + dict) bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions) - bam_splitncigar_interval = bam_splitncigar.map{ meta, bam -> [ meta + [id:meta.sample] - meta.subMap('sample'), bam ] }.groupTuple() + bam_splitncigar_interval = bam_splitncigar.map{ meta, bam_ -> [ meta + [id:meta.sample] - meta.subMap('sample'), bam_ ] }.groupTuple() SAMTOOLS_MERGE(bam_splitncigar_interval, - ch_fasta, - ch_fai.map{ fai -> [[id:fai.baseName], fai] }) + fasta, + fai.map{ fai_ -> [[id:fai_.baseName], fai_] }) splitncigar_bam = SAMTOOLS_MERGE.out.bam ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) @@ -41,14 +41,14 @@ workflow SPLITNCIGAR { splitncigar_bam_bai = splitncigar_bam .join(SAMTOOLS_INDEX.out.bai, remainder: true) .join(SAMTOOLS_INDEX.out.csi, remainder: true) // TODO fix this bottleneck - .map{meta, bam, bai, csi -> - if (bai) [meta, bam, bai] - else [meta, bam, csi] + .map{meta, bam_, bai, csi -> + if (bai) [meta, bam_, bai] + else [meta, bam_, csi] } ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) emit: - bam_bai = splitncigar_bam_bai - versions = ch_versions + bam_bai = splitncigar_bam_bai + versions = ch_versions } diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf index d25801a3..7f3373b6 100644 --- a/subworkflows/local/vcf_annotate_all/main.nf +++ b/subworkflows/local/vcf_annotate_all/main.nf @@ -9,8 +9,8 @@ include { VCF_ANNOTATE_SNPEFF } from '../../nf-core/vc workflow VCF_ANNOTATE_ALL { take: - ch_vcf // channel: [ val(meta), vcf ] - ch_fasta + vcf // channel: [ val(meta), vcf ] + fasta tools // Mandatory, list of tools to apply snpeff_db snpeff_cache @@ -25,42 +25,42 @@ workflow VCF_ANNOTATE_ALL { def vcf_ann = Channel.empty() def tab_ann = Channel.empty() def json_ann = Channel.empty() - def versions = Channel.empty() + def ch_versions = Channel.empty() if (tools.split(',').contains('bcfann')) { - VCF_ANNOTATE_BCFTOOLS(ch_vcf) + VCF_ANNOTATE_BCFTOOLS(vcf) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) - versions = versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions) + ch_versions = ch_versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions) } if (tools.split(',').contains('merge') || tools.split(',').contains('snpeff')) { - VCF_ANNOTATE_SNPEFF(ch_vcf, snpeff_db, snpeff_cache) + VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache) - ch_reports = ch_reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ _meta, reports -> [ reports ] }) + ch_reports = ch_reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ _meta, reports_ -> [ reports_ ] }) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi) - versions = versions.mix(VCF_ANNOTATE_SNPEFF.out.versions) + ch_versions = ch_versions.mix(VCF_ANNOTATE_SNPEFF.out.versions) } if (tools.split(',').contains('merge')) { - vcf_ann_for_merge = VCF_ANNOTATE_SNPEFF.out.vcf_tbi.map{ meta, vcf, _tbi -> [ meta, vcf, [] ] } - VCF_ANNOTATE_MERGE(vcf_ann_for_merge, ch_fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) + vcf_ann_for_merge = VCF_ANNOTATE_SNPEFF.out.vcf_tbi.map{ meta, vcf_, _tbi -> [ meta, vcf_, [] ] } + VCF_ANNOTATE_MERGE(vcf_ann_for_merge, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) ch_reports = ch_reports.mix(VCF_ANNOTATE_MERGE.out.reports) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi) - versions = versions.mix(VCF_ANNOTATE_MERGE.out.versions) + ch_versions = ch_versions.mix(VCF_ANNOTATE_MERGE.out.versions) } if (tools.split(',').contains('vep')) { - vcf_for_vep = ch_vcf.map{ meta, vcf -> [ meta, vcf, [] ] } - VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, ch_fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) + vcf_for_vep = vcf.map{ meta, vcf_ -> [ meta, vcf_, [] ] } + VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) ch_reports = ch_reports.mix(VCF_ANNOTATE_ENSEMBLVEP.out.reports) vcf_ann = vcf_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi) tab_ann = tab_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab) json_ann = json_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json) - versions = versions.mix(VCF_ANNOTATE_ENSEMBLVEP.out.versions) + ch_versions = ch_versions.mix(VCF_ANNOTATE_ENSEMBLVEP.out.versions) } emit: @@ -68,5 +68,5 @@ workflow VCF_ANNOTATE_ALL { tab_ann json_ann reports = ch_reports // path: *.html - versions // path: versions.yml + versions = ch_versions // path: ch_versions.yml } diff --git a/subworkflows/local/vcf_annotate_bcftools/main.nf b/subworkflows/local/vcf_annotate_bcftools/main.nf index fb506f2d..d0327166 100644 --- a/subworkflows/local/vcf_annotate_bcftools/main.nf +++ b/subworkflows/local/vcf_annotate_bcftools/main.nf @@ -8,21 +8,21 @@ include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow VCF_ANNOTATE_BCFTOOLS { take: - ch_vcf // channel: [ val(meta), vcf ] + vcf // channel: [ val(meta), vcf ] main: - ch_versions = Channel.empty() + def ch_versions = Channel.empty() - BCFTOOLS_ANNOTATE(ch_vcf.map { meta, vcf -> [ meta, vcf, [], [], [], []]}) + BCFTOOLS_ANNOTATE(vcf.map { meta, vcf_ -> [ meta, vcf_, [], [], [], []]}) TABIX_TABIX(BCFTOOLS_ANNOTATE.out.vcf) - ch_vcf_tbi = BCFTOOLS_ANNOTATE.out.vcf.join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true) + vcf_tbi = BCFTOOLS_ANNOTATE.out.vcf.join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true) // Gather versions of all tools used ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) emit: - vcf_tbi = ch_vcf_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] + vcf_tbi = vcf_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] versions = ch_versions // path: versions.yml } diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 728511f7..3518a0d5 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -52,17 +52,17 @@ include { paramsSummaryMap } from 'plugin/nf-schema' workflow RNAVAR { take: - ch_input - ch_dbsnp - ch_dbsnp_tbi - ch_dict - ch_exon_bed - ch_fasta - ch_fasta_fai - ch_gtf - ch_known_indels - ch_known_indels_tbi - ch_star_index + input + dbsnp + dbsnp_tbi + dict + exon_bed + fasta + fasta_fai + gtf + known_indels + known_indels_tbi + star_index snpeff_cache vep_genome vep_species @@ -77,11 +77,11 @@ workflow RNAVAR { // To gather all QC reports for MultiQC def ch_reports = Channel.empty() - // To gather used softwares versions for MultiQC + // To gather used softwares ch_versions for MultiQC def ch_versions = Channel.empty() // Parse the input data - ch_parsed_input = ch_input.groupTuple().map{ samplesheet -> checkSamplesAfterGrouping(samplesheet) } + parsed_input = input.groupTuple().map{ samplesheet -> checkSamplesAfterGrouping(samplesheet) } .branch{ meta, fastqs, bam, bai, cram, crai -> single : fastqs.size() == 1 return [ meta, fastqs.flatten() ] @@ -95,20 +95,20 @@ workflow RNAVAR { // MODULE: Prepare the alignment files (convert CRAM -> BAM and index) PREPARE_ALIGNMENT( - ch_parsed_input.cram, - ch_parsed_input.bam, + parsed_input.cram, + parsed_input.bam, ) ch_versions = ch_versions.mix(PREPARE_ALIGNMENT.out.versions) // MODULE: Concatenate FastQ files from same sample if required - CAT_FASTQ(ch_parsed_input.multiple) + CAT_FASTQ(parsed_input.multiple) - def ch_cat_fastq = CAT_FASTQ.out.reads.mix(ch_parsed_input.single) + def cat_fastq = CAT_FASTQ.out.reads.mix(parsed_input.single) ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) // MODULE: Generate QC summary using FastQC - FASTQC(ch_cat_fastq) + FASTQC(cat_fastq) ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ _meta, logs -> logs }) ch_versions = ch_versions.mix(FASTQC.out.versions) @@ -116,20 +116,20 @@ workflow RNAVAR { // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList // - GATK4_BEDTOINTERVALLIST(ch_exon_bed, ch_dict) - def ch_interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list + GATK4_BEDTOINTERVALLIST(exon_bed, dict) + def interval_list = GATK4_BEDTOINTERVALLIST.out.interval_list ch_versions = ch_versions.mix(GATK4_BEDTOINTERVALLIST.out.versions) // // MODULE: Scatter one interval-list into many interval-files using GATK4 IntervalListTools // - def ch_interval_list_split = Channel.empty() + def interval_list_split = Channel.empty() if (!params.skip_intervallisttools) { - GATK4_INTERVALLISTTOOLS(ch_interval_list) - ch_interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.flatten() + GATK4_INTERVALLISTTOOLS(interval_list) + interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.flatten() } else { - ch_interval_list_split = ch_interval_list.map { _meta, bed -> bed } + interval_list_split = interval_list.map { _meta, bed -> bed } } // @@ -137,18 +137,18 @@ workflow RNAVAR { // if (params.aligner == 'star') { - FASTQ_ALIGN_STAR(ch_cat_fastq, - ch_star_index, - ch_gtf, + FASTQ_ALIGN_STAR(cat_fastq, + star_index, + gtf, params.star_ignore_sjdbgtf, seq_platform, seq_center, - ch_fasta, - [[:],[]]) //ch_transcripts_fasta) + fasta, + [[:],[]]) //transcripts_fasta) - def ch_genome_bam = FASTQ_ALIGN_STAR.out.bam + def genome_bam = FASTQ_ALIGN_STAR.out.bam - // Gather QC reports + // Gather QC ch_reports ch_reports = ch_reports.mix(FASTQ_ALIGN_STAR.out.log_out) ch_reports = ch_reports.mix(FASTQ_ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(FASTQ_ALIGN_STAR.out.versions) @@ -156,11 +156,11 @@ workflow RNAVAR { // // SUBWORKFLOW: Mark duplicates with GATK4 // - BAM_MARKDUPLICATES_PICARD(ch_genome_bam, - ch_fasta, - ch_fasta_fai) + BAM_MARKDUPLICATES_PICARD(genome_bam, + fasta, + fasta_fai) - def ch_genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam + def genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam .join(BAM_MARKDUPLICATES_PICARD.out.bai, remainder: true) .join(BAM_MARKDUPLICATES_PICARD.out.csi, remainder: true) // TODO fix this bottleneck .map{meta, bam, bai, csi -> @@ -169,7 +169,7 @@ workflow RNAVAR { } .mix(PREPARE_ALIGNMENT.out.bam) - //Gather QC reports + //Gather QC ch_reports ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.metrics.collect{it[1]}.ifEmpty([])) ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.stats.collect{it[1]}.ifEmpty([])) ch_reports = ch_reports.mix(BAM_MARKDUPLICATES_PICARD.out.flagstat.collect{it[1]}.ifEmpty([])) @@ -181,50 +181,50 @@ workflow RNAVAR { // Splits reads that contain Ns in their cigar string(e.g. spanning splicing events in RNAseq data). // - SPLITNCIGAR(ch_genome_bam_bai, - ch_fasta, - ch_fasta_fai.map { _meta, fai -> fai }, - ch_dict, - ch_interval_list_split + SPLITNCIGAR(genome_bam_bai, + fasta, + fasta_fai.map { _meta, fai -> fai }, + dict, + interval_list_split ) - def ch_splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai + def splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai ch_versions = ch_versions.mix(SPLITNCIGAR.out.versions) // // MODULE: BaseRecalibrator from GATK4 // Generates a recalibration table based on various co-variates // - def ch_bam_variant_calling = Channel.empty() + def bam_variant_calling = Channel.empty() if (!params.skip_baserecalibration) { // known_sites is made by grouping both the dbsnp and the known indels ressources // they can either or both be optional - def ch_known_sites = ch_dbsnp.concat(ch_known_indels).collect() - def ch_known_sites_tbi = ch_dbsnp_tbi.concat(ch_known_indels_tbi).collect() + def known_sites = dbsnp.concat(known_indels).collect() + def known_sites_tbi = dbsnp_tbi.concat(known_indels_tbi).collect() - def ch_interval_list_recalib = ch_interval_list.map{ _meta, bed -> [bed] }.flatten() - def ch_splitncigar_bam_bai_interval = ch_splitncigar_bam_bai.combine(ch_interval_list_recalib) + def interval_list_recalib = interval_list.map{ _meta, bed -> [bed] }.flatten() + def splitncigar_bam_bai_interval = splitncigar_bam_bai.combine(interval_list_recalib) .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] } GATK4_BASERECALIBRATOR( - ch_splitncigar_bam_bai_interval, - ch_fasta.map{ _meta, fasta -> [fasta] }, - ch_fasta_fai.map { _meta, fai -> fai }, - ch_dict.map{ _meta, dict -> [dict] }, - ch_known_sites, - ch_known_sites_tbi + splitncigar_bam_bai_interval, + fasta.map{ _meta, fasta_ -> [fasta_] }, + fasta_fai.map { _meta, fai -> fai }, + dict.map{ _meta, dict_ -> [dict_] }, + known_sites, + known_sites_tbi ) - def ch_bqsr_table = GATK4_BASERECALIBRATOR.out.table + def bqsr_table = GATK4_BASERECALIBRATOR.out.table - // Gather QC reports - ch_reports = ch_reports.mix(ch_bqsr_table.map{ _meta, table -> table}) + // Gather QC ch_reports + ch_reports = ch_reports.mix(bqsr_table.map{ _meta, table -> table}) ch_versions = ch_versions.mix(GATK4_BASERECALIBRATOR.out.versions) - def ch_bam_applybqsr = ch_splitncigar_bam_bai.join(ch_bqsr_table) + def bam_applybqsr = splitncigar_bam_bai.join(bqsr_table) - def ch_interval_list_applybqsr = ch_interval_list.map{ _meta, bed -> [bed] }.flatten() - def ch_applybqsr_bam_bai_interval = ch_bam_applybqsr.combine(ch_interval_list_applybqsr) + def interval_list_applybqsr = interval_list.map{ _meta, bed -> [bed] }.flatten() + def applybqsr_bam_bai_interval = bam_applybqsr.combine(interval_list_applybqsr) .map{ meta, bam, bai, table, interval -> [ meta, bam, bai, table, interval]} // @@ -233,35 +233,35 @@ workflow RNAVAR { // RECALIBRATE( params.skip_multiqc, - ch_applybqsr_bam_bai_interval, - ch_dict.map{ _meta, dict -> [dict] }, - ch_fasta_fai.map { _meta, fai -> fai }, - ch_fasta.map{ _meta, fasta -> [fasta] } + applybqsr_bam_bai_interval, + dict.map{ _meta, dict_ -> [dict_] }, + fasta_fai.map { _meta, fai -> fai }, + fasta.map{ _meta, fasta_ -> [fasta_] } ) - ch_bam_variant_calling = RECALIBRATE.out.bam + bam_variant_calling = RECALIBRATE.out.bam - // Gather QC reports + // Gather QC ch_reports ch_reports = ch_reports.mix(RECALIBRATE.out.qc.collect{it[1]}.ifEmpty([])) ch_versions = ch_versions.mix(RECALIBRATE.out.versions) } else { - ch_bam_variant_calling = ch_splitncigar_bam_bai + bam_variant_calling = splitncigar_bam_bai } // Run haplotyper even in the absence of dbSNP files - def ch_dbsnp_for_haplotypecaller = Channel.empty() - def ch_dbsnp_for_haplotypecaller_tbi = Channel.empty() + def dbsnp_for_haplotypecaller = Channel.empty() + def dbsnp_for_haplotypecaller_tbi = Channel.empty() if (!params.dbsnp){ - ch_dbsnp_for_haplotypecaller = [[id:'null'], []] - ch_dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] + dbsnp_for_haplotypecaller = [[id:'null'], []] + dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] } else { - ch_dbsnp_for_haplotypecaller = ch_dbsnp.map{ vcf -> [[id:'dbsnp'], vcf] } - ch_dbsnp_for_haplotypecaller_tbi = ch_dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } + dbsnp_for_haplotypecaller = dbsnp.map{ vcf -> [[id:'dbsnp'], vcf] } + dbsnp_for_haplotypecaller_tbi = dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } } - ch_haplotypecaller_interval_bam = ch_bam_variant_calling.combine(ch_interval_list_split) - .map{ meta, bam, bai, interval_list -> - [ meta + [ id:meta.id + "_" + interval_list.baseName, sample:meta.id, variantcaller:'haplotypecaller' ], bam, bai, interval_list, [] ] + haplotypecaller_interval_bam = bam_variant_calling.combine(interval_list_split) + .map{ meta, bam, bai, interval_list_ -> + [ meta + [ id:meta.id + "_" + interval_list_.baseName, sample:meta.id, variantcaller:'haplotypecaller' ], bam, bai, interval_list_, [] ] } // @@ -270,39 +270,39 @@ workflow RNAVAR { // GATK4_HAPLOTYPECALLER( - ch_haplotypecaller_interval_bam, - ch_fasta, - ch_fasta_fai, - ch_dict, - ch_dbsnp_for_haplotypecaller, - ch_dbsnp_for_haplotypecaller_tbi + haplotypecaller_interval_bam, + fasta, + fasta_fai, + dict, + dbsnp_for_haplotypecaller, + dbsnp_for_haplotypecaller_tbi ) - def ch_haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() // TODO fix this bottleneck + def haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() // TODO fix this bottleneck ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions) - def ch_haplotypecaller_vcf = Channel.empty() + def haplotypecaller_vcf = Channel.empty() if (!params.generate_gvcf){ // // MODULE: MergeVCFS from GATK4 // Merge multiple VCF files into one VCF // GATK4_MERGEVCFS( - ch_haplotypecaller_raw, - ch_dict + haplotypecaller_raw, + dict ) - ch_haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf + haplotypecaller_vcf = GATK4_MERGEVCFS.out.vcf ch_versions = ch_versions.mix(GATK4_MERGEVCFS.out.versions) // // MODULE: Index the VCF using TABIX // TABIX( - ch_haplotypecaller_vcf + haplotypecaller_vcf ) - def ch_haplotypecaller_vcf_tbi = ch_haplotypecaller_vcf + def haplotypecaller_vcf_tbi = haplotypecaller_vcf .join(TABIX.out.tbi, by: [0], remainder: true) .join(TABIX.out.csi, by: [0], remainder: true) // TODO fix this bottleneck .map{meta, vcf, tbi, csi -> @@ -311,7 +311,7 @@ workflow RNAVAR { } ch_versions = ch_versions.mix(TABIX.out.versions) - def ch_final_vcf = Channel.empty() + def final_vcf = Channel.empty() // // MODULE: VariantFiltration from GATK4 @@ -320,17 +320,17 @@ workflow RNAVAR { if (!params.skip_variantfiltration && !params.bam_csi_index ) { GATK4_VARIANTFILTRATION( - ch_haplotypecaller_vcf_tbi, - ch_fasta, - ch_fasta_fai, - ch_dict + haplotypecaller_vcf_tbi, + fasta, + fasta_fai, + dict ) - def ch_filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf - ch_final_vcf = ch_filtered_vcf + def filtered_vcf = GATK4_VARIANTFILTRATION.out.vcf + final_vcf = filtered_vcf ch_versions = ch_versions.mix(GATK4_VARIANTFILTRATION.out.versions) } else { - ch_final_vcf = ch_haplotypecaller_vcf + final_vcf = haplotypecaller_vcf } // @@ -338,15 +338,15 @@ workflow RNAVAR { // if((!params.skip_variantannotation) && (params.annotate_tools) && (params.annotate_tools.contains('merge') || params.annotate_tools.contains('snpeff') || params.annotate_tools.contains('vep'))) { - def ch_vep_fasta = [[id: 'null'], []] + def vep_fasta = [[id: 'null'], []] if (params.vep_include_fasta) { - ch_vep_fasta = ch_fasta + vep_fasta = fasta } VCF_ANNOTATE_ALL( - ch_final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, - ch_vep_fasta, + final_vcf.map{meta, vcf -> [ meta + [ file_name: vcf.baseName ], vcf ] }, + vep_fasta, params.annotate_tools, params.snpeff_genome ? "${params.snpeff_genome}.${params.snpeff_db}" : "${params.genome}.${params.snpeff_db}", snpeff_cache, @@ -357,13 +357,13 @@ workflow RNAVAR { vep_extra_files, ) - // Gather QC reports + // Gather QC ch_reports ch_reports = ch_reports.mix(VCF_ANNOTATE_ALL.out.reports) ch_versions = ch_versions.mix(VCF_ANNOTATE_ALL.out.versions) } } else { - def ch_combinegvcfs_input = GATK4_HAPLOTYPECALLER.out.vcf + def combinegvcfs_input = GATK4_HAPLOTYPECALLER.out.vcf .join(GATK4_HAPLOTYPECALLER.out.tbi, failOnMismatch:true, failOnDuplicate:true) .map{ meta, vcf, tbi -> def new_meta = meta + [id:meta.sample] @@ -376,18 +376,18 @@ workflow RNAVAR { // Merge multiple GVCF files into one GVCF // GATK4_COMBINEGVCFS( - ch_combinegvcfs_input, - ch_fasta.map { _meta, fasta -> fasta }, - ch_fasta_fai.map { _meta, fai -> fai }, - ch_dict.map { _meta, dict -> dict } + combinegvcfs_input, + fasta.map { _meta, fasta_ -> fasta_ }, + fasta_fai.map { _meta, fai -> fai }, + dict.map { _meta, dict_ -> dict_ } ) - def ch_haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf + def haplotypecaller_gvcf = GATK4_COMBINEGVCFS.out.combined_gvcf ch_versions = ch_versions.mix(GATK4_COMBINEGVCFS.out.versions) // // MODULE: Index the VCF using TABIX // - TABIXGVCF(ch_haplotypecaller_gvcf) + TABIXGVCF(haplotypecaller_gvcf) ch_versions = ch_versions.mix(TABIXGVCF.out.versions) @@ -395,9 +395,9 @@ workflow RNAVAR { } // - // Collate and save software versions + // Collate and save software ch_versions // - def ch_collated_versions = softwareVersionsToYAML(ch_versions).collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) + def collated_versions = softwareVersionsToYAML(ch_versions).collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true) // // MODULE: MultiQC @@ -406,25 +406,25 @@ workflow RNAVAR { def val_multiqc_report = Channel.empty() if (!params.skip_multiqc){ - def ch_multiqc_files = Channel.empty() + def multiqc_files = Channel.empty() - def ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) - def ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() - def ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + def multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) + def multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() + def multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() def summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") - def ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - def ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - def ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description)) + def workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) + def multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) + def methods_description = Channel.value(methodsDescriptionText(multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) + multiqc_files = multiqc_files.mix(workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + multiqc_files = multiqc_files.mix(collated_versions) + multiqc_files = multiqc_files.mix(methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true)) MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList(), + multiqc_files.collect(), + multiqc_config.toList(), + multiqc_custom_config.toList(), + multiqc_logo.toList(), [], [] ) From f54266ece5e325208ac1e0ef0648162b2d337e69 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 9 Jan 2025 16:55:55 +0100 Subject: [PATCH 170/275] fix some tests --- subworkflows/local/vcf_annotate_all/main.nf | 24 +++++++------- tests/all_inputs.nf.test.snap | 18 +++++------ tests/annotation.nf.test.snap | 36 ++++++++++----------- 3 files changed, 39 insertions(+), 39 deletions(-) diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf index 7f3373b6..8782a149 100644 --- a/subworkflows/local/vcf_annotate_all/main.nf +++ b/subworkflows/local/vcf_annotate_all/main.nf @@ -22,15 +22,15 @@ workflow VCF_ANNOTATE_ALL { main: def ch_reports = Channel.empty() - def vcf_ann = Channel.empty() - def tab_ann = Channel.empty() - def json_ann = Channel.empty() + def vcf_annotated = Channel.empty() + def tab_annotated = Channel.empty() + def json_annotated = Channel.empty() def ch_versions = Channel.empty() if (tools.split(',').contains('bcfann')) { VCF_ANNOTATE_BCFTOOLS(vcf) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) ch_versions = ch_versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions) } @@ -39,7 +39,7 @@ workflow VCF_ANNOTATE_ALL { VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache) ch_reports = ch_reports.mix(VCF_ANNOTATE_SNPEFF.out.reports.map{ _meta, reports_ -> [ reports_ ] }) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_SNPEFF.out.vcf_tbi) ch_versions = ch_versions.mix(VCF_ANNOTATE_SNPEFF.out.versions) } @@ -48,7 +48,7 @@ workflow VCF_ANNOTATE_ALL { VCF_ANNOTATE_MERGE(vcf_ann_for_merge, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) ch_reports = ch_reports.mix(VCF_ANNOTATE_MERGE.out.reports) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_MERGE.out.vcf_tbi) ch_versions = ch_versions.mix(VCF_ANNOTATE_MERGE.out.versions) } @@ -57,16 +57,16 @@ workflow VCF_ANNOTATE_ALL { VCF_ANNOTATE_ENSEMBLVEP(vcf_for_vep, fasta, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) ch_reports = ch_reports.mix(VCF_ANNOTATE_ENSEMBLVEP.out.reports) - vcf_ann = vcf_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi) - tab_ann = tab_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab) - json_ann = json_ann.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json) + vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.vcf_tbi) + tab_annotated = tab_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.tab) + json_annotated = json_annotated.mix(VCF_ANNOTATE_ENSEMBLVEP.out.json) ch_versions = ch_versions.mix(VCF_ANNOTATE_ENSEMBLVEP.out.versions) } emit: - vcf_ann // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - tab_ann - json_ann + vcf_ann = vcf_annotated // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] + tab_ann = tab_annotated + json_ann = json_annotated reports = ch_reports // path: *.html versions = ch_versions // path: ch_versions.yml } diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 23afadb6..e3166fc9 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -31,29 +31,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -128,6 +128,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:56:22.79954652" + "timestamp": "2025-01-09T16:41:24.471237186" } } \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index afadab8f..7799c2c2 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -297,29 +297,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -504,7 +504,7 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:37:37.774766173" + "timestamp": "2025-01-09T16:51:32.004274594" }, "Run with profile test | annotation with snpeff": { "content": [ @@ -538,32 +538,32 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SNPEFF_SNPEFF": { "snpeff": "5.1d" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -644,6 +644,6 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:31:39.422563362" + "timestamp": "2025-01-09T16:47:00.48306332" } } \ No newline at end of file From ceeb934198575363549662daca317a4109cf1749 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Thu, 9 Jan 2025 16:35:29 +0000 Subject: [PATCH 171/275] fix snapshots --- tests/annotation.nf.test.snap | 20 ++++++++++---------- tests/bam_csi.nf.test.snap | 20 ++++++++++---------- tests/bam_input.nf.test.snap | 10 +++++----- tests/cram_input.nf.test.snap | 10 +++++----- tests/default.nf.test.snap | 20 ++++++++++---------- tests/removeduplicates.nf.test.snap | 20 ++++++++++---------- tests/skip_baserecalibration.nf.test.snap | 20 ++++++++++---------- 7 files changed, 60 insertions(+), 60 deletions(-) diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 7799c2c2..b32e2859 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -34,32 +34,32 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SNPEFF_SNPEFF": { "snpeff": "5.1d" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -257,10 +257,10 @@ ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:44:12.561904068" + "timestamp": "2025-01-09T16:19:12.045032239" }, "Run with profile test | annotation with vep": { "content": [ diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index f984dd6a..a55345ea 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -28,29 +28,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -100,9 +100,9 @@ ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T14:02:00.162034514" + "timestamp": "2025-01-09T16:22:32.936861849" } } \ No newline at end of file diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index a646d392..8c014b13 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -25,13 +25,13 @@ "gatk4": "4.5.0.0" }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "TABIX": { "tabix": "1.19.1" @@ -71,9 +71,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2025-01-07T17:03:13.667134079" + "timestamp": "2025-01-09T16:24:31.090393575" } } \ No newline at end of file diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index fab0606f..438866ce 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -25,13 +25,13 @@ "gatk4": "4.5.0.0" }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "TABIX": { "tabix": "1.19.1" @@ -71,9 +71,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2025-01-07T17:05:36.02051331" + "timestamp": "2025-01-09T16:26:33.364598229" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index a7c2b652..ddd16443 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -31,29 +31,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -105,9 +105,9 @@ ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T14:15:23.218615886" + "timestamp": "2025-01-09T16:29:28.081229818" } } \ No newline at end of file diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 25ee58b7..a86e9bcb 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -31,29 +31,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -105,9 +105,9 @@ ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T14:21:28.482683082" + "timestamp": "2025-01-09T16:32:25.501338685" } } \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index eb925e0f..bebbdaa5 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -25,29 +25,29 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -97,9 +97,9 @@ ] ], "meta": { - "nf-test": "0.9.1", + "nf-test": "0.9.2", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T14:26:44.327045503" + "timestamp": "2025-01-09T16:35:18.554293763" } } \ No newline at end of file From 64950b74e290939b9df09ed22d852097be798836 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 9 Jan 2025 17:35:47 +0100 Subject: [PATCH 172/275] Update subworkflows/local/prepare_genome/main.nf Co-authored-by: Maxime U Garcia --- subworkflows/local/prepare_genome/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index f3c5f486..193212e1 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -74,7 +74,7 @@ workflow PREPARE_GENOME { star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi - versions = ch_versions // channel: [ ch_versions.yml ] + versions = ch_versions // channel: [ versions.yml ] // bedtools_sort = bedtools_sort // path: sort.bed // bedtools_merge = bedtools_merge // path: merge.bed } From 8a69313150e9778de372893db39889b7b533f52c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 10 Jan 2025 15:54:39 +0100 Subject: [PATCH 173/275] update changelog --- CHANGELOG.md | 4 +++- tests/annotation.nf.test.snap | 18 +++++++++--------- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 83c8d2a7..6b5a0f26 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -54,7 +54,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | fastqc | 0.11.9 | 0.12.1 | | mosdepth | 0.3.3 | 0.3.6 | | multiqc | 1.15 | 1.18 | -| samtools | 1.17 | 1.18 | +| picard | 3.1.0 | 3.3.0 | +| samtools | 1.17 | 1.21 | +| star | 2.7.10a | 2.7.11b | ## [1.0.0] nfcore/rnavar - 2022/06/20 diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 7799c2c2..e2e9ee23 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -34,32 +34,32 @@ "gatk4": "4.5.0.0" }, "PICARD_MARKDUPLICATES": { - "picard": "3.1.1" + "picard": "3.3.0" }, "SAMTOOLS_FLAGSTAT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_IDXSTATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_INDEX": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_MERGE": { "samtools": "1.19.2" }, "SAMTOOLS_SORT": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SNPEFF_SNPEFF": { "snpeff": "5.1d" }, "STAR_ALIGN": { - "star": "2.7.10a", - "samtools": 1.18, + "star": "2.7.11b", + "samtools": 1.21, "gawk": "5.1.0" }, "TABIX": { @@ -260,7 +260,7 @@ "nf-test": "0.9.1", "nextflow": "24.10.3" }, - "timestamp": "2025-01-08T13:44:12.561904068" + "timestamp": "2025-01-09T16:57:22.127665971" }, "Run with profile test | annotation with vep": { "content": [ From b422fbc3d03343a68d15a7849abd67293008f708 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 10 Jan 2025 16:03:09 +0100 Subject: [PATCH 174/275] add this PR --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b5a0f26..f140cbca 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -44,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#144](https://github.com/nf-core/rnavar/pull/144) - Change gatk_vf params from integer to floats - [#145](https://github.com/nf-core/rnavar/issues/145) - Converted `star_index` and `gtf` emit channels from queue to value channels in `PREPARE_GENOME` subworkflow - [#149](https://github.com/nf-core/rnavar/pull/149) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf +- [#158](https://github.com/nf-core/rnavar/pull/158) - Fixed language server errors and warnings ### Dependencies From 3addcd312e438f67fffcc0d75aa770870980cd0f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 13 Jan 2025 11:40:30 +0100 Subject: [PATCH 175/275] fix join bottlenecks --- subworkflows/local/recalibrate/main.nf | 14 ++++++-------- subworkflows/local/splitncigar/main.nf | 26 +++++++++++++------------- workflows/rnavar/main.nf | 23 ++++++++++------------- 3 files changed, 29 insertions(+), 34 deletions(-) diff --git a/subworkflows/local/recalibrate/main.nf b/subworkflows/local/recalibrate/main.nf index 5a03c308..c3e3e223 100644 --- a/subworkflows/local/recalibrate/main.nf +++ b/subworkflows/local/recalibrate/main.nf @@ -30,16 +30,14 @@ workflow RECALIBRATE { ch_versions = ch_versions.mix(APPLYBQSR.out.versions.first()) SAMTOOLS_INDEX(bam_recalibrated) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) - def bam_recalibrated_index = bam_recalibrated - .join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true) - .join(SAMTOOLS_INDEX.out.csi, by: [0], remainder: true) // TODO fix this bottleneck - .map{meta, bam_, bai, csi -> - if (bai) [meta, bam_, bai] - else [meta, bam_, csi] - } + def bam_indices = SAMTOOLS_INDEX.out.bai + .mix(SAMTOOLS_INDEX.out.csi) + .mix(SAMTOOLS_INDEX.out.crai) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first()) + def bam_recalibrated_index = bam_recalibrated + .join(bam_indices, failOnMismatch: true, failOnDuplicate: true) def bam_reports = Channel.empty() diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index ee5575bd..25ad18a3 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -24,29 +24,29 @@ workflow SPLITNCIGAR { fai.map{ fai_ -> [[id:'genome'], fai_] }, dict) - bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam + def bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions) - bam_splitncigar_interval = bam_splitncigar.map{ meta, bam_ -> [ meta + [id:meta.sample] - meta.subMap('sample'), bam_ ] }.groupTuple() + def bam_splitncigar_interval = bam_splitncigar.map{ meta, bam_ -> [ meta + [id:meta.sample] - meta.subMap('sample'), bam_ ] }.groupTuple() - SAMTOOLS_MERGE(bam_splitncigar_interval, + SAMTOOLS_MERGE( + bam_splitncigar_interval, fasta, - fai.map{ fai_ -> [[id:fai_.baseName], fai_] }) + fai.map{ fai_ -> [[id:fai_.baseName], fai_] } + ) - splitncigar_bam = SAMTOOLS_MERGE.out.bam + def splitncigar_bam = SAMTOOLS_MERGE.out.bam ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions) SAMTOOLS_INDEX(splitncigar_bam) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) - splitncigar_bam_bai = splitncigar_bam - .join(SAMTOOLS_INDEX.out.bai, remainder: true) - .join(SAMTOOLS_INDEX.out.csi, remainder: true) // TODO fix this bottleneck - .map{meta, bam_, bai, csi -> - if (bai) [meta, bam_, bai] - else [meta, bam_, csi] - } + def splitncigar_bam_indices = SAMTOOLS_INDEX.out.bai + .mix(SAMTOOLS_INDEX.out.csi) + .mix(SAMTOOLS_INDEX.out.crai) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + def splitncigar_bam_bai = splitncigar_bam + .join(splitncigar_bam_indices, failOnDuplicate: true, failOnMismatch: true) emit: bam_bai = splitncigar_bam_bai diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 3518a0d5..48722838 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -160,13 +160,12 @@ workflow RNAVAR { fasta, fasta_fai) + def markduplicate_indices = BAM_MARKDUPLICATES_PICARD.out.bai + .mix(BAM_MARKDUPLICATES_PICARD.out.csi) + .mix(BAM_MARKDUPLICATES_PICARD.out.crai) + def genome_bam_bai = BAM_MARKDUPLICATES_PICARD.out.bam - .join(BAM_MARKDUPLICATES_PICARD.out.bai, remainder: true) - .join(BAM_MARKDUPLICATES_PICARD.out.csi, remainder: true) // TODO fix this bottleneck - .map{meta, bam, bai, csi -> - if (bai) [meta, bam, bai] - else [meta, bam, csi] - } + .join(markduplicate_indices, failOnDuplicate:true, failOnMismatch:true) .mix(PREPARE_ALIGNMENT.out.bam) //Gather QC ch_reports @@ -301,16 +300,14 @@ workflow RNAVAR { TABIX( haplotypecaller_vcf ) + ch_versions = ch_versions.mix(TABIX.out.versions) + + def haplotypecaller_indices = TABIX.out.tbi + .mix(TABIX.out.csi) def haplotypecaller_vcf_tbi = haplotypecaller_vcf - .join(TABIX.out.tbi, by: [0], remainder: true) - .join(TABIX.out.csi, by: [0], remainder: true) // TODO fix this bottleneck - .map{meta, vcf, tbi, csi -> - if (tbi) [meta, vcf, tbi] - else [meta, vcf, csi] - } + .join(haplotypecaller_indices, failOnDuplicate:true, failOnMismatch: true) - ch_versions = ch_versions.mix(TABIX.out.versions) def final_vcf = Channel.empty() // From ec5740180c42bbc4ac7a78ed10600433bc740771 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 13 Jan 2025 12:06:02 +0100 Subject: [PATCH 176/275] fix a groupTuple bottleneck --- workflows/rnavar/main.nf | 29 +++++++++++++++++------------ 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 48722838..78084a77 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -126,7 +126,7 @@ workflow RNAVAR { def interval_list_split = Channel.empty() if (!params.skip_intervallisttools) { GATK4_INTERVALLISTTOOLS(interval_list) - interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.flatten() + interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.collect() } else { interval_list_split = interval_list.map { _meta, bed -> bed } @@ -184,7 +184,7 @@ workflow RNAVAR { fasta, fasta_fai.map { _meta, fai -> fai }, dict, - interval_list_split + interval_list.map { _meta, bed -> bed } ) def splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai @@ -258,7 +258,12 @@ workflow RNAVAR { dbsnp_for_haplotypecaller_tbi = dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } } - haplotypecaller_interval_bam = bam_variant_calling.combine(interval_list_split) + def haplotypecaller_interval_bam = bam_variant_calling.combine(interval_list_split) + .map { meta, bam, bai, interval_lists -> + def new_meta = meta + [interval_count: interval_lists instanceof List ? interval_lists.size() : 1] + [ new_meta, bam, bai, interval_lists ] + } + .transpose(by:3) .map{ meta, bam, bai, interval_list_ -> [ meta + [ id:meta.id + "_" + interval_list_.baseName, sample:meta.id, variantcaller:'haplotypecaller' ], bam, bai, interval_list_, [] ] } @@ -277,7 +282,13 @@ workflow RNAVAR { dbsnp_for_haplotypecaller_tbi ) - def haplotypecaller_raw = GATK4_HAPLOTYPECALLER.out.vcf.map{ meta, vcf -> [ meta + [id:meta.sample] - meta.subMap('sample'), vcf ] }.groupTuple() // TODO fix this bottleneck + def haplotypecaller_out = GATK4_HAPLOTYPECALLER.out.vcf + .join(GATK4_HAPLOTYPECALLER.out.tbi, failOnMismatch:true, failOnDuplicate:true) + .map{ meta, vcf, tbi -> + def new_meta = meta + [id:meta.sample] - meta.subMap('sample') - meta.subMap("interval_count") + [ groupKey(new_meta, meta.interval_count), vcf, tbi ] + } + .groupTuple() ch_versions = ch_versions.mix(GATK4_HAPLOTYPECALLER.out.versions) @@ -287,6 +298,7 @@ workflow RNAVAR { // MODULE: MergeVCFS from GATK4 // Merge multiple VCF files into one VCF // + def haplotypecaller_raw = haplotypecaller_out.map { meta, vcfs, _tbis -> [ meta, vcfs ]} GATK4_MERGEVCFS( haplotypecaller_raw, dict @@ -360,20 +372,13 @@ workflow RNAVAR { } } else { - def combinegvcfs_input = GATK4_HAPLOTYPECALLER.out.vcf - .join(GATK4_HAPLOTYPECALLER.out.tbi, failOnMismatch:true, failOnDuplicate:true) - .map{ meta, vcf, tbi -> - def new_meta = meta + [id:meta.sample] - [new_meta, vcf, tbi] - } - .groupTuple() // TODO fix this bottleneck // // MODULE: CombineGVCFS from GATK4 // Merge multiple GVCF files into one GVCF // GATK4_COMBINEGVCFS( - combinegvcfs_input, + haplotypecaller_out, fasta.map { _meta, fasta_ -> fasta_ }, fasta_fai.map { _meta, fai -> fai }, dict.map { _meta, dict_ -> dict_ } From ad1f1bcd47157090acfed89435c2a1c50b0d3d40 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 13 Jan 2025 13:24:27 +0100 Subject: [PATCH 177/275] fix splitcigarreads groupTuple bottleneck --- subworkflows/local/splitncigar/main.nf | 19 +++++++++++++++++-- workflows/rnavar/main.nf | 2 +- 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 25ad18a3..43cdfe43 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -17,7 +17,17 @@ workflow SPLITNCIGAR { main: def ch_versions = Channel.empty() - def bam_interval = bam.combine(intervals).map{ meta, bam_, bai, intervals_ -> [ meta + [sample:meta.id], bam_, bai, intervals_ ] } + def bam_interval = bam + .combine(intervals) + .map { meta, bam_, bai, intervals_ -> + def new_meta = meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1] + [ new_meta, bam_, bai, intervals_ ] + } + .transpose(by:3) + .map { meta, bam_, bai, interval -> + def new_meta = meta + [id:"${meta.id}_${interval.baseName}", sample: meta.id] + [ new_meta, bam_, bai, interval ] + } GATK4_SPLITNCIGARREADS(bam_interval, fasta, @@ -27,7 +37,12 @@ workflow SPLITNCIGAR { def bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions) - def bam_splitncigar_interval = bam_splitncigar.map{ meta, bam_ -> [ meta + [id:meta.sample] - meta.subMap('sample'), bam_ ] }.groupTuple() + def bam_splitncigar_interval = bam_splitncigar + .map{ meta, bam_ -> + def new_meta = meta + [id:meta.sample] - meta.subMap('sample') - meta.subMap('interval_count') + [ groupKey(new_meta, meta.interval_count), bam_ ] + } + .groupTuple() SAMTOOLS_MERGE( bam_splitncigar_interval, diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 78084a77..f3c131a7 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -184,7 +184,7 @@ workflow RNAVAR { fasta, fasta_fai.map { _meta, fai -> fai }, dict, - interval_list.map { _meta, bed -> bed } + interval_list_split ) def splitncigar_bam_bai = SPLITNCIGAR.out.bam_bai From 8037ce73e393a25cf73a95e17194779eef0e69f4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 13 Jan 2025 13:57:35 +0100 Subject: [PATCH 178/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f140cbca..8ed24bf2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,6 +45,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#145](https://github.com/nf-core/rnavar/issues/145) - Converted `star_index` and `gtf` emit channels from queue to value channels in `PREPARE_GENOME` subworkflow - [#149](https://github.com/nf-core/rnavar/pull/149) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf - [#158](https://github.com/nf-core/rnavar/pull/158) - Fixed language server errors and warnings +- [#159](https://github.com/nf-core/rnavar/pull/159) - Fixed a couple of bottlenecks in the pipeline ### Dependencies From 0d2bb33c8b5032e7e31e2c5c2b95741daa5feaa9 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 13 Jan 2025 13:58:39 +0100 Subject: [PATCH 179/275] make editorconfig happy --- subworkflows/local/splitncigar/main.nf | 6 +++--- workflows/rnavar/main.nf | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 43cdfe43..4c18afe5 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -24,7 +24,7 @@ workflow SPLITNCIGAR { [ new_meta, bam_, bai, intervals_ ] } .transpose(by:3) - .map { meta, bam_, bai, interval -> + .map { meta, bam_, bai, interval -> def new_meta = meta + [id:"${meta.id}_${interval.baseName}", sample: meta.id] [ new_meta, bam_, bai, interval ] } @@ -38,9 +38,9 @@ workflow SPLITNCIGAR { ch_versions = ch_versions.mix(GATK4_SPLITNCIGARREADS.out.versions) def bam_splitncigar_interval = bam_splitncigar - .map{ meta, bam_ -> + .map{ meta, bam_ -> def new_meta = meta + [id:meta.sample] - meta.subMap('sample') - meta.subMap('interval_count') - [ groupKey(new_meta, meta.interval_count), bam_ ] + [ groupKey(new_meta, meta.interval_count), bam_ ] } .groupTuple() diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index f3c131a7..74faa2f2 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -284,7 +284,7 @@ workflow RNAVAR { def haplotypecaller_out = GATK4_HAPLOTYPECALLER.out.vcf .join(GATK4_HAPLOTYPECALLER.out.tbi, failOnMismatch:true, failOnDuplicate:true) - .map{ meta, vcf, tbi -> + .map{ meta, vcf, tbi -> def new_meta = meta + [id:meta.sample] - meta.subMap('sample') - meta.subMap("interval_count") [ groupKey(new_meta, meta.interval_count), vcf, tbi ] } From 8ef0e6567df0465debff0fa94ca8522a6d05a81e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 14 Jan 2025 16:35:25 +0100 Subject: [PATCH 180/275] Update subworkflows/local/splitncigar/main.nf Co-authored-by: Maxime U Garcia --- subworkflows/local/splitncigar/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 4c18afe5..bcc5ea5c 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -20,8 +20,7 @@ workflow SPLITNCIGAR { def bam_interval = bam .combine(intervals) .map { meta, bam_, bai, intervals_ -> - def new_meta = meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1] - [ new_meta, bam_, bai, intervals_ ] + [ meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1], bam_, bai, intervals_ ] } .transpose(by:3) .map { meta, bam_, bai, interval -> From d477c2149b7f82362a61fb684767f26370268f61 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 14 Jan 2025 16:35:31 +0100 Subject: [PATCH 181/275] Update subworkflows/local/splitncigar/main.nf Co-authored-by: Maxime U Garcia --- subworkflows/local/splitncigar/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index bcc5ea5c..776d6072 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -25,7 +25,7 @@ workflow SPLITNCIGAR { .transpose(by:3) .map { meta, bam_, bai, interval -> def new_meta = meta + [id:"${meta.id}_${interval.baseName}", sample: meta.id] - [ new_meta, bam_, bai, interval ] + [ meta + [id:"${meta.id}_${interval.baseName}", sample: meta.id], bam_, bai, interval ] } GATK4_SPLITNCIGARREADS(bam_interval, From 0c18809fe6bdd7ec478d9343299de8a3d42d473f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 15 Jan 2025 09:19:52 +0100 Subject: [PATCH 182/275] Update workflows/rnavar/main.nf Co-authored-by: Maxime U Garcia --- workflows/rnavar/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/rnavar/main.nf b/workflows/rnavar/main.nf index 74faa2f2..65246ad9 100755 --- a/workflows/rnavar/main.nf +++ b/workflows/rnavar/main.nf @@ -285,7 +285,7 @@ workflow RNAVAR { def haplotypecaller_out = GATK4_HAPLOTYPECALLER.out.vcf .join(GATK4_HAPLOTYPECALLER.out.tbi, failOnMismatch:true, failOnDuplicate:true) .map{ meta, vcf, tbi -> - def new_meta = meta + [id:meta.sample] - meta.subMap('sample') - meta.subMap("interval_count") + def new_meta = meta + [id:meta.sample] - meta.subMap('sample', "interval_count") [ groupKey(new_meta, meta.interval_count), vcf, tbi ] } .groupTuple() From 4035a184da41d5fb75b32f8c6d7512de1ebe2358 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 15 Jan 2025 09:20:17 +0100 Subject: [PATCH 183/275] Update subworkflows/local/splitncigar/main.nf Co-authored-by: Maxime U Garcia --- subworkflows/local/splitncigar/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 776d6072..27320c20 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -24,7 +24,6 @@ workflow SPLITNCIGAR { } .transpose(by:3) .map { meta, bam_, bai, interval -> - def new_meta = meta + [id:"${meta.id}_${interval.baseName}", sample: meta.id] [ meta + [id:"${meta.id}_${interval.baseName}", sample: meta.id], bam_, bai, interval ] } From a2c61fd5cb38c4b3107024eed756601b195e6717 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Wed, 15 Jan 2025 12:17:52 +0000 Subject: [PATCH 184/275] fix tests --- .github/workflows/ci.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d956edf4..c1eaa758 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -48,6 +48,8 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 From 557f18e4b0873c2bd3f7eacbbd9536477bc7ebb1 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Wed, 15 Jan 2025 12:17:57 +0000 Subject: [PATCH 185/275] fix linting --- modules.json | 2 +- modules/nf-core/fastqc/main.nf | 20 ++++++++++---------- modules/nf-core/fastqc/tests/tags.yml | 2 -- 3 files changed, 11 insertions(+), 13 deletions(-) delete mode 100644 modules/nf-core/fastqc/tests/tags.yml diff --git a/modules.json b/modules.json index d73b11a1..3d6bae2b 100755 --- a/modules.json +++ b/modules.json @@ -52,7 +52,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", "installed_by": ["modules"] }, "gatk4/applybqsr": { diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 752c3a10..033f4154 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -1,5 +1,5 @@ process FASTQC { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" @@ -19,30 +19,30 @@ process FASTQC { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of old name and new name pairs to use for renaming in the bash while loop def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') + def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus + def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do + printf "%s %s\\n" ${rename_to} | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done fastqc \\ - $args \\ - --threads $task.cpus \\ - --memory $fastqc_memory \\ - $renamed_files + ${args} \\ + --threads ${task.cpus} \\ + --memory ${fastqc_memory} \\ + ${renamed_files} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294b..00000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** From aee62f0000b2b847212fc047cc4de1713e345287 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Wed, 15 Jan 2025 12:38:37 +0000 Subject: [PATCH 186/275] add report param --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 53d86fba..3fe8e357 100644 --- a/nextflow.config +++ b/nextflow.config @@ -116,6 +116,7 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null + trace_report_suffix = "${new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')}" // Schema validation default options validate_params = true From 02005bd0aeb9a7e618f8341cb69ba38e63606eb2 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Wed, 15 Jan 2025 13:50:32 +0100 Subject: [PATCH 187/275] Update nextflow.config Co-authored-by: Maxime U Garcia --- nextflow.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/nextflow.config b/nextflow.config index 3fe8e357..65c74e93 100644 --- a/nextflow.config +++ b/nextflow.config @@ -308,12 +308,12 @@ manifest { orcid: '' ], [ - name: ' Maxime U Garcia', - affiliation: '', - email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') - orcid: '' + name: 'Maxime U Garcia', + affiliation: 'Seqera', + email: 'maxime.garcia@seqera.io', + github: '@maxulysse', + contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0003-2827-9261' ], ] homePage = 'https://github.com/nf-core/rnavar' From b9ad4803b9b48e38b6b2bb65566a4a713383abad Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 20 Jan 2025 14:38:40 +0000 Subject: [PATCH 188/275] Template update for nf-core/tools version 3.1.2 --- .github/workflows/ci.yml | 2 + .github/workflows/download_pipeline.yml | 28 ++++++++------ .nf-core.yml | 2 +- CITATIONS.md | 4 +- README.md | 10 +++-- conf/test.config | 4 +- nextflow.config | 2 +- ro-crate-metadata.json | 49 +++++++------------------ 8 files changed, 45 insertions(+), 56 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d4714261..f14e881d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -46,6 +46,8 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 13b51e2c..ab06316e 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -34,6 +34,17 @@ jobs: REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} + steps: + - name: Get the repository name and current branch + id: get_repo_properties + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + + download: + runs-on: ubuntu-latest + needs: configure steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -56,21 +67,10 @@ jobs: python -m pip install --upgrade pip pip install git+https://github.com/nf-core/tools.git@dev - - name: Get the repository name and current branch set as environment variable - id: get_repo_properties - run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" - - name: Make a cache directory for the container images run: | mkdir -p ./singularity_container_images - download: - runs-on: ubuntu-latest - needs: configure - steps: - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images @@ -87,6 +87,9 @@ jobs: - name: Inspect download run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + - name: Inspect container images + run: tree ./singularity_container_images | tee ./container_initial + - name: Count the downloaded number of container images id: count_initial run: | @@ -123,7 +126,8 @@ jobs: final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} difference=$((final_count - initial_count)) echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" - tree ./singularity_container_images + tree ./singularity_container_images > ./container_afterwards + diff ./container_initial ./container_afterwards exit 1 else echo "The pipeline can be downloaded successfully!" diff --git a/.nf-core.yml b/.nf-core.yml index 3c023ae2..a0a10252 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,4 @@ -nf_core_version: 3.1.1 +nf_core_version: 3.1.2 repository_type: pipeline template: author: Praveen Raj, Maxime U Garcia diff --git a/CITATIONS.md b/CITATIONS.md index a471b8ee..bda4c349 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,9 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. diff --git a/README.md b/README.md index b1fbaf59..047291a8 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ nf-core/rnavar -[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) + + +[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) @@ -32,7 +34,7 @@ ## Usage > [!NOTE] -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - + + + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/conf/test.config b/conf/test.config index ca6300a9..bb0a1e3f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -25,8 +25,6 @@ params { // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' - - // Genome references + input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'// Genome references genome = 'R64-1-1' } diff --git a/nextflow.config b/nextflow.config index fd3e09f8..34cecfa0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -257,7 +257,7 @@ manifest { // Nextflow plugins plugins { - id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet } validation { diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index eea1f876..dd9bdd91 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T13:10:35+00:00", - "description": "

    \n \n \n \"nf-core/rnavar\"\n \n

    [![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnavar** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/rnavar \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnavar/output).\n\n## Credits\n\nnf-core/rnavar was originally written by Praveen Raj, Maxime U Garcia.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnavar` channel](https://nfcore.slack.com/channels/rnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-01-20T14:38:17+00:00", + "description": "

    \n \n \n \"nf-core/rnavar\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnavar** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/rnavar \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnavar/output).\n\n## Credits\n\nnf-core/rnavar was originally written by Praveen Raj, Maxime U Garcia.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnavar` channel](https://nfcore.slack.com/channels/rnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#cb58e61f-4cc9-4fab-962d-1a7c1ac1c329" + "@id": "#65760387-042a-4b8a-abc5-804ee910b710" } ], "name": "nf-core/rnavar" @@ -121,42 +121,21 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2024-12-20T13:10:35Z", + "dateModified": "2025-01-20T14:38:17Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", - "keywords": [ - "nf-core", - "nextflow", - "gatk4", - "rna", - "rnaseq", - "variant-calling", - "worflow" - ], - "license": [ - "MIT" - ], - "name": [ - "nf-core/rnavar" - ], + "keywords": ["nf-core", "nextflow", "gatk4", "rna", "rnaseq", "variant-calling", "worflow"], + "license": ["MIT"], + "name": ["nf-core/rnavar"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/rnavar", - "https://nf-co.re/rnavar/dev/" - ], - "version": [ - "2.0.0dev" - ] + "url": ["https://github.com/nf-core/rnavar", "https://nf-co.re/rnavar/dev/"], + "version": ["2.0.0dev"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -171,11 +150,11 @@ "version": "!>=24.04.2" }, { - "@id": "#cb58e61f-4cc9-4fab-962d-1a7c1ac1c329", + "@id": "#65760387-042a-4b8a-abc5-804ee910b710", "@type": "TestSuite", "instance": [ { - "@id": "#bbcc4db9-1638-4fd6-9f87-7d2acff32057" + "@id": "#9a74612c-ee78-41b0-a666-d13163eb1a52" } ], "mainEntity": { @@ -184,7 +163,7 @@ "name": "Test suite for nf-core/rnavar" }, { - "@id": "#bbcc4db9-1638-4fd6-9f87-7d2acff32057", + "@id": "#9a74612c-ee78-41b0-a666-d13163eb1a52", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rnavar", "resource": "repos/nf-core/rnavar/actions/workflows/ci.yml", @@ -313,4 +292,4 @@ "url": "https://nf-co.re/" } ] -} \ No newline at end of file +} From 06c1f6c4743b7a50d2893c80f2c4724448c26691 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 27 Jan 2025 14:47:28 +0000 Subject: [PATCH 189/275] Template update for nf-core/tools version 3.2.0 --- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 33 ------------------- .nf-core.yml | 2 +- .pre-commit-config.yaml | 2 +- docs/output.md | 11 +++++-- modules.json | 4 +-- modules/nf-core/fastqc/main.nf | 20 +++++------ modules/nf-core/fastqc/tests/tags.yml | 2 -- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +-- .../nf-core/multiqc/tests/main.nf.test.snap | 24 +++++++------- nextflow.config | 16 ++++----- ro-crate-metadata.json | 12 +++---- 13 files changed, 52 insertions(+), 82 deletions(-) delete mode 100644 modules/nf-core/fastqc/tests/tags.yml diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 0bed96d3..95b6b6af 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 + uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 450b1d5e..76a9e67e 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -27,39 +27,6 @@ jobs: ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics - send-tweet: - runs-on: ubuntu-latest - - steps: - - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.10" - - name: Install dependencies - run: pip install tweepy==4.14.0 - - name: Send tweet - shell: python - run: | - import os - import tweepy - - client = tweepy.Client( - access_token=os.getenv("TWITTER_ACCESS_TOKEN"), - access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), - consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), - consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), - ) - tweet = os.getenv("TWEET") - client.create_tweet(text=tweet) - env: - TWEET: | - Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! - - Please see the changelog: ${{ github.event.release.html_url }} - TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} - TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} - TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} - TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} - bsky-post: runs-on: ubuntu-latest steps: diff --git a/.nf-core.yml b/.nf-core.yml index a0a10252..411a201f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,4 @@ -nf_core_version: 3.1.2 +nf_core_version: 3.2.0 repository_type: pipeline template: author: Praveen Raj, Maxime U Garcia diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9e9f0e1c..1dec8650 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "3.0.3" + rev: "3.1.2" hooks: - id: editorconfig-checker alias: ec diff --git a/docs/output.md b/docs/output.md index 3d490a5f..40fd2f1f 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,7 +12,8 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: -- [FastQC](#fastqc) - Raw read QC- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline +- [FastQC](#fastqc) - Raw read QC +- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -26,7 +27,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
    -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).### MultiQC +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). + +### MultiQC
    Output files @@ -40,7 +43,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . + +### Pipeline information
    Output files diff --git a/modules.json b/modules.json index ce2c1e82..f8fd0627 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164", + "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "f0719ae309075ae4a291533883847c3f7c441dad", "installed_by": ["modules"] } } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 752c3a10..033f4154 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -1,5 +1,5 @@ process FASTQC { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" @@ -19,30 +19,30 @@ process FASTQC { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of old name and new name pairs to use for renaming in the bash while loop def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') + def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus + def memory_in_mb = task.memory ? task.memory.toUnit('MB').toFloat() / task.cpus : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do + printf "%s %s\\n" ${rename_to} | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done fastqc \\ - $args \\ - --threads $task.cpus \\ - --memory $fastqc_memory \\ - $renamed_files + ${args} \\ + --threads ${task.cpus} \\ + --memory ${fastqc_memory} \\ + ${renamed_files} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294b..00000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 6f5b867b..a27122ce 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25.1 + - bioconda::multiqc=1.27 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index cc0643e1..58d9313c 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.27--pyhdfd78af_0' : + 'biocontainers/multiqc:1.27--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 2fcbb5ff..7b7c1322 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:51:46.317523" + "timestamp": "2025-01-27T09:29:57.631982377" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:20.680978" + "timestamp": "2025-01-27T09:30:34.743726958" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-10-02T17:52:09.185842" + "timestamp": "2025-01-27T09:30:21.44383553" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 34cecfa0..e0012c24 100644 --- a/nextflow.config +++ b/nextflow.config @@ -195,14 +195,14 @@ env { } // Set bash options -process.shell = """\ -bash - -set -e # Exit if a tool returns a non-zero status/exit code -set -u # Treat unset variables and parameters as an error -set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute -set -C # No clobber - prevent output redirection from overwriting files. -""" +process.shell = [ + "bash", + "-C", // No clobber - prevent output redirection from overwriting files. + "-e", // Exit if a tool returns a non-zero status/exit code + "-u", // Treat unset variables and parameters as an error + "-o", // Returns the status of the last command to exit.. + "pipefail" // ..with a non-zero status or zero if all successfully execute +] // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index dd9bdd91..d6179d57 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-01-20T14:38:17+00:00", + "datePublished": "2025-01-27T14:47:25+00:00", "description": "

    \n \n \n \"nf-core/rnavar\"\n \n

    \n\n[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/rnavar)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnavar-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnavar)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/rnavar** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/rnavar \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnavar/usage) and the [parameter documentation](https://nf-co.re/rnavar/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnavar/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/rnavar/output).\n\n## Credits\n\nnf-core/rnavar was originally written by Praveen Raj, Maxime U Garcia.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#rnavar` channel](https://nfcore.slack.com/channels/rnavar) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#65760387-042a-4b8a-abc5-804ee910b710" + "@id": "#987cc264-681a-447f-8374-ea9bdd0c5ec8" } ], "name": "nf-core/rnavar" @@ -123,7 +123,7 @@ "@id": "main.nf", "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "dateCreated": "", - "dateModified": "2025-01-20T14:38:17Z", + "dateModified": "2025-01-27T14:47:25Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": ["nf-core", "nextflow", "gatk4", "rna", "rnaseq", "variant-calling", "worflow"], "license": ["MIT"], @@ -150,11 +150,11 @@ "version": "!>=24.04.2" }, { - "@id": "#65760387-042a-4b8a-abc5-804ee910b710", + "@id": "#987cc264-681a-447f-8374-ea9bdd0c5ec8", "@type": "TestSuite", "instance": [ { - "@id": "#9a74612c-ee78-41b0-a666-d13163eb1a52" + "@id": "#be9634be-5830-4d2c-b195-7c068e424c5c" } ], "mainEntity": { @@ -163,7 +163,7 @@ "name": "Test suite for nf-core/rnavar" }, { - "@id": "#9a74612c-ee78-41b0-a666-d13163eb1a52", + "@id": "#be9634be-5830-4d2c-b195-7c068e424c5c", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rnavar", "resource": "repos/nf-core/rnavar/actions/workflows/ci.yml", From 008d464d1df65b7500cb9ef272d1507daba823e3 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Thu, 20 Feb 2025 15:56:43 +0000 Subject: [PATCH 190/275] fix multiqc lint error --- modules.json | 2 +- modules/nf-core/multiqc/environment.yml | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/modules.json b/modules.json index 3d6bae2b..4013f678 100755 --- a/modules.json +++ b/modules.json @@ -127,7 +127,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "picard/markduplicates": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a27122ce..c3b3413f 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda From ca9925973ed0756dbcec539e2342f41f8422abcb Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Thu, 20 Feb 2025 15:59:53 +0000 Subject: [PATCH 191/275] bump changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8ed24bf2..e95f1172 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#140](https://github.com/nf-core/rnavar/pull/140) - Template update for nf-core/tools v2.14.1 - [#153](https://github.com/nf-core/rnavar/pull/153) - Template update for nf-core/tools v3.0.2 - [#153](https://github.com/nf-core/rnavar/pull/153) - Converted pytest tests to nf-test tests +- [#161](https://github.com/nf-core/rnavar/pull/161) - Template update for nf-core/tools v3.2.0 ### Fixed From 04b4d6a20e30bd1c049dd29ae9978e4454d5882b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 21 Feb 2025 15:13:01 +0100 Subject: [PATCH 192/275] remove strandedness --- assets/samplesheet.csv | 8 ++-- assets/schema_input.json | 8 +--- docs/output.md | 4 +- docs/usage.md | 43 +++++++++---------- .../utils_nfcore_rnavar_pipeline/main.nf | 6 --- tests/csv/1.0/all.csv | 8 ++-- tests/csv/1.0/bam.csv | 4 +- tests/csv/1.0/cram.csv | 4 +- tests/csv/1.0/fastq_single.csv | 4 +- 9 files changed, 38 insertions(+), 51 deletions(-) diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 6b6e0ec5..d52bf2ea 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,4 +1,4 @@ -sample,fastq_1,fastq_2,strandedness -RAP1_UNINDUCED_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357073_1.fastq.gz,,reverse -RAP1_UNINDUCED_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357074_1.fastq.gz,,reverse -RAP1_UNINDUCED_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357075_1.fastq.gz,,reverse +sample,fastq_1,fastq_2 +RAP1_UNINDUCED_REP1,s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357073_1.fastq.gz, +RAP1_UNINDUCED_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357074_1.fastq.gz, +RAP1_UNINDUCED_REP2,s3://nf-core-awsmegatests/rnaseq/input_data/minimal/GSE110004/SRR6357075_1.fastq.gz, diff --git a/assets/schema_input.json b/assets/schema_input.json index 97382d08..034adc35 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -27,12 +27,6 @@ "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, - "strandedness": { - "type": "string", - "errorMessage": "Strandedness must be provided and be one of 'forward', 'reverse' or 'unstranded'", - "enum": ["forward", "reverse", "unstranded"], - "meta": ["strandedness"] - }, "bam": { "type": "string", "format": "file-path", @@ -63,7 +57,7 @@ } }, "oneOf": [ - { "required": ["sample", "fastq_1", "strandedness"] }, + { "required": ["sample", "fastq_1"] }, { "required": ["sample", "bam"] }, { "required": ["sample", "cram"] } ] diff --git a/docs/output.md b/docs/output.md index a133cff4..b6f44316 100644 --- a/docs/output.md +++ b/docs/output.md @@ -15,8 +15,8 @@ RNAseq data has been taken from GM12878 GIAB sample SRA Accession [SRR5665260](h A sample sheet has been prepared in the following way to set the FASTQ files to run the analysis. ```console -sample,fastq_1,fastq_2,strandedness -GM12878,/data/GM12878/SRR5665260_1.fastq.gz,/data/GM12878/SRR5665260_2.fastq.gz,reverse +sample,fastq_1,fastq_2 +GM12878,/data/GM12878/SRR5665260_1.fastq.gz,/data/GM12878/SRR5665260_2.fastq.gz ``` ### Execution diff --git a/docs/usage.md b/docs/usage.md index ad29dacf..77955985 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -82,10 +82,10 @@ You will need to create a samplesheet with information about the samples you wou The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: ```console -sample,fastq_1,fastq_2,strandedness -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,unstranded -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,unstranded -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,unstranded +sample,fastq_1,fastq_2 +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz +CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz +CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz ``` #### Full samplesheet @@ -95,26 +95,25 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. ```console -sample,fastq_1,fastq_2,strandedness -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,forward -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,forward -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,reverse -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,reverse -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,reverse -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,reverse +sample,fastq_1,fastq_2 +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz +CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, +TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, ``` -| Column | Description | -| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `bam` | Full path to BAM file created with STAR and duplicate marked. File has to have the extension ".bam". | -| `bai` | Full path to index file of the BAM file. File has to have the extension ".bai". | -| `cram` | Full path to CRAM file created with STAR and duplicate marked. File has to have the extension ".cram". | -| `crai` | Full path to index file of the CRAM file. File has to have the extension ".crai". | -| `strandedness` | Sample strand-specificity. Must be one of `unstranded`, `forward` or `reverse`. | +| Column | Description | +| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `bam` | Full path to BAM file created with STAR and duplicate marked. File has to have the extension ".bam". | +| `bai` | Full path to index file of the BAM file. File has to have the extension ".bai". | +| `cram` | Full path to CRAM file created with STAR and duplicate marked. File has to have the extension ".cram". | +| `crai` | Full path to index file of the CRAM file. File has to have the extension ".crai". | :::note Only one file type per sample is allowed. Supplying FASTQ files and a BAM/CRAM file for the same sample will cause an error in the pipeline. diff --git a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf index 54b14425..2f7f8179 100644 --- a/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_rnavar_pipeline/main.nf @@ -198,12 +198,6 @@ def checkSamplesAfterGrouping(input) { error("Please check input samplesheet -> Detected FASTQ and BAM/CRAM files for the same sample. Please provide only one file type per sample: ${metas[0].id}") } - // Check that multiple runs of the same sample are of the same strandedness - def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1 - if (!strandedness_ok) { - error("Please check input samplesheet -> Multiple runs of a sample must have the same strandedness!: ${metas[0].id}") - } - // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 if (!endedness_ok) { diff --git a/tests/csv/1.0/all.csv b/tests/csv/1.0/all.csv index 09829568..eb9f4a04 100644 --- a/tests/csv/1.0/all.csv +++ b/tests/csv/1.0/all.csv @@ -1,4 +1,4 @@ -sample,fastq_1,fastq_2,bam,bai,cram,crai,strandedness -GM12878_fastq,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,,,,,reverse -GM12878_bam,,,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai,,,reverse -GM12878_cram,,,,,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai,reverse +sample,fastq_1,fastq_2,bam,bai,cram,crai +GM12878_fastq,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,,,, +GM12878_bam,,,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai,, +GM12878_cram,,,,,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai diff --git a/tests/csv/1.0/bam.csv b/tests/csv/1.0/bam.csv index 706a4baa..aea2d964 100644 --- a/tests/csv/1.0/bam.csv +++ b/tests/csv/1.0/bam.csv @@ -1,2 +1,2 @@ -sample,bam,bai,strandedness -GM12878,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai,reverse +sample,bam,bai +GM12878,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai diff --git a/tests/csv/1.0/cram.csv b/tests/csv/1.0/cram.csv index 28ca3dc4..3495d30c 100644 --- a/tests/csv/1.0/cram.csv +++ b/tests/csv/1.0/cram.csv @@ -1,2 +1,2 @@ -sample,cram,crai,strandedness -GM12878,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai,reverse +sample,cram,crai +GM12878,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai diff --git a/tests/csv/1.0/fastq_single.csv b/tests/csv/1.0/fastq_single.csv index 125f9bfd..a0d3b841 100644 --- a/tests/csv/1.0/fastq_single.csv +++ b/tests/csv/1.0/fastq_single.csv @@ -1,2 +1,2 @@ -sample,fastq_1,fastq_2,strandedness -GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz,reverse +sample,fastq_1,fastq_2 +GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz From 8e71d65649da3a94558db3b81f0230eb36f5c3a6 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 21 Feb 2025 16:25:19 +0100 Subject: [PATCH 193/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e95f1172..14be2c7b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#153](https://github.com/nf-core/rnavar/pull/153) - Template update for nf-core/tools v3.0.2 - [#153](https://github.com/nf-core/rnavar/pull/153) - Converted pytest tests to nf-test tests - [#161](https://github.com/nf-core/rnavar/pull/161) - Template update for nf-core/tools v3.2.0 +- [#167](https://github.com/nf-core/rnavar/pull/167) - Removed the strandedness field from the samplesheet as it wasn't used in the pipeline. ### Fixed From 07da1a1f1a9c29ebd04dc97e924fd3f4426967f8 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 09:48:30 +0100 Subject: [PATCH 194/275] allow integer vep_cache_version --- conf/igenomes.config | 20 ++++++++++---------- conf/test.config | 2 +- main.nf | 2 +- nextflow_schema.json | 3 ++- 4 files changed, 14 insertions(+), 13 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 48ed5e9a..7ea8911a 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -19,7 +19,7 @@ params { readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" snpeff_db = '87' snpeff_genome = 'GRCh37' - vep_cache_version = '111' + vep_cache_version = 111 vep_genome = 'GRCh37' vep_species = 'homo_sapiens' } @@ -30,7 +30,7 @@ params { bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" snpeff_db = '105' snpeff_genome = 'GRCh38' - vep_cache_version = '110' + vep_cache_version = 110 vep_genome = 'GRCh38' vep_species = 'homo_sapiens' } @@ -47,7 +47,7 @@ params { readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" snpeff_db = '99' snpeff_genome = 'GRCm38' - vep_cache_version = '102' + vep_cache_version = 102 vep_genome = 'GRCm38' vep_species = 'mus_musculus' } @@ -73,7 +73,7 @@ params { readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" snpeff_db = '75' snpeff_genome = 'UMD3.1' - vep_cache_version = '94' + vep_cache_version = 94 vep_genome = 'UMD3.1' vep_species = 'bos_taurus' } @@ -84,7 +84,7 @@ params { bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" snpeff_db = '105' snpeff_genome = 'WBcel235' - vep_cache_version = '111' + vep_cache_version = 111 vep_genome = 'WBcel235' vep_species = 'caenorhabditis_elegans' } @@ -96,7 +96,7 @@ params { readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" snpeff_db = '99' snpeff_genome = 'CanFam3.1' - vep_cache_version = '104' + vep_cache_version = 104 vep_genome = 'CanFam3.1' vep_species = 'canis_lupus_familiaris' } @@ -178,7 +178,7 @@ params { bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" snpeff_db = '105' snpeff_genome = 'R64-1-1' - vep_cache_version = '111' + vep_cache_version = 111 vep_genome = 'R64-1-1' vep_species = 'saccharomyces_cerevisiae' } @@ -216,7 +216,7 @@ params { bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" snpeff_db = '105' snpeff_genome = 'GRCh38' - vep_cache_version = '111' + vep_cache_version = 111 vep_genome = 'GRCh38' vep_species = 'homo_sapiens' } @@ -228,7 +228,7 @@ params { readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" snpeff_db = '87' snpeff_genome = 'GRCh37' - vep_cache_version = '111' + vep_cache_version = 111 vep_genome = 'GRCh37' vep_species = 'homo_sapiens' } @@ -240,7 +240,7 @@ params { readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" snpeff_db = '99' snpeff_genome = 'GRCm38' - vep_cache_version = '102' + vep_cache_version = 102 vep_genome = 'GRCm38' vep_species = 'mus_musculus' } diff --git a/conf/test.config b/conf/test.config index 7fc184d5..aef4df71 100644 --- a/conf/test.config +++ b/conf/test.config @@ -44,7 +44,7 @@ params { // Annotation snpeff_db = '105' snpeff_genome = 'WBcel235' - vep_cache_version = '110' + vep_cache_version = 110 vep_genome = 'WBcel235' vep_species = 'caenorhabditis_elegans' } diff --git a/main.nf b/main.nf index 7a4f7f4f..96e45207 100644 --- a/main.nf +++ b/main.nf @@ -27,7 +27,7 @@ params.known_indels = getGenomeAttribute('known_indels') params.known_indels_tbi = getGenomeAttribute('known_indels_tbi') params.snpeff_db = getGenomeAttribute('snpeff_db') params.snpeff_genome = getGenomeAttribute('snpeff_genome') -params.vep_cache_version = getGenomeAttribute('vep_cache_version') +params.vep_cache_version = getGenomeAttribute('vep_cache_version') as String params.vep_genome = getGenomeAttribute('vep_genome') params.vep_species = getGenomeAttribute('vep_species') diff --git a/nextflow_schema.json b/nextflow_schema.json index f2cf9d03..87db3677 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -147,7 +147,8 @@ "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively species listed in Ensembl Genomes caches can be used." }, "vep_cache_version": { - "type": "string", + "type": ["integer", "string"], + "minimum": 1, "fa_icon": "fas fa-tag", "description": "VEP cache version.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nAlternatively cache version can be use to specify the correct Ensembl Genomes version number as these differ from the concurrent Ensembl/VEP version numbers" From ab751170c1cc5d5a6b0e474363bf1c6545e50d31 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 09:52:32 +0100 Subject: [PATCH 195/275] allow integer snpeff_db --- conf/igenomes.config | 20 ++++++++++---------- conf/test.config | 2 +- main.nf | 2 +- nextflow_schema.json | 3 ++- 4 files changed, 14 insertions(+), 13 deletions(-) diff --git a/conf/igenomes.config b/conf/igenomes.config index 7ea8911a..8a9861b0 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -17,7 +17,7 @@ params { gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - snpeff_db = '87' + snpeff_db = 87 snpeff_genome = 'GRCh37' vep_cache_version = 111 vep_genome = 'GRCh37' @@ -28,7 +28,7 @@ params { star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - snpeff_db = '105' + snpeff_db = 105 snpeff_genome = 'GRCh38' vep_cache_version = 110 vep_genome = 'GRCh38' @@ -45,7 +45,7 @@ params { gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - snpeff_db = '99' + snpeff_db = 99 snpeff_genome = 'GRCm38' vep_cache_version = 102 vep_genome = 'GRCm38' @@ -71,7 +71,7 @@ params { gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - snpeff_db = '75' + snpeff_db = 75 snpeff_genome = 'UMD3.1' vep_cache_version = 94 vep_genome = 'UMD3.1' @@ -82,7 +82,7 @@ params { star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - snpeff_db = '105' + snpeff_db = 105 snpeff_genome = 'WBcel235' vep_cache_version = 111 vep_genome = 'WBcel235' @@ -94,7 +94,7 @@ params { gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - snpeff_db = '99' + snpeff_db = 99 snpeff_genome = 'CanFam3.1' vep_cache_version = 104 vep_genome = 'CanFam3.1' @@ -176,7 +176,7 @@ params { star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - snpeff_db = '105' + snpeff_db = 105 snpeff_genome = 'R64-1-1' vep_cache_version = 111 vep_genome = 'R64-1-1' @@ -214,7 +214,7 @@ params { star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - snpeff_db = '105' + snpeff_db = 105 snpeff_genome = 'GRCh38' vep_cache_version = 111 vep_genome = 'GRCh38' @@ -226,7 +226,7 @@ params { gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - snpeff_db = '87' + snpeff_db = 87 snpeff_genome = 'GRCh37' vep_cache_version = 111 vep_genome = 'GRCh37' @@ -238,7 +238,7 @@ params { gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - snpeff_db = '99' + snpeff_db = 99 snpeff_genome = 'GRCm38' vep_cache_version = 102 vep_genome = 'GRCm38' diff --git a/conf/test.config b/conf/test.config index aef4df71..187ca9f9 100644 --- a/conf/test.config +++ b/conf/test.config @@ -42,7 +42,7 @@ params { star_index = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/index/star/star.tar.gz" // Annotation - snpeff_db = '105' + snpeff_db = 105 snpeff_genome = 'WBcel235' vep_cache_version = 110 vep_genome = 'WBcel235' diff --git a/main.nf b/main.nf index 96e45207..32d5d10c 100644 --- a/main.nf +++ b/main.nf @@ -25,7 +25,7 @@ params.dbsnp = getGenomeAttribute('dbsnp') params.dbsnp_tbi = getGenomeAttribute('dbsnp_tbi') params.known_indels = getGenomeAttribute('known_indels') params.known_indels_tbi = getGenomeAttribute('known_indels_tbi') -params.snpeff_db = getGenomeAttribute('snpeff_db') +params.snpeff_db = getGenomeAttribute('snpeff_db') as String params.snpeff_genome = getGenomeAttribute('snpeff_genome') params.vep_cache_version = getGenomeAttribute('vep_cache_version') as String params.vep_genome = getGenomeAttribute('vep_genome') diff --git a/nextflow_schema.json b/nextflow_schema.json index 87db3677..614af091 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -123,7 +123,8 @@ "description": "Path to dbSNP VCF index file" }, "snpeff_db": { - "type": "string", + "type": ["integer", "string"], + "minimum": 1, "fa_icon": "fas fa-database", "description": "snpEff DB version.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\nThis is used to specify the database to be use to annotate with.\nAlternatively databases' names can be listed with the `snpEff databases`." From 0881a64dd2b960dd4040b4e99ce74c88b570c6d0 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 09:55:18 +0100 Subject: [PATCH 196/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 14be2c7b..8a5a028e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -48,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#149](https://github.com/nf-core/rnavar/pull/149) - Updated ch_gtf and ch_fasta_fai channels emitted by main.nf - [#158](https://github.com/nf-core/rnavar/pull/158) - Fixed language server errors and warnings - [#159](https://github.com/nf-core/rnavar/pull/159) - Fixed a couple of bottlenecks in the pipeline +- [#168](https://github.com/nf-core/rnavar/pull/168) - Allow integer values for `--vep_cache_version` and `--snpeff_db`. ### Dependencies From c8335c1f8afae72ccd1c4d63f6b7df45069521b1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 10:13:30 +0100 Subject: [PATCH 197/275] add `--star_max_intron_size` --- conf/modules.config | 3 ++- nextflow.config | 1 + nextflow_schema.json | 5 +++++ 3 files changed, 8 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 70acd95b..a0a7248e 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -121,7 +121,8 @@ process { params.star_twopass ? '--twopassMode Basic' : '', params.star_max_memory_bamsort > 0 ? "--limitBAMsortRAM ${params.star_max_memory_bamsort}" : "", params.star_bins_bamsort > 0 ? "--outBAMsortingBinsN ${params.star_bins_bamsort}" : "", - params.star_max_collapsed_junc > 0 ? "--limitOutSJcollapsed ${params.star_max_collapsed_junc}" : "" + params.star_max_collapsed_junc > 0 ? "--limitOutSJcollapsed ${params.star_max_collapsed_junc}" : "", + params.star_max_intron_size ? "--alignIntronMax ${params.star_max_intron_size}" : "" ].flatten().unique(false).join(' ').trim() } publishDir = [ [ diff --git a/nextflow.config b/nextflow.config index 3d4bcd58..af48228b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -29,6 +29,7 @@ params { star_max_memory_bamsort = 0 // STAR parameter limitBAMsortRAM to specify maximum RAM for sorting BAM star_bins_bamsort = 50 // STAR parameter outBAMsortingBinsN to specify number of bins for sorting BAM star_max_collapsed_junc = 1000000 // STAR parameter limitOutSJcollapsed to specify max number of collapsed junctions + star_max_intron_size = null // STAR parameter alignIntronMax to specify the max intron size seq_center = null seq_platform = 'illumina' // Required for preparing for BAM headers for GATK to work bam_csi_index = false diff --git a/nextflow_schema.json b/nextflow_schema.json index f2cf9d03..bb84c146 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -224,6 +224,11 @@ "default": 1000000, "description": "Specifies the maximum number of collapsed junctions" }, + "star_max_intron_size": { + "type": "integer", + "minimum": 0, + "description": "Specifies the maximum intron size" + }, "seq_center": { "type": "string", "description": "Sequencing center information to be added to read group of BAM files.", From cf6998214cc9aa866c09d35c93fd3a1939e75d04 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 10:15:56 +0100 Subject: [PATCH 198/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 14be2c7b..4fff5e44 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#116](https://github.com/nf-core/rnavar/pull/116) - Added `unzip` from nf-core modules for working with unzipped fasta and gtf files - [#157](https://github.com/nf-core/rnavar/pull/157) - Added support for `bam` and `cram` input files +- [#169](https://github.com/nf-core/rnavar/pull/169) - Added the `--star_max_intron_size` parameter to set the `--alignIntronMax` argument in STAR ### Changed From b155b1175d6c250da6d58b96e25955e9dc63cad9 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 10:30:23 +0100 Subject: [PATCH 199/275] fix --skip_intervallisttools --- subworkflows/local/splitncigar/main.nf | 2 +- workflows/rnavar.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 27320c20..b2f12366 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -20,7 +20,7 @@ workflow SPLITNCIGAR { def bam_interval = bam .combine(intervals) .map { meta, bam_, bai, intervals_ -> - [ meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1], bam_, bai, intervals_ ] + [ meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1], bam_, bai, [intervals_] ] } .transpose(by:3) .map { meta, bam_, bai, interval -> diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 99e81b7e..08d55d74 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -261,7 +261,7 @@ workflow RNAVAR { def haplotypecaller_interval_bam = bam_variant_calling.combine(interval_list_split) .map { meta, bam, bai, interval_lists -> def new_meta = meta + [interval_count: interval_lists instanceof List ? interval_lists.size() : 1] - [ new_meta, bam, bai, interval_lists ] + [ new_meta, bam, bai, new_meta.interval_count > 1 ? interval_lists : [interval_lists] ] } .transpose(by:3) .map{ meta, bam, bai, interval_list_ -> From 761440b5256c768f82a3b55ae8eb6763aaf1b13b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 10:32:33 +0100 Subject: [PATCH 200/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a5a028e..b588ecb4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -49,6 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#158](https://github.com/nf-core/rnavar/pull/158) - Fixed language server errors and warnings - [#159](https://github.com/nf-core/rnavar/pull/159) - Fixed a couple of bottlenecks in the pipeline - [#168](https://github.com/nf-core/rnavar/pull/168) - Allow integer values for `--vep_cache_version` and `--snpeff_db`. +- [#170](https://github.com/nf-core/rnavar/pull/170) - Fixed pipeline failure when running `--skip_intervallisttools`. ### Dependencies From 13821ee6b9b44fe2c01ec90dd75b8f959ad9dc9a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 10:47:30 +0100 Subject: [PATCH 201/275] added a missing check --- subworkflows/local/splitncigar/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index b2f12366..7e6bb515 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -20,7 +20,8 @@ workflow SPLITNCIGAR { def bam_interval = bam .combine(intervals) .map { meta, bam_, bai, intervals_ -> - [ meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1], bam_, bai, [intervals_] ] + def new_meta = meta + [interval_count:intervals_ instanceof List ? intervals_.size() : 1] + [ new_meta, bam_, bai, new_meta.interval_count > 1 ? intervals_ : [intervals_] ] } .transpose(by:3) .map { meta, bam_, bai, interval -> From b725e359035dce19e128b0ba2c3631ec64de5d43 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 13:24:40 +0100 Subject: [PATCH 202/275] rework dbsnp handling and implement bgzip of dbsnp --- main.nf | 18 +++---- subworkflows/local/prepare_genome/main.nf | 57 +++++++++++++++-------- workflows/rnavar.nf | 19 ++------ 3 files changed, 51 insertions(+), 43 deletions(-) diff --git a/main.nf b/main.nf index 32d5d10c..3bf55163 100644 --- a/main.nf +++ b/main.nf @@ -62,13 +62,13 @@ workflow NFCORE_RNAVAR { ch_versions = Channel.empty() // Initialize fasta file with meta map: - ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() + ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() // Initialize file channels based on params, defined in the params.genomes[params.genome] scope - ch_dbsnp = params.dbsnp ? Channel.fromPath(params.dbsnp).collect() : Channel.value([]) - ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([]) - ch_gff = params.gff ? Channel.fromPath(params.gff).collect() : Channel.empty() - ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() + ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]} : Channel.value([]) + ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([]) + ch_gff = params.gff ? Channel.fromPath(params.gff).collect() : Channel.empty() + ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() // Initialize variant annotation associated channels snpeff_db = params.snpeff_db ?: Channel.empty() @@ -103,7 +103,7 @@ workflow NFCORE_RNAVAR { ch_fasta_raw, ch_gff, ch_gtf_raw, - ch_dbsnp, + ch_dbsnp_raw, ch_known_indels, params.feature_type) @@ -116,8 +116,10 @@ workflow NFCORE_RNAVAR { : PREPARE_GENOME.out.fasta_fai ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() : PREPARE_GENOME.out.exon_bed - ch_dbsnp_tbi = params.dbsnp ? params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).collect() - : PREPARE_GENOME.out.dbsnp_tbi : Channel.value([]) + ch_dbsnp = params.dbsnp && params.dbsnp.endsWith(".gz") ? ch_dbsnp_raw : PREPARE_GENOME.out.dbsnp + ch_dbsnp_tbi = params.dbsnp.toString().endsWith(".gz") && params.dbsnp_tbi + ? Channel.fromPath(params.dbsnp_tbi).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() + : PREPARE_GENOME.out.dbsnp_tbi ch_known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() : PREPARE_GENOME.out.known_indels_tbi : Channel.value([]) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 193212e1..be81e4d5 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -2,29 +2,30 @@ // Prepare reference genome files // -include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' -include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtools/sort/main' -include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GFFREAD } from '../../../modules/nf-core/gffread/main' -include { GTF2BED } from '../../../modules/local/gtf2bed' -include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' -include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' -include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' -include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/tabix/main' +include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' +include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtools/sort/main' +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GFFREAD } from '../../../modules/nf-core/gffread/main' +include { GTF2BED } from '../../../modules/local/gtf2bed' +include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' +include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' +include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' +include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_BGZIPTABIX as BGZIPTABIX_DBSNP } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/tabix/main' workflow PREPARE_GENOME { take: - fasta_raw // file: /path/to/genome.fasta - gff // file: /path/to/genome.gff - gtf_raw // file: /path/to/genome.gtf - dbsnp - known_indels + fasta_raw // channel: /path/to/genome.fasta + gff // channel: /path/to/genome.gff + gtf_raw // channel: /path/to/genome.gtf + dbsnp // file: /path/to/dbnsp.vcf.gz + known_indels // file: /path/to/known_indels.vcf.gz feature_type main: - ch_versions = Channel.empty() + def ch_versions = Channel.empty() //Unzip reference genome files if needed @@ -46,10 +47,26 @@ workflow PREPARE_GENOME { gtf = gtf_raw } + def ch_dbsnp = Channel.value([[],[]]) + def ch_dbsnp_tbi = Channel.value([[],[]]) + if (params.dbsnp && !params.dbsnp.endsWith(".gz")) { + BGZIPTABIX_DBSNP( + dbsnp + ) + ch_versions = ch_versions.mix(BGZIPTABIX_DBSNP.out.versions.first()) + ch_dbsnp = BGZIPTABIX_DBSNP.out.gz_tbi.map { meta, vcf, _tbi -> [ meta, vcf ] }.collect() + ch_dbsnp_tbi = BGZIPTABIX_DBSNP.out.gz_tbi.map { meta, _vcf, tbi -> [ meta, tbi ] }.collect() + } else if(params.dbsnp && !params.dbsnp_tbi) { + TABIX_DBSNP( + dbsnp + ) + ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions.first()) + ch_dbsnp_tbi = TABIX_DBSNP.out.tbi.collect() + } + GATK4_CREATESEQUENCEDICTIONARY(fasta) GFFREAD(gff, fasta) SAMTOOLS_FAIDX(fasta, [['id':'genome'], []]) - TABIX_DBSNP(dbsnp.flatten().map{ it -> [ [ id:it.baseName ], it ] }) TABIX_KNOWN_INDELS(known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) gtf = gtf.mix(GFFREAD.out.gtf) @@ -62,7 +79,6 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(GTF2BED.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) - ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions) ch_versions = ch_versions.mix(TABIX_KNOWN_INDELS.out.versions) emit: @@ -72,7 +88,8 @@ workflow PREPARE_GENOME { fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai gtf = gtf.first() // path: genome.gtf star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ - dbsnp_tbi = TABIX_DBSNP.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: dbsnb.vcf.gz.tbi + dbsnp = ch_dbsnp // path: dbsnp.vcf.gz + dbsnp_tbi = ch_dbsnp_tbi // path: dbsnp.vcf.gz.tbi known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi versions = ch_versions // channel: [ versions.yml ] // bedtools_sort = bedtools_sort // path: sort.bed diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 08d55d74..5815a3ee 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -199,8 +199,8 @@ workflow RNAVAR { if (!params.skip_baserecalibration) { // known_sites is made by grouping both the dbsnp and the known indels ressources // they can either or both be optional - def known_sites = dbsnp.concat(known_indels).collect() - def known_sites_tbi = dbsnp_tbi.concat(known_indels_tbi).collect() + def known_sites = dbsnp.map { _meta, dbsnp_ -> dbsnp_ }.concat(known_indels).collect() + def known_sites_tbi = dbsnp_tbi.map { _meta, tbi -> tbi }.concat(known_indels_tbi).collect() def interval_list_recalib = interval_list.map{ _meta, bed -> [bed] }.flatten() def splitncigar_bam_bai_interval = splitncigar_bam_bai.combine(interval_list_recalib) @@ -247,17 +247,6 @@ workflow RNAVAR { bam_variant_calling = splitncigar_bam_bai } - // Run haplotyper even in the absence of dbSNP files - def dbsnp_for_haplotypecaller = Channel.empty() - def dbsnp_for_haplotypecaller_tbi = Channel.empty() - if (!params.dbsnp){ - dbsnp_for_haplotypecaller = [[id:'null'], []] - dbsnp_for_haplotypecaller_tbi = [[id:'null'], []] - } else { - dbsnp_for_haplotypecaller = dbsnp.map{ vcf -> [[id:'dbsnp'], vcf] } - dbsnp_for_haplotypecaller_tbi = dbsnp_tbi.map{ tbi -> [[id:'dbsnp'], tbi] } - } - def haplotypecaller_interval_bam = bam_variant_calling.combine(interval_list_split) .map { meta, bam, bai, interval_lists -> def new_meta = meta + [interval_count: interval_lists instanceof List ? interval_lists.size() : 1] @@ -278,8 +267,8 @@ workflow RNAVAR { fasta, fasta_fai, dict, - dbsnp_for_haplotypecaller, - dbsnp_for_haplotypecaller_tbi + dbsnp, + dbsnp_tbi ) def haplotypecaller_out = GATK4_HAPLOTYPECALLER.out.vcf From 439a7b05009de8eaa5073a5824370c3453f59fba Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 13:51:31 +0100 Subject: [PATCH 203/275] rework known_indels handling and allow uncompressed files --- main.nf | 11 ++-- subworkflows/local/prepare_genome/main.nf | 74 ++++++++++++++++------- 2 files changed, 60 insertions(+), 25 deletions(-) diff --git a/main.nf b/main.nf index 3bf55163..d80fd7d8 100644 --- a/main.nf +++ b/main.nf @@ -66,7 +66,8 @@ workflow NFCORE_RNAVAR { // Initialize file channels based on params, defined in the params.genomes[params.genome] scope ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]} : Channel.value([]) - ch_known_indels = params.known_indels ? Channel.fromPath(params.known_indels).collect() : Channel.value([]) + ch_known_indels_raw = params.known_indels ? Channel.fromPath(params.known_indels) : Channel.empty() + ch_known_indels_tbi_raw = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : Channel.empty() ch_gff = params.gff ? Channel.fromPath(params.gff).collect() : Channel.empty() ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() @@ -104,7 +105,8 @@ workflow NFCORE_RNAVAR { ch_gff, ch_gtf_raw, ch_dbsnp_raw, - ch_known_indels, + ch_known_indels_raw, + ch_known_indels_tbi_raw, params.feature_type) ch_fasta = PREPARE_GENOME.out.fasta @@ -120,8 +122,9 @@ workflow NFCORE_RNAVAR { ch_dbsnp_tbi = params.dbsnp.toString().endsWith(".gz") && params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() : PREPARE_GENOME.out.dbsnp_tbi - ch_known_indels_tbi = params.known_indels ? params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi).collect() - : PREPARE_GENOME.out.known_indels_tbi : Channel.value([]) + ch_known_indels = params.known_indels ? PREPARE_GENOME.out.known_indels : Channel.value([]) + ch_known_indels_tbi = params.known_indels ? PREPARE_GENOME.out.known_indels_tbi : Channel.value([]) + // Download cache if (params.download_cache) { diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index be81e4d5..60ed6c0e 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -2,26 +2,28 @@ // Prepare reference genome files // -include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' -include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtools/sort/main' -include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' -include { GFFREAD } from '../../../modules/nf-core/gffread/main' -include { GTF2BED } from '../../../modules/local/gtf2bed' -include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' -include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' -include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' -include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' -include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' -include { TABIX_BGZIPTABIX as BGZIPTABIX_DBSNP } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/tabix/main' +include { BEDTOOLS_MERGE } from '../../../modules/nf-core/bedtools/merge/main' +include { BEDTOOLS_SORT } from '../../../modules/nf-core/bedtools/sort/main' +include { GATK4_CREATESEQUENCEDICTIONARY } from '../../../modules/nf-core/gatk4/createsequencedictionary/main' +include { GFFREAD } from '../../../modules/nf-core/gffread/main' +include { GTF2BED } from '../../../modules/local/gtf2bed' +include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' +include { STAR_GENOMEGENERATE } from '../../../modules/nf-core/star/genomegenerate/main' +include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip/main' +include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip/main' +include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_BGZIPTABIX as BGZIPTABIX_DBSNP } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_BGZIPTABIX as BGZIPTABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/bgziptabix/main' workflow PREPARE_GENOME { take: - fasta_raw // channel: /path/to/genome.fasta - gff // channel: /path/to/genome.gff - gtf_raw // channel: /path/to/genome.gtf - dbsnp // file: /path/to/dbnsp.vcf.gz - known_indels // file: /path/to/known_indels.vcf.gz + fasta_raw // channel: /path/to/genome.fasta + gff // channel: /path/to/genome.gff + gtf_raw // channel: /path/to/genome.gtf + dbsnp // channel: /path/to/dbnsp.vcf.gz + known_indels // channel: [/path/to/known_indels] + known_indels_tbi // channel: [/path/to/known_indels_index] feature_type main: @@ -49,7 +51,7 @@ workflow PREPARE_GENOME { def ch_dbsnp = Channel.value([[],[]]) def ch_dbsnp_tbi = Channel.value([[],[]]) - if (params.dbsnp && !params.dbsnp.endsWith(".gz")) { + if (params.dbsnp && !params.dbsnp.toString().endsWith(".gz")) { BGZIPTABIX_DBSNP( dbsnp ) @@ -64,10 +66,40 @@ workflow PREPARE_GENOME { ch_dbsnp_tbi = TABIX_DBSNP.out.tbi.collect() } + def ch_known_indels_input = known_indels.map { file -> [[id:file.name], file ] } + .join(known_indels_tbi.map { file -> [[id:file.baseName], file ] }, failOnDuplicate:true, remainder:true) + .branch { meta, file, index -> + plain: !file.toString().endsWith(".gz") + return [ meta, file ] + bgzip_noindex: !index && file.toString().endsWith(".gz") + return [ meta, file ] + bgzip_index: true + return [ meta, file, index ] + } + + BGZIPTABIX_KNOWN_INDELS( + ch_known_indels_input.plain + ) + ch_versions = ch_versions.mix(BGZIPTABIX_KNOWN_INDELS.out.versions.first()) + + TABIX_KNOWN_INDELS( + ch_known_indels_input.bgzip_noindex + ) + ch_versions = ch_versions.mix(TABIX_KNOWN_INDELS.out.versions.first()) + + def ch_known_indels = BGZIPTABIX_KNOWN_INDELS.out.gz_tbi.map { _meta, file, _index -> file } + .mix(ch_known_indels_input.bgzip_noindex.map { _meta, file -> file }) + .mix(ch_known_indels_input.bgzip_index.map { _meta, file, _index -> file }) + .collect() + + def ch_known_indels_tbi = BGZIPTABIX_KNOWN_INDELS.out.gz_tbi.map { _meta, _file, index -> index } + .mix(TABIX_KNOWN_INDELS.out.tbi.map { _meta, tbi -> tbi }) + .mix(ch_known_indels_input.bgzip_index.map { _meta, _file, index -> index }) + .collect() + GATK4_CREATESEQUENCEDICTIONARY(fasta) GFFREAD(gff, fasta) SAMTOOLS_FAIDX(fasta, [['id':'genome'], []]) - TABIX_KNOWN_INDELS(known_indels.flatten().map{ it -> [ [ id:it.baseName ], it ] } ) gtf = gtf.mix(GFFREAD.out.gtf) @@ -79,7 +111,6 @@ workflow PREPARE_GENOME { ch_versions = ch_versions.mix(GTF2BED.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) - ch_versions = ch_versions.mix(TABIX_KNOWN_INDELS.out.versions) emit: dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict @@ -90,7 +121,8 @@ workflow PREPARE_GENOME { star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp = ch_dbsnp // path: dbsnp.vcf.gz dbsnp_tbi = ch_dbsnp_tbi // path: dbsnp.vcf.gz.tbi - known_indels_tbi = TABIX_KNOWN_INDELS.out.tbi.map{ _meta, tbi -> [tbi] }.collect() // path: {known_indels*}.vcf.gz.tbi + known_indels = ch_known_indels // path: {known_indels*}.vcf.gz + known_indels_tbi = ch_known_indels_tbi // path: {known_indels*}.vcf.gz.tbi versions = ch_versions // channel: [ versions.yml ] // bedtools_sort = bedtools_sort // path: sort.bed // bedtools_merge = bedtools_merge // path: merge.bed From 4576a781020ef434559c320fee5de603cfd9ef7a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 13:56:08 +0100 Subject: [PATCH 204/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b588ecb4..1b181eba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -50,6 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#159](https://github.com/nf-core/rnavar/pull/159) - Fixed a couple of bottlenecks in the pipeline - [#168](https://github.com/nf-core/rnavar/pull/168) - Allow integer values for `--vep_cache_version` and `--snpeff_db`. - [#170](https://github.com/nf-core/rnavar/pull/170) - Fixed pipeline failure when running `--skip_intervallisttools`. +- [#171](https://github.com/nf-core/rnavar/pull/171) - Fixed the `--dbnsp` and `--known_indels` handling. Uncompressed files are now allowed as inputs to the pipeline as the pipeline will automatically compress these. ### Dependencies From dc3c008ef9a949cb8ed22a509ab01317dba51e1a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 13:57:52 +0100 Subject: [PATCH 205/275] update the params schema --- nextflow_schema.json | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 614af091..325d92ec 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -108,19 +108,27 @@ }, "known_indels": { "type": "string", - "description": "Path to known indels VCF file" + "description": "Path to known indels VCF file", + "format": "file-path-pattern", + "exists": true }, "known_indels_tbi": { "type": "string", - "description": "Path to known indels index file" + "description": "Path to known indels index file", + "format": "file-path-pattern", + "exists": true }, "dbsnp": { "type": "string", - "description": "Path to dbSNP VCF file" + "description": "Path to dbSNP VCF file", + "format": "file-path", + "exists": true }, "dbsnp_tbi": { "type": "string", - "description": "Path to dbSNP VCF index file" + "description": "Path to dbSNP VCF index file", + "format": "file-path", + "exists": true }, "snpeff_db": { "type": ["integer", "string"], From ecfe4fc8b8dafc15c0f5917cfae5f0ccb027c5c5 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 14:00:02 +0100 Subject: [PATCH 206/275] small improvement to known indels description --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 325d92ec..3d5387b5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -108,13 +108,13 @@ }, "known_indels": { "type": "string", - "description": "Path to known indels VCF file", + "description": "Path to known indels VCF file(s)", "format": "file-path-pattern", "exists": true }, "known_indels_tbi": { "type": "string", - "description": "Path to known indels index file", + "description": "Path to known indels index file(s)", "format": "file-path-pattern", "exists": true }, From c073e241f9bf9a8a8af3d00385cec0f72133f977 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Mon, 24 Feb 2025 14:03:00 +0000 Subject: [PATCH 207/275] add a missing .collect --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index d80fd7d8..683c7251 100644 --- a/main.nf +++ b/main.nf @@ -65,7 +65,7 @@ workflow NFCORE_RNAVAR { ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() // Initialize file channels based on params, defined in the params.genomes[params.genome] scope - ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]} : Channel.value([]) + ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() : Channel.value([]) ch_known_indels_raw = params.known_indels ? Channel.fromPath(params.known_indels) : Channel.empty() ch_known_indels_tbi_raw = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : Channel.empty() ch_gff = params.gff ? Channel.fromPath(params.gff).collect() : Channel.empty() From 4ea81c25e6974b15c30078e23101a58e1f609948 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 15:32:40 +0100 Subject: [PATCH 208/275] first batch of schema updates --- nextflow_schema.json | 45 ++++++++++++++++++++++++++++++++------------ 1 file changed, 33 insertions(+), 12 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index aa7446ba..d29142f9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -14,14 +14,13 @@ "properties": { "input": { "description": "Path to comma-separated file containing information about the samples in the experiment.", - "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/rnavar/usage#input).", + "help_text": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a tab or comma-separated file with a header row or a JSON/YAML file. See [usage docs](https://nf-co.re/rnavar/usage#input).", "fa_icon": "fas fa-file-csv", "type": "string", "format": "file-path", "exists": true, "schema": "assets/schema_input.json", - "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$" + "pattern": "^\\S+\\.(csv|tsv|yaml|yml|json)$" }, "outdir": { "type": "string", @@ -71,33 +70,49 @@ }, "dict": { "type": "string", + "format": "file-path", + "exists": true, "fa_icon": "fas fa-file", + "pattern": "^\\S+\\.dict$", "description": "Path to FASTA dictionary file.", "help_text": "> **NB** If none provided, will be generated automatically from the FASTA reference." }, "fasta_fai": { "type": "string", "fa_icon": "fas fa-file", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.fai$", "help_text": "> **NB** If none provided, will be generated automatically from the FASTA reference", "description": "Path to FASTA reference index." }, "gtf": { "type": "string", + "format": "file-path", "description": "Path to GTF annotation file.", + "exists": true, + "pattern": "^\\S+\\.gtf$", "help_text": "This parameter is *mandatory* if `--genome` is not specified." }, "gff": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.gff$", "description": "Path to GFF3 annotation file.", "help_text": "This parameter must be specified if `--genome` or `--gtf` are not specified." }, "exon_bed": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.bed$", "description": "Path to BED file containing exon intervals. This will be created from the GTF file if not specified." }, "read_length": { "type": "number", "default": 150, + "minimum": 1, "description": "Read length", "help_text": "Specify the read length for the STAR aligner." }, @@ -157,7 +172,8 @@ "feature_type": { "type": "string", "description": "Type of feature to parse from annotation file", - "help_text": "This parameter value can be exon, transcript or gene. Default exon" + "enum": ["exon", "transcript", "gene"], + "default": "exon" }, "download_cache": { "type": "boolean", @@ -191,11 +207,14 @@ "aligner": { "type": "string", "default": "star", - "description": "Specifies the alignment algorithm to use. Currently available option is 'star'", - "help_text": "This parameter define which aligner is to be used for aligning the RNA reads to the reference genome. Currently only STAR aligner is supported. So use 'star' as the value for this option." + "enum": ["star"], + "description": "Specifies the alignment algorithm to use.", + "help_text": "This parameter define which aligner is to be used for aligning the RNA reads to the reference genome." }, "star_index": { "type": "string", + "format": "path", + "exists": true, "description": "Path to STAR index folder or compressed file (tar.gz)", "help_text": "This parameter can be used if there is an pre-defined STAR index available. You can either give the full path to the index directory or a compressed file in tar.gz format." }, @@ -206,24 +225,27 @@ }, "star_ignore_sjdbgtf": { "type": "boolean", - "description": "Do not use GTF file during STAR index buidling step", + "description": "Do not use GTF file during STAR index building step", "help_text": "Do not use parameter --sjdbGTFfile during the STAR genomeGenerate process." }, "star_max_memory_bamsort": { "type": "integer", "default": 0, + "minimum": 0, "description": "Option to limit RAM when sorting BAM file. Value to be specified in bytes. If 0, will be set to the genome index size.", "help_text": "This parameter specifies the maximum available RAM (bytes) for sorting BAM during STAR alignment." }, "star_bins_bamsort": { "type": "integer", "default": 50, + "minimum": 0, "description": "Specifies the number of genome bins for coordinate-sorting", "help_text": "This parameter specifies the number of bins to be used for coordinate sorting during STAR alignment step." }, "star_max_collapsed_junc": { "type": "integer", "default": 1000000, + "minimum": 0, "description": "Specifies the maximum number of collapsed junctions" }, "star_max_intron_size": { @@ -261,8 +283,7 @@ "preprocessing": { "title": "Preprocessing of alignment", "type": "object", - "description": "", - "default": "", + "description": "Parameters for preprocessing analysis.", "fa_icon": "fas fa-toolbox", "properties": { "remove_duplicates": { @@ -277,13 +298,13 @@ "variant_calling": { "title": "Variant calling", "type": "object", - "description": "", - "default": "", + "description": "Parameters for variant calling tools.", "fa_icon": "fas fa-toolbox", "properties": { "gatk_hc_call_conf": { - "type": "number", + "type": "integer", "default": 20, + "minimum": 0, "fa_icon": "fas fa-hammer", "description": "The minimum phred-scaled confidence threshold at which variants should be called.", "help_text": "Specify the minimum phred-scaled confidence threshold at which variants should be called.", From 37f64fe493ffa4d627c9668fc1b288afb4ee942e Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Mon, 24 Feb 2025 14:55:47 +0000 Subject: [PATCH 209/275] update snapshots --- tests/all_inputs.nf.test.snap | 14 +++----- tests/annotation.nf.test.snap | 40 ++++++++--------------- tests/bam_csi.nf.test.snap | 12 +++---- tests/bam_input.nf.test.snap | 12 +++---- tests/cram_input.nf.test.snap | 12 +++---- tests/default.nf.test.snap | 12 +++---- tests/removeduplicates.nf.test.snap | 12 +++---- tests/skip_baserecalibration.nf.test.snap | 12 +++---- 8 files changed, 43 insertions(+), 83 deletions(-) diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index e3166fc9..5183b0b4 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 79, + 77, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -117,17 +117,13 @@ "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.vcf.gz", - "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878_fastq/GM12878_fastq.haplotypecaller.vcf.gz.tbi" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:41:24.471237186" + "timestamp": "2025-02-24T14:23:18.179475664" } } \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index b32e2859..e51c3135 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | annotation with merge": { "content": [ - 47, + 45, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -249,22 +249,18 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:19:12.045032239" + "timestamp": "2025-02-24T14:34:43.581063475" }, "Run with profile test | annotation with vep": { "content": [ - 44, + 42, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -493,22 +489,18 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:51:32.004274594" + "timestamp": "2025-02-24T14:30:05.490462421" }, "Run with profile test | annotation with snpeff": { "content": [ - 44, + 42, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -633,17 +625,13 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.10.3" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:47:00.48306332" + "timestamp": "2025-02-24T14:26:26.781658411" } } \ No newline at end of file diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index a55345ea..58226c69 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | bam_csi_index": { "content": [ - 40, + 38, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -92,17 +92,13 @@ "variant_calling", "variant_calling/GM12878", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.csi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.csi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.csi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.csi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:22:32.936861849" + "timestamp": "2025-02-24T14:38:46.62830248" } } \ No newline at end of file diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 8c014b13..c9f200ef 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 28, + 26, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -63,17 +63,13 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:24:31.090393575" + "timestamp": "2025-02-24T14:41:05.2347019" } } \ No newline at end of file diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index 438866ce..ce685b04 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 28, + 26, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -63,17 +63,13 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:26:33.364598229" + "timestamp": "2025-02-24T14:43:24.758766571" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ddd16443..3eecbc12 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 41, + 39, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -97,17 +97,13 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:29:28.081229818" + "timestamp": "2025-02-24T14:46:26.029862753" } } \ No newline at end of file diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index a86e9bcb..043f69e9 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | remove_duplicates": { "content": [ - 41, + 39, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -97,17 +97,13 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:32:25.501338685" + "timestamp": "2025-02-24T14:49:58.665114628" } } \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index bebbdaa5..7c1ef258 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | skip_baserecalibration": { "content": [ - 37, + 35, { "CAT_FASTQ": { "cat": 8.3 @@ -89,17 +89,13 @@ "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", - "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", - "variant_calling/dbsnp_146.hg38.vcf", - "variant_calling/dbsnp_146.hg38.vcf/dbsnp_146.hg38.vcf.gz.tbi", - "variant_calling/mills_and_1000G.indels.vcf", - "variant_calling/mills_and_1000G.indels.vcf/mills_and_1000G.indels.vcf.gz.tbi" + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.3" + "nextflow": "24.10.4" }, - "timestamp": "2025-01-09T16:35:18.554293763" + "timestamp": "2025-02-24T14:52:44.06475637" } } \ No newline at end of file From 84cafed3f2d3062c6105b3e24a18ccfd317dd7b6 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 24 Feb 2025 16:06:20 +0100 Subject: [PATCH 210/275] second batch of schema updates --- CHANGELOG.md | 2 ++ conf/modules.config | 8 ++++---- nextflow_schema.json | 38 ++++++++++++++++++++++++++++++++------ 3 files changed, 38 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4405039e..5da472e4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#153](https://github.com/nf-core/rnavar/pull/153) - Converted pytest tests to nf-test tests - [#161](https://github.com/nf-core/rnavar/pull/161) - Template update for nf-core/tools v3.2.0 - [#167](https://github.com/nf-core/rnavar/pull/167) - Removed the strandedness field from the samplesheet as it wasn't used in the pipeline. +- [#172](https://github.com/nf-core/rnavar/pull/172) - Added support for TSV, JSON and YAML samplesheets ### Fixed @@ -51,6 +52,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#159](https://github.com/nf-core/rnavar/pull/159) - Fixed a couple of bottlenecks in the pipeline - [#168](https://github.com/nf-core/rnavar/pull/168) - Allow integer values for `--vep_cache_version` and `--snpeff_db`. - [#170](https://github.com/nf-core/rnavar/pull/170) - Fixed pipeline failure when running `--skip_intervallisttools`. +- [#172](https://github.com/nf-core/rnavar/pull/172) - Fixed the parameters JSON schema so the pipeline does better input validation. ### Dependencies diff --git a/conf/modules.config b/conf/modules.config index a0a7248e..7dc4b339 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -322,10 +322,10 @@ process { withName: GATK4_VARIANTFILTRATION { ext.prefix = {"${meta.id}.haplotypecaller.filtered"} ext.args = [ - params.gatk_vf_window_size ? "--window $params.gatk_vf_window_size" : '', - params.gatk_vf_cluster_size ? "--cluster $params.gatk_vf_cluster_size" : '', - params.gatk_vf_fs_filter ? "--filter-name \"FS\" --filter \"FS > $params.gatk_vf_fs_filter\" " : '', - params.gatk_vf_qd_filter ? "--filter-name \"QD\" --filter \"QD < $params.gatk_vf_qd_filter\" " : '', + params.gatk_vf_window_size ? "--cluster-window-size $params.gatk_vf_window_size" : '', + params.gatk_vf_cluster_size ? "--cluster-size $params.gatk_vf_cluster_size" : '', + params.gatk_vf_fs_filter ? "--filter-name \"FS\" --filter-expression \"FS > $params.gatk_vf_fs_filter\" " : '', + params.gatk_vf_qd_filter ? "--filter-name \"QD\" --filter-expression \"QD < $params.gatk_vf_qd_filter\" " : '', ].join(' ').trim() publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, diff --git a/nextflow_schema.json b/nextflow_schema.json index d29142f9..64657b3f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -320,8 +320,7 @@ "variant_annotation": { "title": "Variant Annotation", "type": "object", - "description": "", - "default": "", + "description": "Parameters for variant annotation tools.", "fa_icon": "fas fa-toolbox", "properties": { "annotate_tools": { @@ -334,6 +333,8 @@ }, "vep_cache": { "type": "string", + "format": "directory-path", + "exists": true, "fa_icon": "fas fa-file", "default": "s3://annotation-cache/vep_cache/", "description": "Path to VEP cache.", @@ -342,6 +343,8 @@ "snpeff_cache": { "type": "string", "fa_icon": "fas fa-file", + "format": "directory-path", + "exists": true, "default": "s3://annotation-cache/snpeff_cache/", "description": "Path to snpEff cache.", "help_text": "Path to snpEff cache which should contain the relevant genome and build directory in the path ${snpeff_species}.${snpeff_version}" @@ -362,6 +365,9 @@ }, "dbnsfp": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.gz$", "fa_icon": "fas fa-file", "description": "Path to dbNSFP processed file.", "help_text": "To be used with `--vep_dbnsfp`.\ndbNSFP files and more information are available at https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#dbnsfp and https://sites.google.com/site/jpopgen/dbNSFP/", @@ -369,6 +375,9 @@ }, "dbnsfp_tbi": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.tbi$", "fa_icon": "fas fa-file", "description": "Path to dbNSFP tabix indexed file.", "help_text": "To be used with `--vep_dbnsfp`.", @@ -405,6 +414,9 @@ }, "spliceai_snv": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.vcf\\.gz$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores snv file.", "help_text": "To be used with `--vep_spliceai`.", @@ -412,6 +424,9 @@ }, "spliceai_snv_tbi": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.tbi$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores snv tabix indexed file.", "help_text": "To be used with `--vep_spliceai`.", @@ -419,6 +434,9 @@ }, "spliceai_indel": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.vcf\\.gz$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores indel file.", "help_text": "To be used with `--vep_spliceai`.", @@ -426,6 +444,9 @@ }, "spliceai_indel_tbi": { "type": "string", + "format": "file-path", + "exists": true, + "pattern": "^\\S+\\.tbi$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores indel tabix indexed file.", "help_text": "To be used with `--vep_spliceai`.", @@ -443,7 +464,7 @@ "default": "--everything --filter_common --per_gene --total_length --offline --format vcf", "fa_icon": "fas fa-toolbox", "description": "Add an extra custom argument to VEP.", - "help_text": "Using this params you can add custom args to VEP." + "help_text": "Using this parameter, you can add custom args to VEP." }, "use_annotation_cache_keys": { "type": "boolean", @@ -463,7 +484,7 @@ "default": "vcf", "description": "VEP output-file format.", "enum": ["json", "tab", "vcf"], - "help_text": "Sets the format of the output-file from VEP. Available formats: json, tab and vcf.", + "help_text": "Sets the format of the output-file from VEP.", "fa_icon": "fas fa-table", "hidden": true } @@ -511,6 +532,7 @@ "gatk_interval_scatter_count": { "type": "integer", "default": 25, + "minimum": 1, "description": "Number of times the gene interval list to be split in order to run GATK haplotype caller in parallel", "help_text": "Set this parameter to decide the number of splits for the gene interval list file." }, @@ -522,26 +544,30 @@ "gatk_vf_window_size": { "type": "integer", "default": 35, + "minimum": 0, "description": "The window size (in bases) in which to evaluate clustered SNPs.", "help_text": "This parameter is used by GATK variant filteration step. It defines the window size (in bases) in which to evaluate clustered SNPs. It has to be used together with the other option 'cluster'." }, "gatk_vf_cluster_size": { "type": "integer", "default": 3, + "minimum": 2, "description": "The number of SNPs which make up a cluster. Must be at least 2.", "help_text": "This parameter is used by GATK variant filteration step. It defines the number of SNPs which make up a cluster within a window. Must be at least 2." }, "gatk_vf_fs_filter": { "type": "number", "default": 30.0, + "minimum": 0.0, "description": "Value to be used for the FisherStrand (FS) filter", - "help_text": "This parameter defines the value to use for the FisherStrand (FS) filter in the GATK variant-filtering step. \nThe value should given in a float number format. Default is 30.0" + "help_text": "This parameter defines the value to use for the FisherStrand (FS) filter in the GATK variant-filtering step. \nThe value should given in a float number format." }, "gatk_vf_qd_filter": { "type": "number", "default": 2.0, + "minimum": 0.0, "description": "Value to be used for the QualByDepth (QD) filter", - "help_text": "This parameter defines the value to use for the QualByDepth (QD) filter in the GATK variant-filtering step. \nThe value should given in a float number format. Default is 2.0" + "help_text": "This parameter defines the value to use for the QualByDepth (QD) filter in the GATK variant-filtering step. \nThe value should given in a float number format." } } }, From 6cb4be3449d4d3cb3b983f622645e858f5906237 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 25 Feb 2025 14:38:52 +0100 Subject: [PATCH 211/275] add star index error handling --- conf/test.config | 2 + main.nf | 2 + modules.json | 5 + .../nf-core/star/indexversion/environment.yml | 10 ++ modules/nf-core/star/indexversion/main.nf | 41 +++++ modules/nf-core/star/indexversion/meta.yml | 36 +++++ .../star/indexversion/tests/main.nf.test | 36 +++++ .../star/indexversion/tests/main.nf.test.snap | 48 ++++++ subworkflows/local/prepare_genome/main.nf | 133 +++++++++++++-- .../local/prepare_genome/main.nf.test | 151 ++++++++++++++++++ 10 files changed, 450 insertions(+), 14 deletions(-) create mode 100644 modules/nf-core/star/indexversion/environment.yml create mode 100644 modules/nf-core/star/indexversion/main.nf create mode 100644 modules/nf-core/star/indexversion/meta.yml create mode 100644 modules/nf-core/star/indexversion/tests/main.nf.test create mode 100644 modules/nf-core/star/indexversion/tests/main.nf.test.snap create mode 100644 subworkflows/local/prepare_genome/main.nf.test diff --git a/conf/test.config b/conf/test.config index 187ca9f9..63d78afa 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,6 +22,8 @@ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + // Input data input = "${projectDir}/tests/csv/1.0/fastq_single.csv" diff --git a/main.nf b/main.nf index 683c7251..27ef1cc9 100644 --- a/main.nf +++ b/main.nf @@ -70,6 +70,7 @@ workflow NFCORE_RNAVAR { ch_known_indels_tbi_raw = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : Channel.empty() ch_gff = params.gff ? Channel.fromPath(params.gff).collect() : Channel.empty() ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() + ch_star_index_raw = params.star_index ? Channel.fromPath(params.star_index).map { index -> [[id:index.baseName], index]} : Channel.value([[],[]]) // Initialize variant annotation associated channels snpeff_db = params.snpeff_db ?: Channel.empty() @@ -102,6 +103,7 @@ workflow NFCORE_RNAVAR { PREPARE_GENOME( ch_fasta_raw, + ch_star_index_raw, ch_gff, ch_gtf_raw, ch_dbsnp_raw, diff --git a/modules.json b/modules.json index 4013f678..06988fe3 100755 --- a/modules.json +++ b/modules.json @@ -195,6 +195,11 @@ "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", "installed_by": ["modules"] }, + "star/indexversion": { + "branch": "master", + "git_sha": "752700e3dd94798d73e247b523cbbf003b2bfbe4", + "installed_by": ["modules"] + }, "tabix/bgziptabix": { "branch": "master", "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", diff --git a/modules/nf-core/star/indexversion/environment.yml b/modules/nf-core/star/indexversion/environment.yml new file mode 100644 index 00000000..1d05c52a --- /dev/null +++ b/modules/nf-core/star/indexversion/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 + - bioconda::star=2.7.11b + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/indexversion/main.nf b/modules/nf-core/star/indexversion/main.nf new file mode 100644 index 00000000..70dbb4e4 --- /dev/null +++ b/modules/nf-core/star/indexversion/main.nf @@ -0,0 +1,41 @@ +process STAR_INDEXVERSION { + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d/data' : + 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }" + + output: + path("*.txt") , emit: index_version + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "index_version" + """ + STAR --help | grep 'versionGenome' | sed -e 's/versionGenome[ \t]*//' | sed -e 's/ .*//' > ${prefix}.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "index_version" + """ + STAR --help | grep 'versionGenome' | sed -e 's/versionGenome[ \t]*//' | sed -e 's/ .*//' > ${prefix}.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/star/indexversion/meta.yml b/modules/nf-core/star/indexversion/meta.yml new file mode 100644 index 00000000..c35587c0 --- /dev/null +++ b/modules/nf-core/star/indexversion/meta.yml @@ -0,0 +1,36 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "star_indexversion" +description: Get the minimal allowed index version from STAR +keywords: + - index + - version + - rna +tools: + - star: + description: | + STAR is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: https://github.com/alexdobin/STAR + manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf + doi: 10.1093/bioinformatics/bts635 + licence: ["MIT"] + identifier: biotools:star + +output: + - index_version: + - "*.txt": + type: file + description: File with the minimal index version + pattern: "*.txt" + + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/star/indexversion/tests/main.nf.test b/modules/nf-core/star/indexversion/tests/main.nf.test new file mode 100644 index 00000000..d0509e37 --- /dev/null +++ b/modules/nf-core/star/indexversion/tests/main.nf.test @@ -0,0 +1,36 @@ +nextflow_process { + + name "Test Process STAR_INDEXVERSION" + script "../main.nf" + process "STAR_INDEXVERSION" + + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/indexversion" + + test("normal run") { + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("stub run") { + + options "-stub" + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/star/indexversion/tests/main.nf.test.snap b/modules/nf-core/star/indexversion/tests/main.nf.test.snap new file mode 100644 index 00000000..50130c26 --- /dev/null +++ b/modules/nf-core/star/indexversion/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "normal run": { + "content": [ + { + "0": [ + "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd" + ], + "1": [ + "versions.yml:md5,003e8e66b98a702010f209d5049eeabc" + ], + "index_version": [ + "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd" + ], + "versions": [ + "versions.yml:md5,003e8e66b98a702010f209d5049eeabc" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T13:06:11.149770431" + }, + "stub run": { + "content": [ + { + "0": [ + "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd" + ], + "1": [ + "versions.yml:md5,003e8e66b98a702010f209d5049eeabc" + ], + "index_version": [ + "index_version.txt:md5,184a6b325b4ac98bd08ffc0bd8f046cd" + ], + "versions": [ + "versions.yml:md5,003e8e66b98a702010f209d5049eeabc" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T13:06:16.834272136" + } +} \ No newline at end of file diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 60ed6c0e..79fbdbb4 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -15,10 +15,13 @@ include { TABIX_TABIX as TABIX_DBSNP } from '../../../modules include { TABIX_BGZIPTABIX as BGZIPTABIX_DBSNP } from '../../../modules/nf-core/tabix/bgziptabix/main' include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/tabix/main' include { TABIX_BGZIPTABIX as BGZIPTABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/bgziptabix/main' +include { UNTAR } from '../../../modules/nf-core/untar' +include { STAR_INDEXVERSION } from '../../../modules/nf-core/star/indexversion' workflow PREPARE_GENOME { take: fasta_raw // channel: /path/to/genome.fasta + star_index // channel: /path/to/star_index gff // channel: /path/to/genome.gff gtf_raw // channel: /path/to/genome.gtf dbsnp // channel: /path/to/dbnsp.vcf.gz @@ -31,22 +34,24 @@ workflow PREPARE_GENOME { //Unzip reference genome files if needed + def ch_fasta = Channel.empty() if (params.fasta.endsWith('.gz')) { GUNZIP_FASTA(fasta_raw) - fasta = GUNZIP_FASTA.out.gunzip + ch_fasta = GUNZIP_FASTA.out.gunzip } else { - fasta = fasta_raw + ch_fasta = fasta_raw } + def ch_gtf = Channel.empty() if (params.gtf.endsWith('.gz')) { GUNZIP_GTF(gtf_raw) - gtf = GUNZIP_GTF.out.gunzip + ch_gtf = GUNZIP_GTF.out.gunzip } else { - gtf = gtf_raw + ch_gtf = gtf_raw } def ch_dbsnp = Channel.value([[],[]]) @@ -97,28 +102,77 @@ workflow PREPARE_GENOME { .mix(ch_known_indels_input.bgzip_index.map { _meta, _file, index -> index }) .collect() - GATK4_CREATESEQUENCEDICTIONARY(fasta) - GFFREAD(gff, fasta) - SAMTOOLS_FAIDX(fasta, [['id':'genome'], []]) + GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) + GFFREAD(gff, ch_fasta) + SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) - gtf = gtf.mix(GFFREAD.out.gtf) + ch_gtf = ch_gtf.mix(GFFREAD.out.gtf) - GTF2BED(gtf, feature_type) - STAR_GENOMEGENERATE(fasta, gtf) + GTF2BED(ch_gtf, feature_type) + + // + // STAR index handling + // + + def star_index_input = star_index.branch { _meta, index -> + tarzipped: index.name.endsWith(".tar.gz") + no_index: !index + index: true + } + + UNTAR( + star_index_input.tarzipped + ) + ch_versions = ch_versions.mix(UNTAR.out.versions) + + STAR_INDEXVERSION() + ch_versions = ch_versions.mix(STAR_INDEXVERSION.out.versions) + + def star_index_check = star_index_input.index + .mix(UNTAR.out.untar) + .combine(STAR_INDEXVERSION.out.index_version) + .branch { meta, index, version_file -> + def minimal_version = version_file.text.replace("\n", "") + def index_version = file("${index.toUri()}/genomeParameters.txt", checkIfExists:true) + .text + .readLines() + .find { line -> line.startsWith("versionGenome") } + .tokenize("\t")[-1] + def is_compatible = isCompatibleStarIndex(index_version, minimal_version) + if(!is_compatible) { + log.warn("Detected a wrong version of the STAR index, expected a minimum version of ${minimal_version}. Automatically recreating the index of STAR...") + } + compatible: is_compatible + return [ meta, index] + incompatible: !is_compatible + return [ meta, [] ] + } + + def genomegenerate_input = star_index_check.incompatible + .mix(star_index_input.no_index) + .combine(ch_fasta) + .map { _meta1, _wrong_index, meta2, fasta -> + [ meta2, fasta ] + } + + STAR_GENOMEGENERATE(genomegenerate_input, ch_gtf) + ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) + + def star_index_output = STAR_GENOMEGENERATE.out.index + .mix(star_index_check.compatible) ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) ch_versions = ch_versions.mix(GFFREAD.out.versions) ch_versions = ch_versions.mix(GTF2BED.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) - ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) emit: dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed - fasta = fasta + fasta = ch_fasta fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai - gtf = gtf.first() // path: genome.gtf - star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ + gtf = ch_gtf.first() // path: genome.gtf + star_index = star_index_output.first( ) // path: star/index/ dbsnp = ch_dbsnp // path: dbsnp.vcf.gz dbsnp_tbi = ch_dbsnp_tbi // path: dbsnp.vcf.gz.tbi known_indels = ch_known_indels // path: {known_indels*}.vcf.gz @@ -127,3 +181,54 @@ workflow PREPARE_GENOME { // bedtools_sort = bedtools_sort // path: sort.bed // bedtools_merge = bedtools_merge // path: merge.bed } + +def isCompatibleStarIndex(index_version, minimal_index_version) { + def is_compatible = true + if(minimal_index_version.isNumber()) { + // Older version of STAR used a numerical versioning. + // Return true if the index doesn't use the numerical versioning anymore + if(!index_version.isNumber()) { + is_compatible = true + } else { + is_compatible = index_version.toInteger() >= minimal_index_version.toInteger() + } + } else { + if(index_version.isNumber()) { + is_compatible = false + } else { + // Correctly compare semantic version strings: e.g 2.7.11b > 2.7.4a + def min_list = convertVersionToList(minimal_index_version) + def ind_list = convertVersionToList(index_version) + ind_list.eachWithIndex { digit, idx -> + if(digit > min_list[idx]) { + is_compatible = true + return + } else if(digit < min_list[idx]) { + is_compatible = false + return + } + } + } + } + return is_compatible +} + +def convertVersionToList(version) { + def init_list = version.tokenize(".") + if(!init_list[-1].isNumber()) { + // Handle cases where the last digit in the version contains a character: e.g. 2.7.11b + def last_digit = init_list[-1] + def numbers = "" + def characters = "" + last_digit.each { d -> + if(d.isNumber()) { + numbers += d + } else { + characters += d + } + } + init_list[-1] = numbers + init_list.add(characters) + } + return init_list.collect { num -> num.isNumber() ? num.toInteger() : num } +} diff --git a/subworkflows/local/prepare_genome/main.nf.test b/subworkflows/local/prepare_genome/main.nf.test new file mode 100644 index 00000000..e93b854f --- /dev/null +++ b/subworkflows/local/prepare_genome/main.nf.test @@ -0,0 +1,151 @@ + +nextflow_function { + + name "Test Functions" + script "subworkflows/local/prepare_genome/main.nf" + function "isCompatibleStarIndex" + + test("Test Function isCompatibleStarIndex - matching numbers") { + + when { + function { + """ + input[0] = "020101" // index version + input[1] = "020101" // minimal allowed version + """ + } + } + + then { + assert function.success + assert function.result + } + + } + + test("Test Function isCompatibleStarIndex - diff numbers i>m") { + + when { + function { + """ + input[0] = "020101" // index version + input[1] = "010101" // minimal allowed version + """ + } + } + + then { + assert function.success + assert function.result + } + + } + + test("Test Function isCompatibleStarIndex - diff numbers im") { + + when { + function { + """ + input[0] = "2.7.11b" // index version + input[1] = "2.7.4a" // minimal allowed version + """ + } + } + + then { + assert function.success + assert function.result + } + + } + + test("Test Function isCompatibleStarIndex - diff strings i Date: Tue, 25 Feb 2025 14:42:10 +0100 Subject: [PATCH 212/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e6ce8895..94d4e92c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -54,6 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#170](https://github.com/nf-core/rnavar/pull/170) - Fixed pipeline failure when running `--skip_intervallisttools`. - [#171](https://github.com/nf-core/rnavar/pull/171) - Fixed the `--dbnsp` and `--known_indels` handling. Uncompressed files are now allowed as inputs to the pipeline as the pipeline will automatically compress these. - [#172](https://github.com/nf-core/rnavar/pull/172) - Fixed the parameters JSON schema so the pipeline does better input validation. +- [#173](https://github.com/nf-core/rnavar/pull/173) - Added STAR index version control, the pipeline will now automatically detect a wrong STAR index version an create the correct index instead. ### Dependencies From d69e4d8f9060ecd9e68e3ca6862df2d80d62bd3b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 25 Feb 2025 15:18:09 +0100 Subject: [PATCH 213/275] don't output untar output --- conf/modules.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 7dc4b339..da7d300e 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -37,6 +37,12 @@ process { ext.args = params.read_length ? "--sjdbOverhang ${params.read_length - 1}" : '' } + withName: '.*PREPARE_GENOME:UNTAR' { + publishDir = [ + enabled: false + ] + } + withName: 'STAR_GENOMEGENERATE' { publishDir = [ path: { "${params.outdir}/genome/index" }, From b8ee14485840dcc950a7aebd693c35524b24b8bf Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 25 Feb 2025 15:24:55 +0100 Subject: [PATCH 214/275] also test functions --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c1eaa758..f46805b6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: NXF_VER: - "24.04.2" - "latest-everything" - filter: ["pipeline"] + filter: ["pipeline", "function"] # filter: ["process", "workflow", "function", "pipeline"] profile: ["conda", "docker", "singularity"] shard: [1, 2, 3, 4] From 9876aa51d15e823a402f5a4ff3dc1f6c43f88e0c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 25 Feb 2025 15:25:17 +0100 Subject: [PATCH 215/275] fix linting --- modules.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules.json b/modules.json index 06988fe3..b48f0e02 100755 --- a/modules.json +++ b/modules.json @@ -197,7 +197,7 @@ }, "star/indexversion": { "branch": "master", - "git_sha": "752700e3dd94798d73e247b523cbbf003b2bfbe4", + "git_sha": "f495fdd6f4d28424ecf1465dbd5704d2752094bf", "installed_by": ["modules"] }, "tabix/bgziptabix": { From 6709df00abe1555540c7d6db7c3c68913ebfdb48 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 25 Feb 2025 15:41:49 +0100 Subject: [PATCH 216/275] don't output star index version output --- conf/modules.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index da7d300e..c79bf8f8 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -37,6 +37,12 @@ process { ext.args = params.read_length ? "--sjdbOverhang ${params.read_length - 1}" : '' } + withName: STAR_INDEXVERSION { + publishDir = [ + enabled: false + ] + } + withName: '.*PREPARE_GENOME:UNTAR' { publishDir = [ enabled: false From e5adc8c0a630022222f2e55cf1b428a8168538e0 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Tue, 25 Feb 2025 15:36:04 +0000 Subject: [PATCH 217/275] fix tests --- tests/all_inputs.nf.test.snap | 4 ++-- tests/annotation.nf.test.snap | 12 ++++++------ tests/bam_csi.nf.test.snap | 4 ++-- tests/bam_input.nf.test.snap | 4 ++-- tests/cram_input.nf.test.snap | 4 ++-- tests/default.nf.test.snap | 4 ++-- tests/removeduplicates.nf.test.snap | 4 ++-- tests/skip_baserecalibration.nf.test.snap | 4 ++-- 8 files changed, 20 insertions(+), 20 deletions(-) diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 5183b0b4..13f7afa4 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 77, + 78, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -124,6 +124,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:23:18.179475664" + "timestamp": "2025-02-25T14:57:34.430760569" } } \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index e51c3135..8b105ff6 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | annotation with merge": { "content": [ - 45, + 46, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -256,11 +256,11 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:34:43.581063475" + "timestamp": "2025-02-25T15:11:24.746104582" }, "Run with profile test | annotation with vep": { "content": [ - 42, + 43, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -496,11 +496,11 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:30:05.490462421" + "timestamp": "2025-02-25T15:06:02.448281966" }, "Run with profile test | annotation with snpeff": { "content": [ - 42, + 43, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -632,6 +632,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:26:26.781658411" + "timestamp": "2025-02-25T15:01:56.312581883" } } \ No newline at end of file diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index 58226c69..9b1fc5ba 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | bam_csi_index": { "content": [ - 38, + 39, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -99,6 +99,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:38:46.62830248" + "timestamp": "2025-02-25T15:14:54.577109459" } } \ No newline at end of file diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index c9f200ef..d645e1b4 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 26, + 27, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -70,6 +70,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:41:05.2347019" + "timestamp": "2025-02-25T15:17:16.889089376" } } \ No newline at end of file diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index ce685b04..261fe9b9 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 26, + 27, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -70,6 +70,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:43:24.758766571" + "timestamp": "2025-02-25T15:19:49.488420316" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 3eecbc12..c5de7a8a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 39, + 40, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -104,6 +104,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:46:26.029862753" + "timestamp": "2025-02-25T15:23:04.679999134" } } \ No newline at end of file diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 043f69e9..c4d4e100 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | remove_duplicates": { "content": [ - 39, + 40, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -104,6 +104,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:49:58.665114628" + "timestamp": "2025-02-25T15:26:28.065950585" } } \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index 7c1ef258..fd2bd66c 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | skip_baserecalibration": { "content": [ - 35, + 36, { "CAT_FASTQ": { "cat": 8.3 @@ -96,6 +96,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-24T14:52:44.06475637" + "timestamp": "2025-02-25T15:30:01.903327387" } } \ No newline at end of file From f0026c6a94c6a11b134ca95eabc5cb7301095317 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 25 Feb 2025 17:31:41 +0100 Subject: [PATCH 218/275] first steps to gff handling fixes --- conf/test.config | 2 +- main.nf | 6 +++++- modules/local/gtf2bed/main.nf | 16 ++++++++++++--- subworkflows/local/prepare_genome/main.nf | 24 ++++++++++++----------- test.gff | 0 5 files changed, 32 insertions(+), 16 deletions(-) create mode 100644 test.gff diff --git a/conf/test.config b/conf/test.config index 187ca9f9..da0214da 100644 --- a/conf/test.config +++ b/conf/test.config @@ -31,7 +31,7 @@ params { fasta = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta" dict = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.dict" gtf = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" - + gtf = null // Known genome resources (optional) dbsnp = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_tbi = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" diff --git a/main.nf b/main.nf index 683c7251..94031a08 100644 --- a/main.nf +++ b/main.nf @@ -61,6 +61,10 @@ workflow NFCORE_RNAVAR { ch_versions = Channel.empty() + if(params.gtf && params.gff) { + error("Using both --gtf and --gff is not supported. Please use only one of these parameters") + } + // Initialize fasta file with meta map: ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() @@ -68,7 +72,7 @@ workflow NFCORE_RNAVAR { ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() : Channel.value([]) ch_known_indels_raw = params.known_indels ? Channel.fromPath(params.known_indels) : Channel.empty() ch_known_indels_tbi_raw = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : Channel.empty() - ch_gff = params.gff ? Channel.fromPath(params.gff).collect() : Channel.empty() + ch_gff = params.gff ? Channel.fromPath(params.gff).map{ gff -> [ [ id:gff.baseName ], gff ] }.collect() : Channel.empty() ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() // Initialize variant annotation associated channels diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf index b18a63d4..4129d5cf 100755 --- a/modules/local/gtf2bed/main.nf +++ b/modules/local/gtf2bed/main.nf @@ -12,13 +12,13 @@ process GTF2BED { val feature_type output: - path '*.bed' , emit: bed - path "versions.yml", emit: versions + tuple val(meta), path('*.bed') , emit: bed + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when - script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/ + script: def allowed_type = ["exon", "transcript", "gene"]; if (feature_type){ feature_type = allowed_type.contains(feature_type) ? feature_type : "exon" @@ -38,4 +38,14 @@ process GTF2BED { Rscript: \$(echo \$(Rscript --version 2>&1) | sed 's/R scripting front-end version //') END_VERSIONS """ + + stub: + """ + touch exome.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + Rscript: \$(echo \$(Rscript --version 2>&1) | sed 's/R scripting front-end version //') + END_VERSIONS + """ } diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 60ed6c0e..a20b3e94 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -40,13 +40,19 @@ workflow PREPARE_GENOME { fasta = fasta_raw } - if (params.gtf.endsWith('.gz')) { + def ch_gtf = Channel.empty() + if (params.gtf.toString().endsWith('.gz')) { GUNZIP_GTF(gtf_raw) + ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions) - gtf = GUNZIP_GTF.out.gunzip + ch_gtf = GUNZIP_GTF.out.gunzip + } else if(params.gff) { + GFFREAD(gff, fasta.map { _meta, fasta_ -> fasta_}.collect()) + ch_versions = ch_versions.mix(GFFREAD.out.versions) + ch_gtf = GFFREAD.out.gtf } else { - gtf = gtf_raw + ch_gtf = gtf_raw } def ch_dbsnp = Channel.value([[],[]]) @@ -98,26 +104,22 @@ workflow PREPARE_GENOME { .collect() GATK4_CREATESEQUENCEDICTIONARY(fasta) - GFFREAD(gff, fasta) SAMTOOLS_FAIDX(fasta, [['id':'genome'], []]) - gtf = gtf.mix(GFFREAD.out.gtf) - - GTF2BED(gtf, feature_type) - STAR_GENOMEGENERATE(fasta, gtf) + GTF2BED(ch_gtf, feature_type) + STAR_GENOMEGENERATE(fasta, ch_gtf) ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) - ch_versions = ch_versions.mix(GFFREAD.out.versions) ch_versions = ch_versions.mix(GTF2BED.out.versions) ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) ch_versions = ch_versions.mix(STAR_GENOMEGENERATE.out.versions) emit: dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict - exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed + exon_bed = GTF2BED.out.bed.collect() // path: exon.bed fasta = fasta fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai - gtf = gtf.first() // path: genome.gtf + gtf = ch_gtf // path: genome.gtf star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ dbsnp = ch_dbsnp // path: dbsnp.vcf.gz dbsnp_tbi = ch_dbsnp_tbi // path: dbsnp.vcf.gz.tbi diff --git a/test.gff b/test.gff new file mode 100644 index 00000000..e69de29b From cfb156b5a1b9ca4dfd0ebe2ea57956d33d94b71c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 11:54:26 +0100 Subject: [PATCH 219/275] update cat/fastq --- modules.json | 2 +- modules/nf-core/cat/fastq/environment.yml | 11 +- modules/nf-core/cat/fastq/main.nf | 41 ++- modules/nf-core/cat/fastq/meta.yml | 43 +-- modules/nf-core/cat/fastq/tests/main.nf.test | 226 +++++++++++++- .../nf-core/cat/fastq/tests/main.nf.test.snap | 295 ++++++++++++++++-- 6 files changed, 538 insertions(+), 80 deletions(-) diff --git a/modules.json b/modules.json index b48f0e02..a6e4a074 100755 --- a/modules.json +++ b/modules.json @@ -37,7 +37,7 @@ }, "cat/fastq": { "branch": "master", - "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e", + "git_sha": "c03f4019225fce21c11f194ff32eca396963f305", "installed_by": ["modules"] }, "ensemblvep/download": { diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121..9b926b1f 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,7 +1,12 @@ -name: cat_fastq +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - conda-forge::coreutils=8.30 + - conda-forge::coreutils=9.5 + - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index f132b2ad..acfb6d0e 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -1,26 +1,25 @@ process CAT_FASTQ { - tag "$meta.id" + tag "${meta.id}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: tuple val(meta), path(reads, stageAs: "input*/*") output: tuple val(meta), path("*.merged.fastq.gz"), emit: reads - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] + def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()] if (meta.single_end) { if (readList.size >= 1) { """ @@ -31,12 +30,15 @@ process CAT_FASTQ { cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') END_VERSIONS """ + } else { + error("Could not find any FASTQ files to concatenate in the process input") } - } else { + } + else { if (readList.size >= 2) { def read1 = [] def read2 = [] - readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v } + readList.eachWithIndex { v, ix -> (ix & 1 ? read2 : read1) << v } """ cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz @@ -46,34 +48,41 @@ process CAT_FASTQ { cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') END_VERSIONS """ + } else { + error("Could not find any FASTQ file pairs to concatenate in the process input") } } stub: def prefix = task.ext.prefix ?: "${meta.id}" - def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] + def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()] if (meta.single_end) { - if (readList.size > 1) { + if (readList.size >= 1) { """ - touch ${prefix}.merged.fastq.gz + echo '' | gzip > ${prefix}.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') END_VERSIONS """ + } else { + error("Could not find any FASTQ files to concatenate in the process input") } - } else { - if (readList.size > 2) { + } + else { + if (readList.size >= 2) { """ - touch ${prefix}_1.merged.fastq.gz - touch ${prefix}_2.merged.fastq.gz + echo '' | gzip > ${prefix}_1.merged.fastq.gz + echo '' | gzip > ${prefix}_2.merged.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') END_VERSIONS """ + } else { + error("Could not find any FASTQ file pairs to concatenate in the process input") } } } diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index db4ac3c7..91ff2fb5 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,30 +10,33 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test index a71dcb8d..013c1d0f 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -1,5 +1,3 @@ -// NOTE The version snaps may not be consistant -// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035 nextflow_process { name "Test Process CAT_FASTQ" @@ -13,9 +11,6 @@ nextflow_process { test("test_cat_fastq_single_end") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -38,9 +33,6 @@ nextflow_process { test("test_cat_fastq_paired_end") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -65,9 +57,6 @@ nextflow_process { test("test_cat_fastq_single_end_same_name") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -90,9 +79,6 @@ nextflow_process { test("test_cat_fastq_paired_end_same_name") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = Channel.of([ @@ -117,9 +103,129 @@ nextflow_process { test("test_cat_fastq_single_end_single_file") { when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file - stub") { + + options "-stub" + + when { process { """ input[0] = Channel.of([ @@ -137,4 +243,92 @@ nextflow_process { ) } } + + test("test_cat_fastq_single_end_no_files") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } + + test("test_cat_fastq_paired_end_no_files") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } + + test("test_cat_fastq_single_end_no_files - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } + + test("test_cat_fastq_paired_end_no_files - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [] + ]) + """ + } + } + + then { + assertAll( + { assert process.failed }, + { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() } + ) + } + } } diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap index 43dfe28f..ee5ab364 100644 --- a/modules/nf-core/cat/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -1,4 +1,131 @@ { + "test_cat_fastq_paired_end_no_files - stub": { + "content": [ + " Could not find any FASTQ file pairs to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:51.248685461" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:24:04.902821069" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:23:57.476357974" + }, + "test_cat_fastq_paired_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:24:34.615815265" + }, "test_cat_fastq_single_end": { "content": [ { @@ -12,7 +139,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -24,11 +151,15 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], - "timestamp": "2024-01-17T17:30:39.816981" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:23:32.489874386" }, "test_cat_fastq_single_end_same_name": { "content": [ @@ -43,7 +174,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -55,13 +186,17 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], - "timestamp": "2024-01-17T17:32:35.229332" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:23:49.184759506" }, - "test_cat_fastq_single_end_single_file": { + "test_cat_fastq_single_end - stub": { "content": [ { "0": [ @@ -70,11 +205,11 @@ "id": "test", "single_end": true }, - "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -82,17 +217,76 @@ "id": "test", "single_end": true }, - "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], - "timestamp": "2024-01-17T17:34:00.058829" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:24:12.857293744" }, - "test_cat_fastq_paired_end_same_name": { + "test_cat_fastq_paired_end_no_files": { + "content": [ + " Could not find any FASTQ file pairs to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:40.806088747" + }, + "test_cat_fastq_single_end_no_files - stub": { + "content": [ + " Could not find any FASTQ files to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:45.852365218" + }, + "test_cat_fastq_single_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:24:27.816080065" + }, + "test_cat_fastq_paired_end": { "content": [ { "0": [ @@ -108,7 +302,7 @@ ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -123,13 +317,27 @@ ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], - "timestamp": "2024-01-17T17:33:33.031555" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:23:41.739469187" }, - "test_cat_fastq_paired_end": { + "test_cat_fastq_single_end_no_files": { + "content": [ + " Could not find any FASTQ files to concatenate in the process input" + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:14:35.695192409" + }, + "test_cat_fastq_paired_end - stub": { "content": [ { "0": [ @@ -139,13 +347,13 @@ "single_end": false }, [ - "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", - "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], "1": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ], "reads": [ [ @@ -154,16 +362,55 @@ "single_end": false }, [ - "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", - "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], "versions": [ - "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:24:21.178950408" + }, + "test_cat_fastq_single_end_single_file - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6ef4fd28546a005865b9454bbedbf81a" ] } ], - "timestamp": "2024-01-17T17:32:02.270935" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-25T17:24:40.851404993" } } \ No newline at end of file From 6985871e201079fb8e6d2c8eb607aaa0df1b5993 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 13:54:46 +0100 Subject: [PATCH 220/275] correctly handle more ref data --- conf/test.config | 2 +- main.nf | 29 ++++++++------- subworkflows/local/prepare_genome/main.nf | 45 +++++++++++++++++------ subworkflows/local/splitncigar/main.nf | 10 ++--- workflows/rnavar.nf | 3 +- 5 files changed, 57 insertions(+), 32 deletions(-) diff --git a/conf/test.config b/conf/test.config index c631f8f2..63d78afa 100644 --- a/conf/test.config +++ b/conf/test.config @@ -33,7 +33,7 @@ params { fasta = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta" dict = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.dict" gtf = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" - gtf = null + // Known genome resources (optional) dbsnp = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_tbi = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" diff --git a/main.nf b/main.nf index 559f7c4a..e90dbfeb 100644 --- a/main.nf +++ b/main.nf @@ -66,15 +66,18 @@ workflow NFCORE_RNAVAR { } // Initialize fasta file with meta map: - ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() + ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() // Initialize file channels based on params, defined in the params.genomes[params.genome] scope - ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() : Channel.value([]) - ch_known_indels_raw = params.known_indels ? Channel.fromPath(params.known_indels) : Channel.empty() - ch_known_indels_tbi_raw = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : Channel.empty() - ch_gff = params.gff ? Channel.fromPath(params.gff).map{ gff -> [ [ id:gff.baseName ], gff ] }.collect() : Channel.empty() - ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() - ch_star_index_raw = params.star_index ? Channel.fromPath(params.star_index).map { index -> [[id:index.baseName], index]} : Channel.value([[],[]]) + ch_dict_raw = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() + ch_fai_raw = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() + ch_dbsnp_raw = params.dbsnp ? Channel.fromPath(params.dbsnp).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() : Channel.value([]) + ch_known_indels_raw = params.known_indels ? Channel.fromPath(params.known_indels) : Channel.empty() + ch_known_indels_tbi_raw = params.known_indels_tbi ? Channel.fromPath(params.known_indels_tbi) : Channel.empty() + ch_gff = params.gff ? Channel.fromPath(params.gff).map{ gff -> [ [ id:gff.baseName ], gff ] }.collect() : Channel.empty() + ch_gtf_raw = params.gtf ? Channel.fromPath(params.gtf).map{ gtf -> [ [ id:gtf.baseName ], gtf ] }.collect() : Channel.empty() + ch_star_index_raw = params.star_index ? Channel.fromPath(params.star_index).map { index -> [[id:index.baseName], index]} : Channel.value([[],[]]) + ch_exon_bed_raw = params.exon_bed ? Channel.fromPath(params.exon_bed).map { it -> [[id:it.baseName], it]} : Channel.empty() // Initialize variant annotation associated channels snpeff_db = params.snpeff_db ?: Channel.empty() @@ -107,9 +110,12 @@ workflow NFCORE_RNAVAR { PREPARE_GENOME( ch_fasta_raw, + ch_dict_raw, + ch_fai_raw, ch_star_index_raw, ch_gff, ch_gtf_raw, + ch_exon_bed_raw, ch_dbsnp_raw, ch_known_indels_raw, ch_known_indels_tbi_raw, @@ -118,12 +124,9 @@ workflow NFCORE_RNAVAR { ch_fasta = PREPARE_GENOME.out.fasta ch_star_index = PREPARE_GENOME.out.star_index ch_gtf = PREPARE_GENOME.out.gtf - ch_dict = params.dict ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect() - : PREPARE_GENOME.out.dict - ch_fasta_fai = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fasta_fai'], it ] }.collect() - : PREPARE_GENOME.out.fasta_fai - ch_exon_bed = params.exon_bed ? Channel.fromPath(params.exon_bed).map{ it -> [ [id:'exon_bed'], it ] }.collect() - : PREPARE_GENOME.out.exon_bed + ch_dict = PREPARE_GENOME.out.dict + ch_fasta_fai = PREPARE_GENOME.out.fasta_fai + ch_exon_bed = PREPARE_GENOME.out.exon_bed ch_dbsnp = params.dbsnp && params.dbsnp.endsWith(".gz") ? ch_dbsnp_raw : PREPARE_GENOME.out.dbsnp ch_dbsnp_tbi = params.dbsnp.toString().endsWith(".gz") && params.dbsnp_tbi ? Channel.fromPath(params.dbsnp_tbi).map { dbsnp -> [[id:dbsnp.baseName], dbsnp]}.collect() diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index d717e556..4a199886 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -21,9 +21,12 @@ include { STAR_INDEXVERSION } from '../../../modules workflow PREPARE_GENOME { take: fasta_raw // channel: /path/to/genome.fasta + dict_raw // channel: /path/to/genome.dict + fai_raw // channel: /path/to/genome.fasta.fai star_index // channel: /path/to/star_index gff // channel: /path/to/genome.gff gtf_raw // channel: /path/to/genome.gtf + exon_bed_raw // channel: /path/to/genome.bed dbsnp // channel: /path/to/dbnsp.vcf.gz known_indels // channel: [/path/to/known_indels] known_indels_tbi // channel: [/path/to/known_indels_index] @@ -59,6 +62,15 @@ workflow PREPARE_GENOME { ch_gtf = gtf_raw } + def ch_exon_bed = Channel.empty() + if(!params.exon_bed) { + GTF2BED(ch_gtf, feature_type) + ch_versions = ch_versions.mix(GTF2BED.out.versions) + ch_exon_bed = GTF2BED.out.bed + } else { + ch_exon_bed = exon_bed_raw + } + def ch_dbsnp = Channel.value([[],[]]) def ch_dbsnp_tbi = Channel.value([[],[]]) if (params.dbsnp && !params.dbsnp.toString().endsWith(".gz")) { @@ -107,11 +119,24 @@ workflow PREPARE_GENOME { .mix(ch_known_indels_input.bgzip_index.map { _meta, _file, index -> index }) .collect() - GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) - SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) + def ch_dict = Channel.empty() + if(!params.dict) { + GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) + ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) + ch_dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict + } else { + ch_dict = dict_raw + } - GTF2BED(ch_gtf, feature_type) + def ch_fai = Channel.empty() + if(!params.fasta_fai) { + SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) + ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) + ch_fai = SAMTOOLS_FAIDX.out.fai + } else { + ch_fai = fai_raw + } // // STAR index handling @@ -167,17 +192,13 @@ workflow PREPARE_GENOME { def star_index_output = STAR_GENOMEGENERATE.out.index .mix(star_index_check.compatible) - ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) - ch_versions = ch_versions.mix(GTF2BED.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) - emit: - dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict // path: genome.fasta.dict - exon_bed = GTF2BED.out.bed.map{ bed -> [ [ id:bed.baseName ], bed ] }.collect() // path: exon.bed + dict = ch_dict // path: genome.fasta.dict + exon_bed = ch_exon_bed // path: exon.bed fasta = ch_fasta - fasta_fai = SAMTOOLS_FAIDX.out.fai // path: genome.fasta.fai - gtf = ch_gtf // path: genome.gtf - star_index = STAR_GENOMEGENERATE.out.index.first() // path: star/index/ + fasta_fai = ch_fai // path: genome.fasta.fai + gtf = ch_gtf.collect() // path: genome.gtf + star_index = star_index_output // path: star/index/ dbsnp = ch_dbsnp // path: dbsnp.vcf.gz dbsnp_tbi = ch_dbsnp_tbi // path: dbsnp.vcf.gz.tbi known_indels = ch_known_indels // path: {known_indels*}.vcf.gz diff --git a/subworkflows/local/splitncigar/main.nf b/subworkflows/local/splitncigar/main.nf index 7e6bb515..a39731b5 100644 --- a/subworkflows/local/splitncigar/main.nf +++ b/subworkflows/local/splitncigar/main.nf @@ -9,9 +9,9 @@ include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index workflow SPLITNCIGAR { take: bam // channel: [ val(meta), [ bam ], [bai] ] - fasta // channel: [ fasta ] - fai // channel: [ fai ] - dict // channel: [ dict ] + fasta // channel: [ val(meta), fasta ] + fai // channel: [ val(meta), fai ] + dict // channel: [ val(meta), dict ] intervals // channel: [ interval_list] main: @@ -30,7 +30,7 @@ workflow SPLITNCIGAR { GATK4_SPLITNCIGARREADS(bam_interval, fasta, - fai.map{ fai_ -> [[id:'genome'], fai_] }, + fai, dict) def bam_splitncigar = GATK4_SPLITNCIGARREADS.out.bam @@ -46,7 +46,7 @@ workflow SPLITNCIGAR { SAMTOOLS_MERGE( bam_splitncigar_interval, fasta, - fai.map{ fai_ -> [[id:fai_.baseName], fai_] } + fai ) def splitncigar_bam = SAMTOOLS_MERGE.out.bam diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 5815a3ee..6156acfa 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -127,6 +127,7 @@ workflow RNAVAR { if (!params.skip_intervallisttools) { GATK4_INTERVALLISTTOOLS(interval_list) interval_list_split = GATK4_INTERVALLISTTOOLS.out.interval_list.map{ _meta, bed -> [bed] }.collect() + ch_versions = ch_versions.mix(GATK4_INTERVALLISTTOOLS.out.versions) } else { interval_list_split = interval_list.map { _meta, bed -> bed } @@ -182,7 +183,7 @@ workflow RNAVAR { SPLITNCIGAR(genome_bam_bai, fasta, - fasta_fai.map { _meta, fai -> fai }, + fasta_fai, dict, interval_list_split ) From 9072f4a7c128f247fcd8bf748d3f5c819f79c9b2 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 14:36:42 +0100 Subject: [PATCH 221/275] fix some edge cases --- main.nf | 2 ++ nextflow_schema.json | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/main.nf b/main.nf index e90dbfeb..695f0b7c 100644 --- a/main.nf +++ b/main.nf @@ -63,6 +63,8 @@ workflow NFCORE_RNAVAR { if(params.gtf && params.gff) { error("Using both --gtf and --gff is not supported. Please use only one of these parameters") + } else if(!params.gtf && !params.gff) { + error("Missing required parameters: --gtf or --gff") } // Initialize fasta file with meta map: diff --git a/nextflow_schema.json b/nextflow_schema.json index d5be5f91..6b67b7d5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -51,6 +51,7 @@ "type": "object", "fa_icon": "fas fa-dna", "description": "Reference genome related files and options required for the workflow.", + "required": ["fasta"], "properties": { "genome": { "type": "string", @@ -98,7 +99,7 @@ "type": "string", "format": "file-path", "exists": true, - "pattern": "^\\S+\\.gff$", + "pattern": "^\\S+\\.gff\\d?$", "description": "Path to GFF3 annotation file.", "help_text": "This parameter must be specified if `--genome` or `--gtf` are not specified." }, From 4ae9887e44fa0a812b770569955d7a6638b470cb Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 14:40:11 +0100 Subject: [PATCH 222/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 94d4e92c..23ba7972 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -55,6 +55,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#171](https://github.com/nf-core/rnavar/pull/171) - Fixed the `--dbnsp` and `--known_indels` handling. Uncompressed files are now allowed as inputs to the pipeline as the pipeline will automatically compress these. - [#172](https://github.com/nf-core/rnavar/pull/172) - Fixed the parameters JSON schema so the pipeline does better input validation. - [#173](https://github.com/nf-core/rnavar/pull/173) - Added STAR index version control, the pipeline will now automatically detect a wrong STAR index version an create the correct index instead. +- [#175](https://github.com/nf-core/rnavar/pull/175) - Fixed the handling of GFF files so they are now correctly being used. ### Dependencies From 60f61a662e01c75881441bdb7e198ba9469dd285 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 15:42:52 +0100 Subject: [PATCH 223/275] move test data + fix snapshots --- conf/test.config | 5 +++-- conf/test_full.config | 2 +- tests/all_inputs.nf.test | 1 - tests/all_inputs.nf.test.snap | 9 ++++++--- tests/annotation.nf.test | 1 - tests/annotation.nf.test.snap | 23 ++++++++++++++++------- tests/bam_csi.nf.test | 1 - tests/bam_csi.nf.test.snap | 9 ++++++--- tests/bam_input.nf.test | 1 - tests/bam_input.nf.test.snap | 7 +++++-- tests/cram_input.nf.test | 1 - tests/cram_input.nf.test.snap | 7 +++++-- tests/default.nf.test | 1 - tests/default.nf.test.snap | 7 +++++-- tests/removeduplicates.nf.test | 1 - tests/removeduplicates.nf.test.snap | 9 ++++++--- tests/skip_baserecalibration.nf.test | 1 - tests/skip_baserecalibration.nf.test.snap | 9 ++++++--- 18 files changed, 59 insertions(+), 36 deletions(-) diff --git a/conf/test.config b/conf/test.config index 63d78afa..e949cc0d 100644 --- a/conf/test.config +++ b/conf/test.config @@ -22,7 +22,7 @@ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/refs/heads/rnavar/data' // Input data input = "${projectDir}/tests/csv/1.0/fastq_single.csv" @@ -32,7 +32,8 @@ params { fasta = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.fasta" dict = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.dict" - gtf = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" + // gtf = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.gtf" + gff = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/genome.gff3" // Known genome resources (optional) dbsnp = "${params.pipelines_testdata_base_path}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" diff --git a/conf/test_full.config b/conf/test_full.config index 81133bdc..947d4652 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,7 +15,7 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Parameters for full-size test - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.0/samplesheet_full.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnavar/samplesheet/v1.2/samplesheet_full.csv' read_length = 101 genome = 'GRCh38' } diff --git a/tests/all_inputs.nf.test b/tests/all_inputs.nf.test index ee55eb6e..b2f22e86 100644 --- a/tests/all_inputs.nf.test +++ b/tests/all_inputs.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" input = "${projectDir}/tests/csv/1.0/all.csv" } diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 13f7afa4..0ed921ff 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -1,13 +1,13 @@ { "Run with profile test": { "content": [ - 78, + 77, { "APPLYBQSR": { "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "FASTQC": { "fastqc": "0.12.1" @@ -21,6 +21,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -126,4 +129,4 @@ }, "timestamp": "2025-02-25T14:57:34.430760569" } -} \ No newline at end of file +} diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test index c2677c9e..050a3107 100644 --- a/tests/annotation.nf.test +++ b/tests/annotation.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'snpeff' download_cache = true diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 8b105ff6..d9e2787f 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,13 +1,13 @@ { "Run with profile test | annotation with merge": { "content": [ - 46, + 45, { "APPLYBQSR": { "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "ENSEMBLVEP_VEP": { "ensemblvep": 111.0 @@ -24,6 +24,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -260,13 +263,13 @@ }, "Run with profile test | annotation with vep": { "content": [ - 43, + 42, { "APPLYBQSR": { "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "ENSEMBLVEP_VEP": { "ensemblvep": 111.0 @@ -283,6 +286,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -500,13 +506,13 @@ }, "Run with profile test | annotation with snpeff": { "content": [ - 43, + 42, { "APPLYBQSR": { "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "FASTQC": { "fastqc": "0.12.1" @@ -520,6 +526,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -634,4 +643,4 @@ }, "timestamp": "2025-02-25T15:01:56.312581883" } -} \ No newline at end of file +} diff --git a/tests/bam_csi.nf.test b/tests/bam_csi.nf.test index 7e3fd41f..d2f2ea4c 100644 --- a/tests/bam_csi.nf.test +++ b/tests/bam_csi.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" bam_csi_index = true } diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index 9b1fc5ba..a04374a8 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -1,13 +1,13 @@ { "Run with profile test | bam_csi_index": { "content": [ - 39, + 38, { "APPLYBQSR": { "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "FASTQC": { "fastqc": "0.12.1" @@ -21,6 +21,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -101,4 +104,4 @@ }, "timestamp": "2025-02-25T15:14:54.577109459" } -} \ No newline at end of file +} diff --git a/tests/bam_input.nf.test b/tests/bam_input.nf.test index 7e78259c..d6307164 100644 --- a/tests/bam_input.nf.test +++ b/tests/bam_input.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" input = "${projectDir}/tests/csv/1.0/bam.csv" } diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index d645e1b4..9dfb3b1f 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 27, + 26, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -15,6 +15,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -72,4 +75,4 @@ }, "timestamp": "2025-02-25T15:17:16.889089376" } -} \ No newline at end of file +} diff --git a/tests/cram_input.nf.test b/tests/cram_input.nf.test index 315a7041..6380f90f 100644 --- a/tests/cram_input.nf.test +++ b/tests/cram_input.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" input = "${projectDir}/tests/csv/1.0/cram.csv" } diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index 261fe9b9..460d79f8 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 27, + 26, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -15,6 +15,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -72,4 +75,4 @@ }, "timestamp": "2025-02-25T15:19:49.488420316" } -} \ No newline at end of file +} diff --git a/tests/default.nf.test b/tests/default.nf.test index e0904024..0509f2b3 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index c5de7a8a..286cb4d2 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -7,7 +7,7 @@ "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "FASTQC": { "fastqc": "0.12.1" @@ -21,6 +21,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -106,4 +109,4 @@ }, "timestamp": "2025-02-25T15:23:04.679999134" } -} \ No newline at end of file +} diff --git a/tests/removeduplicates.nf.test b/tests/removeduplicates.nf.test index 8d3d6116..597e84e4 100644 --- a/tests/removeduplicates.nf.test +++ b/tests/removeduplicates.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" remove_duplicates = true } diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index c4d4e100..11e81aa7 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,13 +1,13 @@ { "Run with profile test | remove_duplicates": { "content": [ - 40, + 39, { "APPLYBQSR": { "gatk4": "4.5.0.0" }, "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "FASTQC": { "fastqc": "0.12.1" @@ -21,6 +21,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -106,4 +109,4 @@ }, "timestamp": "2025-02-25T15:26:28.065950585" } -} \ No newline at end of file +} diff --git a/tests/skip_baserecalibration.nf.test b/tests/skip_baserecalibration.nf.test index 4599ba8f..a70b70c0 100644 --- a/tests/skip_baserecalibration.nf.test +++ b/tests/skip_baserecalibration.nf.test @@ -9,7 +9,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" skip_baserecalibration = true } diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index fd2bd66c..835a1513 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -1,10 +1,10 @@ { "Run with profile test | skip_baserecalibration": { "content": [ - 36, + 35, { "CAT_FASTQ": { - "cat": 8.3 + "cat": 9.5 }, "FASTQC": { "fastqc": "0.12.1" @@ -15,6 +15,9 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, "GATK4_MERGEVCFS": { "gatk4": "4.5.0.0" }, @@ -98,4 +101,4 @@ }, "timestamp": "2025-02-25T15:30:01.903327387" } -} \ No newline at end of file +} From 5228dc2e5e113eaa6fb125dbae7342994e113cc1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 16:11:27 +0100 Subject: [PATCH 224/275] fix more issues with tests --- tests/all_inputs.nf.test.snap | 2 +- tests/annotation.nf.test | 2 -- tests/annotation.nf.test.snap | 4 ++-- tests/bam_input.nf.test.snap | 2 +- tests/cram_input.nf.test.snap | 2 +- tests/removeduplicates.nf.test.snap | 2 +- 6 files changed, 6 insertions(+), 8 deletions(-) diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 0ed921ff..eae55e86 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 77, + 78, { "APPLYBQSR": { "gatk4": "4.5.0.0" diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test index 050a3107..8f9195e1 100644 --- a/tests/annotation.nf.test +++ b/tests/annotation.nf.test @@ -38,7 +38,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'vep' download_cache = true @@ -68,7 +67,6 @@ nextflow_pipeline { when { params { - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' outdir = "$outputDir" annotate_tools = 'merge' download_cache = true diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index d9e2787f..55021873 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -263,7 +263,7 @@ }, "Run with profile test | annotation with vep": { "content": [ - 42, + 43, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -506,7 +506,7 @@ }, "Run with profile test | annotation with snpeff": { "content": [ - 42, + 43, { "APPLYBQSR": { "gatk4": "4.5.0.0" diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 9dfb3b1f..20c79bc4 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 26, + 27, { "APPLYBQSR": { "gatk4": "4.5.0.0" diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index 460d79f8..422e65d7 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 26, + 27, { "APPLYBQSR": { "gatk4": "4.5.0.0" diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 11e81aa7..553909be 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | remove_duplicates": { "content": [ - 39, + 40, { "APPLYBQSR": { "gatk4": "4.5.0.0" From ad567169b1f458ae3d8fda66049ea53aac7634d8 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 16:25:22 +0100 Subject: [PATCH 225/275] fix snapshot --- tests/annotation.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 55021873..20cc0415 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | annotation with merge": { "content": [ - 45, + 46, { "APPLYBQSR": { "gatk4": "4.5.0.0" From d7b83c77ac1b6d46756d6c945a4de855528157ae Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 17:36:42 +0100 Subject: [PATCH 226/275] add exon bed filter step (credits to @Shaun-Regenbaum) --- bin/remove_unknown_regions.py | 36 ++++++++++++++++ conf/modules.config | 10 +++++ .../remove_unkown_regions/environment.yml | 7 ++++ modules/local/remove_unkown_regions/main.nf | 42 +++++++++++++++++++ nextflow.config | 1 + nextflow_schema.json | 5 +++ subworkflows/local/prepare_genome/main.nf | 38 +++++++++++------ 7 files changed, 126 insertions(+), 13 deletions(-) create mode 100755 bin/remove_unknown_regions.py create mode 100644 modules/local/remove_unkown_regions/environment.yml create mode 100755 modules/local/remove_unkown_regions/main.nf diff --git a/bin/remove_unknown_regions.py b/bin/remove_unknown_regions.py new file mode 100755 index 00000000..97cbc0c7 --- /dev/null +++ b/bin/remove_unknown_regions.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python + +import argparse +import os + +def load_sequences_from_dict(dict_file): + sequences = set() + with open(dict_file, 'r') as file: + for line in file: + if line.startswith('@SQ'): + parts = line.split('\t') + for part in parts: + if part.startswith('SN:'): + sequences.add(part.split(':')[1]) + return sequences + +def filter_bed_file(bed_file, sequences, output_file): + with open(bed_file, 'r') as file, open(output_file, 'w') as out: + for line in file: + sequence = line.split('\t')[0] + if sequence in sequences: + out.write(line) + +def main(bed_file, dict_file, output_file): + sequences = load_sequences_from_dict(dict_file) + filter_bed_file(bed_file, sequences, output_file) + print(f"Output file {output_file} created in {os.getcwd()}") + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Remove unknown regions from a BED file") + parser.add_argument('bed', metavar='FILE', type=str, help="The BED file to remove unknown regions of") + parser.add_argument('dict', metavar='FILE', type=str, help="The DICT file to get known regions from") + parser.add_argument('output', metavar='FILE', type=str, help="The name of the output file") + + args = parser.parse_args() + main(args.bed, args.dict, args.output) diff --git a/conf/modules.config b/conf/modules.config index c79bf8f8..40c600c9 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -49,6 +49,16 @@ process { ] } + withName: REMOVE_UNKNOWN_REGIONS { + ext.prefix = { "${meta.id}.exon" } + publishDir = [ + path: { "${params.outdir}/genome" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + enabled: params.save_reference + ] + } + withName: 'STAR_GENOMEGENERATE' { publishDir = [ path: { "${params.outdir}/genome/index" }, diff --git a/modules/local/remove_unkown_regions/environment.yml b/modules/local/remove_unkown_regions/environment.yml new file mode 100644 index 00000000..e2c586b0 --- /dev/null +++ b/modules/local/remove_unkown_regions/environment.yml @@ -0,0 +1,7 @@ +name: remove_unknown_regions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::python=3.8.3 diff --git a/modules/local/remove_unkown_regions/main.nf b/modules/local/remove_unkown_regions/main.nf new file mode 100755 index 00000000..9f178336 --- /dev/null +++ b/modules/local/remove_unkown_regions/main.nf @@ -0,0 +1,42 @@ +process REMOVE_UNKNOWN_REGIONS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.8.3' : + 'quay.io/biocontainers/python:3.8.3' }" + + input: + tuple val(meta), path(bed) + tuple val(meta2), path(dict) + + output: + tuple val(meta), path('*.bed') , emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + remove_unknown_regions.py $bed $dict ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$(python --version | sed 's/Python //g') + END_VERSIONS + """ +} diff --git a/nextflow.config b/nextflow.config index af48228b..e1733145 100644 --- a/nextflow.config +++ b/nextflow.config @@ -70,6 +70,7 @@ params { skip_intervallisttools = false skip_variantfiltration = false skip_variantannotation = false + skip_exon_bed_check = false // GATK intervallist parameters gatk_interval_scatter_count = 25 diff --git a/nextflow_schema.json b/nextflow_schema.json index 6b67b7d5..23814f0e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -529,6 +529,11 @@ "type": "boolean", "description": "Skip MultiQC reports", "help_text": "This parameter disable all QC reports" + }, + "skip_exon_bed_check": { + "type": "boolean", + "description": "Skip the check of the exon bed", + "help_text": "Set this parameter if you don't want to the pipeline to check and filter unknown regions in the exon bed file." } } }, diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 4a199886..c07460df 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -17,6 +17,7 @@ include { TABIX_TABIX as TABIX_KNOWN_INDELS } from '../../../modules include { TABIX_BGZIPTABIX as BGZIPTABIX_KNOWN_INDELS } from '../../../modules/nf-core/tabix/bgziptabix/main' include { UNTAR } from '../../../modules/nf-core/untar' include { STAR_INDEXVERSION } from '../../../modules/nf-core/star/indexversion' +include { REMOVE_UNKNOWN_REGIONS } from '../../../modules/local/remove_unkown_regions' workflow PREPARE_GENOME { take: @@ -47,6 +48,15 @@ workflow PREPARE_GENOME { ch_fasta = fasta_raw } + def ch_dict = Channel.empty() + if(!params.dict) { + GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) + ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) + ch_dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict + } else { + ch_dict = dict_raw + } + def ch_gtf = Channel.empty() if (params.gtf.toString().endsWith('.gz')) { GUNZIP_GTF(gtf_raw) @@ -62,13 +72,25 @@ workflow PREPARE_GENOME { ch_gtf = gtf_raw } - def ch_exon_bed = Channel.empty() + def ch_exon_bed_raw = Channel.empty() if(!params.exon_bed) { GTF2BED(ch_gtf, feature_type) ch_versions = ch_versions.mix(GTF2BED.out.versions) - ch_exon_bed = GTF2BED.out.bed + ch_exon_bed_raw = GTF2BED.out.bed } else { - ch_exon_bed = exon_bed_raw + ch_exon_bed_raw = exon_bed_raw + } + + def ch_exon_bed = Channel.empty() + if(!params.skip_exon_bed_check) { + REMOVE_UNKNOWN_REGIONS( + ch_exon_bed_raw, + ch_dict + ) + ch_versions = ch_versions.mix(REMOVE_UNKNOWN_REGIONS.out.versions) + ch_exon_bed = REMOVE_UNKNOWN_REGIONS.out.bed + } else { + ch_exon_bed = ch_exon_bed_raw } def ch_dbsnp = Channel.value([[],[]]) @@ -119,16 +141,6 @@ workflow PREPARE_GENOME { .mix(ch_known_indels_input.bgzip_index.map { _meta, _file, index -> index }) .collect() - def ch_dict = Channel.empty() - if(!params.dict) { - GATK4_CREATESEQUENCEDICTIONARY(ch_fasta) - ch_versions = ch_versions.mix(GATK4_CREATESEQUENCEDICTIONARY.out.versions) - ch_dict = GATK4_CREATESEQUENCEDICTIONARY.out.dict - } else { - ch_dict = dict_raw - } - - def ch_fai = Channel.empty() if(!params.fasta_fai) { SAMTOOLS_FAIDX(ch_fasta, [['id':'genome'], []]) From deb39f77747d9f53bb2b7d959ab7e92cfdfde584 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Thu, 27 Feb 2025 17:38:40 +0100 Subject: [PATCH 227/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 23ba7972..4e47aa9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -56,6 +56,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#172](https://github.com/nf-core/rnavar/pull/172) - Fixed the parameters JSON schema so the pipeline does better input validation. - [#173](https://github.com/nf-core/rnavar/pull/173) - Added STAR index version control, the pipeline will now automatically detect a wrong STAR index version an create the correct index instead. - [#175](https://github.com/nf-core/rnavar/pull/175) - Fixed the handling of GFF files so they are now correctly being used. +- [#177](https://github.com/nf-core/rnavar/pull/177) - Added a check and filter step for unknown regions in the exon BED. You can disable this check with `--skip_exon_bed_check`. ### Dependencies From 2506c94f7deb346a992438d1fdd5288e40bb1104 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 17:42:13 +0100 Subject: [PATCH 228/275] implement automatic sharding for nf-test --- .github/actions/get-shards/action.yml | 66 ++++++++++++ .github/actions/nf-test/action.yml | 114 +++++++++++++++++++++ .github/workflows/nf-test.yml | 139 ++++++++++++++++++++++++++ 3 files changed, 319 insertions(+) create mode 100644 .github/actions/get-shards/action.yml create mode 100644 .github/actions/nf-test/action.yml create mode 100644 .github/workflows/nf-test.yml diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml new file mode 100644 index 00000000..6d388be6 --- /dev/null +++ b/.github/actions/get-shards/action.yml @@ -0,0 +1,66 @@ +name: "Get number of shards" +description: "Get the number of nf-test shards for the current CI job" +inputs: + max_shards: + description: "Maximum number of shards allowed" + required: true + paths: + description: "Component paths to test" + required: false +outputs: + shard: + description: "Array of shard numbers" + value: ${{ steps.shards.outputs.shard }} + total_shards: + description: "Total number of shards" + value: ${{ steps.shards.outputs.total_shards }} +runs: + using: "composite" + steps: + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} + - name: Get number of shards + id: shards + shell: bash + run: | + # Run nf-test with dynamic parameter + nftest_output=$(nf-test test \ + --dry-run \ + --profile +docker \ + --filter function,workflow,pipeline \ + --ci \ + --changed-since HEAD^) || { + echo "nf-test command failed with exit code $?" + echo "Full output: $nftest_output" + exit 1 + } + echo "nf-test dry-run output: $nftest_output" + + # Default values for shard and total_shards + shard="[]" + total_shards=0 + + # Check if there are related tests + if echo "$nftest_output" | grep -q 'No tests to execute'; then + echo "No related tests found." + else + # Extract the number of related tests + number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') + if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then + shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) + shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) + total_shards="$shards_to_run" + else + echo "Unexpected output format. Falling back to default values." + fi + fi + + # Write to GitHub Actions outputs + echo "shard=$shard" >> $GITHUB_OUTPUT + echo "total_shards=$total_shards" >> $GITHUB_OUTPUT + + # Debugging output + echo "Final shard array: $shard" + echo "Total number of shards: $total_shards" diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml new file mode 100644 index 00000000..75a93f70 --- /dev/null +++ b/.github/actions/nf-test/action.yml @@ -0,0 +1,114 @@ +name: "nf-test Action" +description: "Runs nf-test with common setup steps" +inputs: + profile: + description: "Profile to use" + required: true + shard: + description: "Shard number for this CI job" + required: true + total_shards: + description: "Total number of test shards(NOT the total number of matrix jobs)" + required: true + paths: + description: "Test paths" + required: true + +runs: + using: "composite" + steps: + - name: Setup Nextflow + uses: nf-core/setup-nextflow@v2 + with: + version: "${{ env.NXF_VERSION }}" + + - name: Set up Python + uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5 + with: + python-version: "3.11" + + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: "${{ env.NFT_VER }}" + + - name: Setup apptainer + if: contains(inputs.profile, 'singularity') + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: contains(inputs.profile, 'singularity') + shell: bash + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Conda setup + if: ${{inputs.profile == 'conda'}} + uses: conda-incubator/setup-miniconda@505e6394dae86d6a5c7fbb6e3fb8938e3e863830 # v3 + with: + auto-update-conda: true + conda-solver: libmamba + conda-remove-defaults: true + + - name: Install pdiff + shell: bash + run: | + python -m pip install pdiff + + # TODO Skip failing conda tests and document their failures + # https://github.com/nf-core/modules/issues/7017 + - name: Run nf-test + shell: bash + env: + NFT_DIFF: ${{ env.NFT_DIFF }} + NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + run: | + nf-test test \ + --profile=+${{ inputs.profile }} \ + --tap=test.tap \ + --verbose \ + --ci \ + --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \ + --filter function,workflow,pipeline + + # Save the absolute path of the test.tap file to the output + echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT + + - name: Generate test summary + if: always() + shell: bash + run: | + # Add header if it doesn't exist (using a token file to track this) + if [ ! -f ".summary_header" ]; then + echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY + echo "" >> $GITHUB_STEP_SUMMARY + echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY + echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY + touch .summary_header + fi + + if [ -f test.tap ]; then + while IFS= read -r line; do + if [[ $line =~ ^ok ]]; then + test_name="${line#ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + elif [[ $line =~ ^not\ ok ]]; then + test_name="${line#not ok }" + # Remove the test number from the beginning + test_name="${test_name#* }" + echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + done < test.tap + else + echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY + fi + + - name: Clean up + if: always() + shell: bash + run: | + sudo rm -rf /home/ubuntu/tests/ diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml new file mode 100644 index 00000000..c5227d13 --- /dev/null +++ b/.github/workflows/nf-test.yml @@ -0,0 +1,139 @@ +name: Run nf-test +on: + push: + branches: + # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging + - "renovate/**" # branches Renovate creates + pull_request: + branches: [dev] + workflow_dispatch: + inputs: + runners: + description: "Runners to test on" + type: choice + options: + - "ubuntu-latest" + - "self-hosted" + default: "ubuntu-latest" + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" + # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver + NFT_VER: "0.9.2" + NFT_WORKDIR: "~" + NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + +jobs: + nf-test-changes: + name: nf-test-changes + runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} + outputs: + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} + steps: + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 + + - name: get number of shards + id: set-shards + uses: ./.github/actions/get-shards + env: + NFT_VER: ${{ env.NFT_VER }} + with: + max_shards: 7 + + - name: debug + run: | + echo ${{ steps.set-shards.outputs.shard }} + echo ${{ steps.set-shards.outputs.total_shards }} + + nf-test: + runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} + name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" + needs: [nf-test-changes] + if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} + strategy: + fail-fast: false + matrix: + shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }} + profile: [conda, docker, singularity] + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" + NXF_VER: + # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver + - "24.10.2" + - "latest-everything" + env: + NXF_ANSI_LOG: false + TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }} + + steps: + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + fetch-depth: 0 + + - name: Run nf-test + uses: ./.github/actions/nf-test + env: + NFT_DIFF: ${{ env.NFT_DIFF }} + NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }} + NFT_WORKDIR: ${{ env.NFT_WORKDIR }} + with: + profile: ${{ matrix.profile }} + shard: ${{ matrix.shard }} + total_shards: ${{ env.TOTAL_SHARDS }} + + confirm-pass: + runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} + needs: [nf-test] + if: always() + steps: + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + + - name: debug-print + if: always() + run: | + echo "::group::DEBUG: `needs` Contents" + echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}" + echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" + echo "::endgroup::" + + - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner + if: always() + run: | + ls -la ./ + rm -rf ./* || true + rm -rf ./.??* || true + ls -la ./ From d36fd58f24fc7831b75560cf6bdc9237a11c060d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 17:42:23 +0100 Subject: [PATCH 229/275] implement automatic sharding for nf-test --- .github/workflows/ci.yml | 124 --------------------------------------- 1 file changed, 124 deletions(-) delete mode 100644 .github/workflows/ci.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index f46805b6..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,124 +0,0 @@ -name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors -on: - push: - branches: - - dev - pull_request: - release: - types: [published] - workflow_dispatch: - -env: - NFT_DIFF: "pdiff" - NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" - NFT_VER: "0.9.0" - NFT_WORKDIR: "~" - NXF_ANSI_LOG: false - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - -concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true - -jobs: - test: - name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5" - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnavar') }}" - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - NXF_VER: - - "24.04.2" - - "latest-everything" - filter: ["pipeline", "function"] - # filter: ["process", "workflow", "function", "pipeline"] - profile: ["conda", "docker", "singularity"] - shard: [1, 2, 3, 4] - isMaster: - - ${{ github.base_ref == 'master' }} - exclude: - - isMaster: false - profile: "conda" - - isMaster: false - profile: "singularity" - steps: - - name: Check out pipeline code - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - fetch-depth: 0 - - - name: Set up Nextflow - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Set up nf-test - uses: nf-core/setup-nf-test@v1 - with: - version: ${{ env.NFT_VER }} - - - name: Set up Apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Cache pdiff - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 - id: cache-pip-pdiff - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-pdiff - - - name: Set up pdiff to see diff between nf-test snapshots - run: | - python -m pip install --upgrade pip - pip install pdiff cryptography - - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/5" - run: | - nf-test test \ - --ci \ - --junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ - --shard ${{ matrix.shard }}/5 \ - --changed-since HEAD^ \ - --follow-dependencies \ - --profile "+${{ matrix.profile }}" \ - --filter ${{ matrix.filter }} - - - name: Publish Test Report - uses: mikepenz/action-junit-report@v4 - if: success() || failure() # always run even if the previous step fails - with: - report_paths: "TEST-*.xml" - - - name: Clean up - if: always() - run: | - sudo rm -rf /home/ubuntu/tests/ From dc1da86f1239f16c45fb3d0a4ef953fa7cecb676 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 17:45:00 +0100 Subject: [PATCH 230/275] update nf-test.config file --- nf-test.config | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/nf-test.config b/nf-test.config index 69ef7315..b7213127 100644 --- a/nf-test.config +++ b/nf-test.config @@ -1,17 +1,20 @@ config { - // location for all nf-tests + // location for all nf-test tests testsDir "." // nf-test directory including temporary files for each test - workDir ".nf-test" + workDir System.getenv("NFT_WORKDIR") ?: ".nf-test" // location of an optional nextflow.config file specific for executing tests - configFile "conf/test.config" + configFile "tests/nextflow.config" // run all test with defined profile(s) from the main nextflow.config profile "test" - // Include plugins + // list of filenames or patterns that should be trigger a full test run + triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config' + + // load the necessary plugins plugins { load "nft-bam@0.4.0" load "nft-utils@0.0.3" From 85b9d239a92f014f8b1a09929b161196ea3655e5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 17:46:13 +0100 Subject: [PATCH 231/275] add missing file --- tests/nextflow.config | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 tests/nextflow.config diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..8c817b3a --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,12 @@ +/* +======================================================================================== + Nextflow config file for running nf-test tests +======================================================================================== +*/ + +// Specify any additional parameters here +// Or any resources requirements + +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' +} From 02701ea0e69a08f6d9cb4015332026d68530732e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 17:47:50 +0100 Subject: [PATCH 232/275] fix linting --- .nf-core.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index 411a201f..3ff492a1 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,3 +1,6 @@ +lint: + files_exist: + - .github/workflows/ci.yml nf_core_version: 3.2.0 repository_type: pipeline template: From 8097e6626930a63c2d3ff66b23854a211dafca96 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 17:48:43 +0100 Subject: [PATCH 233/275] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 23ba7972..e7764045 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#161](https://github.com/nf-core/rnavar/pull/161) - Template update for nf-core/tools v3.2.0 - [#167](https://github.com/nf-core/rnavar/pull/167) - Removed the strandedness field from the samplesheet as it wasn't used in the pipeline. - [#172](https://github.com/nf-core/rnavar/pull/172) - Added support for TSV, JSON and YAML samplesheets +- [#178](https://github.com/nf-core/rnavar/pull/178) - Implement automatic sharding for nf-test tests ### Fixed From 44dd7d4cfe31ecbe00661e9cf1cc365743ce2aaf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 27 Feb 2025 19:09:10 +0100 Subject: [PATCH 234/275] better name for tests --- tests/all_inputs.nf.test | 4 ++-- tests/all_inputs.nf.test.snap | 8 ++++---- tests/annotation.nf.test | 8 ++++---- tests/annotation.nf.test.snap | 20 ++++++++++---------- tests/bam_csi.nf.test | 4 ++-- tests/bam_csi.nf.test.snap | 10 +++++----- tests/bam_input.nf.test | 4 ++-- tests/bam_input.nf.test.snap | 8 ++++---- tests/cram_input.nf.test | 4 ++-- tests/cram_input.nf.test.snap | 8 ++++---- tests/default.nf.test | 2 +- tests/default.nf.test.snap | 8 ++++---- tests/removeduplicates.nf.test | 4 ++-- tests/removeduplicates.nf.test.snap | 8 ++++---- tests/skip_baserecalibration.nf.test | 4 ++-- tests/skip_baserecalibration.nf.test.snap | 10 +++++----- 16 files changed, 57 insertions(+), 57 deletions(-) diff --git a/tests/all_inputs.nf.test b/tests/all_inputs.nf.test index b2f22e86..43cff003 100644 --- a/tests/all_inputs.nf.test +++ b/tests/all_inputs.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | all inputs" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test") { + test("-profile test --input all.csv") { when { params { diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index eae55e86..4a00da86 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -1,5 +1,5 @@ { - "Run with profile test": { + "-profile test --input all.csv": { "content": [ 78, { @@ -125,8 +125,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T14:57:34.430760569" + "timestamp": "2025-02-27T18:32:03.285344136" } -} +} \ No newline at end of file diff --git a/tests/annotation.nf.test b/tests/annotation.nf.test index 8f9195e1..3d94a9da 100644 --- a/tests/annotation.nf.test +++ b/tests/annotation.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | annotation" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test | annotation with snpeff") { + test("-profile test --annotate_tools snpeff") { when { params { @@ -34,7 +34,7 @@ nextflow_pipeline { } } - test("Run with profile test | annotation with vep") { + test("-profile test --annotate_tools vep") { when { params { @@ -63,7 +63,7 @@ nextflow_pipeline { } } - test("Run with profile test | annotation with merge") { + test("-profile test --annotate_tools merge") { when { params { diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 20cc0415..81b15270 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,5 +1,5 @@ { - "Run with profile test | annotation with merge": { + "-profile test --annotate_tools merge": { "content": [ 46, { @@ -257,11 +257,11 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:11:24.746104582" + "timestamp": "2025-02-27T18:46:36.717730874" }, - "Run with profile test | annotation with vep": { + "-profile test --annotate_tools vep": { "content": [ 43, { @@ -500,11 +500,11 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:06:02.448281966" + "timestamp": "2025-02-27T18:41:59.716595012" }, - "Run with profile test | annotation with snpeff": { + "-profile test --annotate_tools snpeff": { "content": [ 43, { @@ -639,8 +639,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:01:56.312581883" + "timestamp": "2025-02-27T18:36:46.359170223" } -} +} \ No newline at end of file diff --git a/tests/bam_csi.nf.test b/tests/bam_csi.nf.test index d2f2ea4c..88f2a2f0 100644 --- a/tests/bam_csi.nf.test +++ b/tests/bam_csi.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | bam_csi_index" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test | bam_csi_index") { + test("-profile test --bam_csi_index") { when { params { diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index a04374a8..2235b017 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -1,7 +1,7 @@ { - "Run with profile test | bam_csi_index": { + "-profile test --bam_csi_index": { "content": [ - 38, + 39, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -100,8 +100,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:14:54.577109459" + "timestamp": "2025-02-27T18:50:47.33970351" } -} +} \ No newline at end of file diff --git a/tests/bam_input.nf.test b/tests/bam_input.nf.test index d6307164..7cddb491 100644 --- a/tests/bam_input.nf.test +++ b/tests/bam_input.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | bam input" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test") { + test("-profile test --input bam.csv") { when { params { diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 20c79bc4..0960fb22 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,5 +1,5 @@ { - "Run with profile test": { + "-profile test --input bam.csv": { "content": [ 27, { @@ -71,8 +71,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:17:16.889089376" + "timestamp": "2025-02-27T18:53:38.97099769" } -} +} \ No newline at end of file diff --git a/tests/cram_input.nf.test b/tests/cram_input.nf.test index 6380f90f..66a48826 100644 --- a/tests/cram_input.nf.test +++ b/tests/cram_input.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | cram input" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test") { + test("-profile test --input cram.csv") { when { params { diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index 422e65d7..5d1e4899 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -1,5 +1,5 @@ { - "Run with profile test": { + "-profile test --input cram.csv": { "content": [ 27, { @@ -71,8 +71,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:19:49.488420316" + "timestamp": "2025-02-27T18:57:38.534910684" } -} +} \ No newline at end of file diff --git a/tests/default.nf.test b/tests/default.nf.test index 0509f2b3..49783cc7 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test") { + test("-profile test") { when { params { diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 286cb4d2..d2262f26 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,5 +1,5 @@ { - "Run with profile test": { + "-profile test": { "content": [ 40, { @@ -105,8 +105,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:23:04.679999134" + "timestamp": "2025-02-27T19:02:10.37030655" } -} +} \ No newline at end of file diff --git a/tests/removeduplicates.nf.test b/tests/removeduplicates.nf.test index 597e84e4..4f78e18b 100644 --- a/tests/removeduplicates.nf.test +++ b/tests/removeduplicates.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | remove_duplicates" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test | remove_duplicates") { + test("-profile test --remove_duplicates") { when { params { diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 553909be..7631ff10 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,5 +1,5 @@ { - "Run with profile test | remove_duplicates": { + "-profile test --remove_duplicates": { "content": [ 40, { @@ -105,8 +105,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:26:28.065950585" + "timestamp": "2025-02-27T19:05:51.886924986" } -} +} \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test b/tests/skip_baserecalibration.nf.test index a70b70c0..b8addd26 100644 --- a/tests/skip_baserecalibration.nf.test +++ b/tests/skip_baserecalibration.nf.test @@ -1,11 +1,11 @@ nextflow_pipeline { - name "Test pipeline | skip_baserecalibration" + name "Test pipeline" script "../main.nf" tag "pipeline" tag "pipeline_rnavar" - test("Run with profile test | skip_baserecalibration") { + test("-profile test --skip_baserecalibration") { when { params { diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index 835a1513..38123272 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -1,7 +1,7 @@ { - "Run with profile test | skip_baserecalibration": { + "-profile test --skip_baserecalibration": { "content": [ - 35, + 36, { "CAT_FASTQ": { "cat": 9.5 @@ -97,8 +97,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T15:30:01.903327387" + "timestamp": "2025-02-27T19:08:25.175823741" } -} +} \ No newline at end of file From ba040dbe8bcc1eded3cca9a41f8b453ad25f9491 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Fri, 28 Feb 2025 14:09:12 +0000 Subject: [PATCH 235/275] fix snapshots --- tests/all_inputs.nf.test.snap | 6 +++--- tests/annotation.nf.test.snap | 14 +++++++------- tests/bam_csi.nf.test.snap | 6 +++--- tests/bam_input.nf.test.snap | 6 +++--- tests/cram_input.nf.test.snap | 6 +++--- tests/default.nf.test.snap | 6 +++--- tests/removeduplicates.nf.test.snap | 6 +++--- tests/skip_baserecalibration.nf.test.snap | 6 +++--- 8 files changed, 28 insertions(+), 28 deletions(-) diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index eae55e86..119a135f 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 78, + 79, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -127,6 +127,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T14:57:34.430760569" + "timestamp": "2025-02-28T13:33:31.371268626" } -} +} \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 20cc0415..0a8a49cd 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | annotation with merge": { "content": [ - 46, + 47, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -259,11 +259,11 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:11:24.746104582" + "timestamp": "2025-02-28T13:46:27.75077738" }, "Run with profile test | annotation with vep": { "content": [ - 43, + 44, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -502,11 +502,11 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:06:02.448281966" + "timestamp": "2025-02-28T13:41:21.446868258" }, "Run with profile test | annotation with snpeff": { "content": [ - 43, + 44, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -641,6 +641,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:01:56.312581883" + "timestamp": "2025-02-28T13:36:52.683033566" } -} +} \ No newline at end of file diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index a04374a8..f47f216b 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | bam_csi_index": { "content": [ - 38, + 40, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -102,6 +102,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:14:54.577109459" + "timestamp": "2025-02-28T13:51:12.605457529" } -} +} \ No newline at end of file diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 20c79bc4..5e2994fd 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 27, + 28, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -73,6 +73,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:17:16.889089376" + "timestamp": "2025-02-28T13:54:12.491719133" } -} +} \ No newline at end of file diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index 422e65d7..d5926438 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 27, + 28, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -73,6 +73,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:19:49.488420316" + "timestamp": "2025-02-28T13:57:55.375924294" } -} +} \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 286cb4d2..1f225707 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test": { "content": [ - 40, + 41, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -107,6 +107,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:23:04.679999134" + "timestamp": "2025-02-28T14:01:49.031861331" } -} +} \ No newline at end of file diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 553909be..388fbac2 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | remove_duplicates": { "content": [ - 40, + 41, { "APPLYBQSR": { "gatk4": "4.5.0.0" @@ -107,6 +107,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:26:28.065950585" + "timestamp": "2025-02-28T14:05:08.874427283" } -} +} \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index 835a1513..d7e07a4e 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -1,7 +1,7 @@ { "Run with profile test | skip_baserecalibration": { "content": [ - 35, + 37, { "CAT_FASTQ": { "cat": 9.5 @@ -99,6 +99,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T15:30:01.903327387" + "timestamp": "2025-02-28T14:08:15.055621292" } -} +} \ No newline at end of file From 1d5d5b22f0fd77f0059820d26b69b234b227601e Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 28 Feb 2025 17:18:19 +0100 Subject: [PATCH 236/275] fix s3 file resolving --- subworkflows/local/prepare_genome/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index c07460df..d28f6001 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -175,7 +175,7 @@ workflow PREPARE_GENOME { def is_compatible = true if(!workflow.stubRun) { def minimal_version = version_file.text.replace("\n", "") - def index_version = file("${index.toUri()}/genomeParameters.txt", checkIfExists:true) + def index_version = index.resolve("genomeParameters.txt") .text .readLines() .find { line -> line.startsWith("versionGenome") } From e8281bd0e62a65514b0dbeb4527e6ee35edc1450 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 3 Mar 2025 13:03:44 +0100 Subject: [PATCH 237/275] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 34ddd0d5..061a81a1 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/rnavar/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/rnavar/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnavar/actions/workflows/linting.yml) [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnavar/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.6669636-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.6669636) From ba09a023333fad9adadace8377ad58bf643b8884 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 13:08:15 +0100 Subject: [PATCH 238/275] Add UMI extraction --- conf/modules.config | 10 ++ main.nf | 4 + modules.json | 5 + .../nf-core/umitools/extract/environment.yml | 7 + modules/nf-core/umitools/extract/main.nf | 74 ++++++++ modules/nf-core/umitools/extract/meta.yml | 60 +++++++ .../umitools/extract/tests/main.nf.test | 106 +++++++++++ .../umitools/extract/tests/main.nf.test.snap | 167 ++++++++++++++++++ .../umitools/extract/tests/nextflow.config | 9 + .../nf-core/umitools/extract/tests/tags.yml | 2 + nextflow.config | 5 + nextflow_schema.json | 31 ++++ workflows/rnavar.nf | 20 ++- 13 files changed, 499 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/umitools/extract/environment.yml create mode 100644 modules/nf-core/umitools/extract/main.nf create mode 100644 modules/nf-core/umitools/extract/meta.yml create mode 100644 modules/nf-core/umitools/extract/tests/main.nf.test create mode 100644 modules/nf-core/umitools/extract/tests/main.nf.test.snap create mode 100644 modules/nf-core/umitools/extract/tests/nextflow.config create mode 100644 modules/nf-core/umitools/extract/tests/tags.yml diff --git a/conf/modules.config b/conf/modules.config index 40c600c9..eac39d86 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -132,6 +132,16 @@ process { // ALIGNMENT process { + // UMITOOLS_EXTRACT + withName: UMITOOLS_EXTRACT { + ext.args = { [ + params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '', + params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '', + params.umitools_bc_pattern2 && !meta.single_end ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '', + params.umitools_umi_separator ? "--umi-separator='${params.umitools_umi_separator}'" : '' + ].join(' ').trim() } + } + // ALIGN_STAR withName: STAR_ALIGN { diff --git a/main.nf b/main.nf index 695f0b7c..a4017512 100644 --- a/main.nf +++ b/main.nf @@ -67,6 +67,10 @@ workflow NFCORE_RNAVAR { error("Missing required parameters: --gtf or --gff") } + if(params.extract_umi && !params.umitools_bc_pattern) { + error("Expected --umitools_bc_pattern when --extract_umi is specified.") + } + // Initialize fasta file with meta map: ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() diff --git a/modules.json b/modules.json index a6e4a074..37894473 100755 --- a/modules.json +++ b/modules.json @@ -210,6 +210,11 @@ "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, + "umitools/extract": { + "branch": "master", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "installed_by": ["modules"] + }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml new file mode 100644 index 00000000..e5721f1e --- /dev/null +++ b/modules/nf-core/umitools/extract/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf new file mode 100644 index 00000000..b97900e0 --- /dev/null +++ b/modules/nf-core/umitools/extract/main.nf @@ -0,0 +1,74 @@ +process UMITOOLS_EXTRACT { + tag "$meta.id" + label "process_single" + label "process_long" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/umi_tools:1.1.5--py39hf95cd2a_0' : + 'biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.fastq.gz"), emit: reads + tuple val(meta), path("*.log") , emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if (meta.single_end) { + """ + umi_tools \\ + extract \\ + -I $reads \\ + -S ${prefix}.umi_extract.fastq.gz \\ + $args \\ + > ${prefix}.umi_extract.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ + } else { + """ + umi_tools \\ + extract \\ + -I ${reads[0]} \\ + --read2-in=${reads[1]} \\ + -S ${prefix}.umi_extract_1.fastq.gz \\ + --read2-out=${prefix}.umi_extract_2.fastq.gz \\ + $args \\ + > ${prefix}.umi_extract.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ + } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if (meta.single_end) { + output_command = "echo '' | gzip > ${prefix}.umi_extract.fastq.gz" + } else { + output_command = "echo '' | gzip > ${prefix}.umi_extract_1.fastq.gz ;" + output_command += "echo '' | gzip > ${prefix}.umi_extract_2.fastq.gz" + } + """ + touch ${prefix}.umi_extract.log + ${output_command} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml new file mode 100644 index 00000000..648ffbd2 --- /dev/null +++ b/modules/nf-core/umitools/extract/meta.yml @@ -0,0 +1,60 @@ +name: umitools_extract +description: Extracts UMI barcode from a read and add it to the read name, leaving + any sample barcode in place +keywords: + - UMI + - barcode + - extract + - umitools +tools: + - umi_tools: + description: > + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + documentation: https://umi-tools.readthedocs.io/en/latest/ + license: "MIT" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. +output: + - reads: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: > + Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. + | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Logfile for umi_tools + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test new file mode 100644 index 00000000..bb8a0658 --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/main.nf.test @@ -0,0 +1,106 @@ +nextflow_process { + + name "Test Process UMITOOLS_EXTRACT" + script "../main.nf" + process "UMITOOLS_EXTRACT" + config "./nextflow.config" + tag "modules_nfcore" + tag "modules" + tag "umitools" + tag "umitools/extract" + + test("single end") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.reads.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.log.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + } + + test("single end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("pair end") { + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.reads[0][1][0]).name, + file(process.out.reads[0][1][1]).name, + process.out.log.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + } + + test("pair end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test.snap b/modules/nf-core/umitools/extract/tests/main.nf.test.snap new file mode 100644 index 00000000..b1159054 --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/main.nf.test.snap @@ -0,0 +1,167 @@ +{ + "pair end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.umi_extract_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.umi_extract_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T15:05:20.008312" + }, + "single end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.umi_extract.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.umi_extract.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T15:04:12.145999" + }, + "pair end": { + "content": [ + "test.umi_extract_1.fastq.gz", + "test.umi_extract_2.fastq.gz", + [ + [ + { + "id": "test", + "single_end": false + }, + "test.umi_extract.log" + ] + ], + [ + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T15:21:09.578031" + }, + "single end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.umi_extract.fastq.gz" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.umi_extract.log" + ] + ], + [ + "versions.yml:md5,568d243174c081a0301e74ed42e59b48" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-02T15:03:52.464606" + } +} \ No newline at end of file diff --git a/modules/nf-core/umitools/extract/tests/nextflow.config b/modules/nf-core/umitools/extract/tests/nextflow.config new file mode 100644 index 00000000..c866f5a0 --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: UMITOOLS_EXTRACT { + ext.args = '--bc-pattern="NNNN"' + } + +} diff --git a/modules/nf-core/umitools/extract/tests/tags.yml b/modules/nf-core/umitools/extract/tests/tags.yml new file mode 100644 index 00000000..c3fb23de --- /dev/null +++ b/modules/nf-core/umitools/extract/tests/tags.yml @@ -0,0 +1,2 @@ +umitools/extract: + - modules/nf-core/umitools/extract/** diff --git a/nextflow.config b/nextflow.config index e1733145..6d8a6e5f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -38,6 +38,11 @@ params { // Preprocessing of alignment remove_duplicates = false + extract_umi = false + umitools_extract_method = 'string' + umitools_bc_pattern = null + umitools_bc_pattern2 = null + umitools_umi_separator = null // Variant calling no_intervals = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 23814f0e..62d15274 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -301,6 +301,37 @@ "description": "Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.", "help_text": "Specify true for removing duplicates from BAM file during Picard MarkDuplicates step.", "hidden": false + }, + "extract_umi": { + "type": "boolean", + "fa_icon": "fas fa-hammer", + "description": "Specify whether to remove UMIs from the reads with UMI-tools extract." + }, + "umitools_extract_method": { + "type": "string", + "default": "string", + "fa_icon": "fas fa-barcode", + "description": "UMI pattern to use. Can be either 'string' (default) or 'regex'.", + "help_text": "More details can be found in the [UMI-tools documentation](https://umi-tools.readthedocs.io/en/latest/reference/extract.html#extract-method).\n", + "enum": ["string", "regex"] + }, + "umitools_bc_pattern": { + "type": "string", + "fa_icon": "fas fa-barcode", + "help_text": "More details can be found in the [UMI-tools documentation](https://umi-tools.readthedocs.io/en/latest/reference/extract.html#extract-method).", + "description": "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI.", + "pattern": "^[NXC]*$" + }, + "umitools_bc_pattern2": { + "type": "string", + "fa_icon": "fas fa-barcode", + "description": "The UMI barcode pattern to use if the UMI is located in read 2.", + "pattern": "^[NXC]*$" + }, + "umitools_umi_separator": { + "type": "string", + "fa_icon": "fas fa-star-half-alt", + "description": "The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with UMI-tools and used other software." } } }, diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 6156acfa..01b3096b 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -22,6 +22,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc' include { SAMTOOLS_INDEX } from '../modules/nf-core/samtools/index' include { TABIX_TABIX as TABIX } from '../modules/nf-core/tabix/tabix' include { TABIX_TABIX as TABIXGVCF } from '../modules/nf-core/tabix/tabix' +include { UMITOOLS_EXTRACT } from '../modules/nf-core/umitools/extract' // local include { RECALIBRATE } from '../subworkflows/local/recalibrate' @@ -112,6 +113,22 @@ workflow RNAVAR { ch_reports = ch_reports.mix(FASTQC.out.zip.collect{ _meta, logs -> logs }) ch_versions = ch_versions.mix(FASTQC.out.versions) + // + // MODULE: Extract UMIs from reads + // + + def umi_extracted_reads = Channel.empty() + if(params.extract_umi) { + UMITOOLS_EXTRACT( + cat_fastq + ) + ch_versions = ch_versions.mix(UMITOOLS_EXTRACT.out.versions.first()) + umi_extracted_reads = UMITOOLS_EXTRACT.out.reads + } else { + umi_extracted_reads = cat_fastq + } + + // // MODULE: Prepare the interval list from the GTF file using GATK4 BedToIntervalList // @@ -138,7 +155,8 @@ workflow RNAVAR { // if (params.aligner == 'star') { - FASTQ_ALIGN_STAR(cat_fastq, + FASTQ_ALIGN_STAR( + umi_extracted_reads, star_index, gtf, params.star_ignore_sjdbgtf, From 04a5f229663080fee4639c2a1579a9bd7b4201ca Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 13:10:36 +0100 Subject: [PATCH 239/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e47aa9b..bcee8917 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#116](https://github.com/nf-core/rnavar/pull/116) - Added `unzip` from nf-core modules for working with unzipped fasta and gtf files - [#157](https://github.com/nf-core/rnavar/pull/157) - Added support for `bam` and `cram` input files - [#169](https://github.com/nf-core/rnavar/pull/169) - Added the `--star_max_intron_size` parameter to set the `--alignIntronMax` argument in STAR +- [#180](https://github.com/nf-core/rnavar/pull/180) - Added support for UMI extraction. Specify `--extract_umi` to enable this feature ### Changed From 756293c88ab8128f3dde0c5208912dfb77f6663d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 13:11:34 +0100 Subject: [PATCH 240/275] update actions/cache --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f46805b6..a1bafd97 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,7 +72,7 @@ jobs: mkdir -p $NXF_SINGULARITY_LIBRARYDIR - name: Cache pdiff - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + uses: actions/cache@v4 # v4 id: cache-pip-pdiff with: path: ~/.cache/pip From 05a5eb93613461c3c055de928558a71c55d34b21 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 13:27:17 +0100 Subject: [PATCH 241/275] add tests --- tests/csv/1.0/fastq_single_end.csv | 2 + tests/extract_umi.nf.test | 37 ++++++++++ tests/extract_umi.nf.test.snap | 115 +++++++++++++++++++++++++++++ 3 files changed, 154 insertions(+) create mode 100644 tests/csv/1.0/fastq_single_end.csv create mode 100644 tests/extract_umi.nf.test create mode 100644 tests/extract_umi.nf.test.snap diff --git a/tests/csv/1.0/fastq_single_end.csv b/tests/csv/1.0/fastq_single_end.csv new file mode 100644 index 00000000..ece90513 --- /dev/null +++ b/tests/csv/1.0/fastq_single_end.csv @@ -0,0 +1,2 @@ +sample,fastq_1 +GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz diff --git a/tests/extract_umi.nf.test b/tests/extract_umi.nf.test new file mode 100644 index 00000000..fad10013 --- /dev/null +++ b/tests/extract_umi.nf.test @@ -0,0 +1,37 @@ +nextflow_pipeline { + + name "Test pipeline | extract_umi" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Run with profile test | extract_umi") { + + when { + params { + input = "${projectDir}/tests/csv/1.0/fastq_single_end.csv" + outdir = "$outputDir" + extract_umi = true + umitools_bc_pattern = "NNNXC" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/extract_umi.nf.test.snap b/tests/extract_umi.nf.test.snap new file mode 100644 index 00000000..0ecf7a8e --- /dev/null +++ b/tests/extract_umi.nf.test.snap @@ -0,0 +1,115 @@ +{ + "Run with profile test | extract_umi": { + "content": [ + 41, + { + "APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.5.0.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.5.0.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.5.0.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.5.0.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.5.0.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.3.0" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.21 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.21 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.21 + }, + "SAMTOOLS_MERGE": { + "samtools": "1.19.2" + }, + "SAMTOOLS_SORT": { + "samtools": 1.21 + }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, + "STAR_ALIGN": { + "star": "2.7.11b", + "samtools": 1.21, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": "1.19.1" + }, + "UMITOOLS_EXTRACT": { + "umitools": "1.1.5" + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "umitools", + "umitools/GM12878.umi_extract.fastq.gz", + "umitools/GM12878.umi_extract.log", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-03T13:25:38.180578622" + } +} \ No newline at end of file From 36350b9e34ceff890ac29dc3808401a11f178b54 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 16:06:34 +0100 Subject: [PATCH 242/275] bump all modules --- CHANGELOG.md | 6 +- modules.json | 68 +- .../nf-core/bcftools/annotate/environment.yml | 6 +- modules/nf-core/bcftools/annotate/main.nf | 24 +- modules/nf-core/bcftools/annotate/meta.yml | 90 ++- .../bcftools/annotate/tests/bcf.config | 8 +- .../bcftools/annotate/tests/main.nf.test | 326 ++++++++- .../bcftools/annotate/tests/main.nf.test.snap | 358 +++++++++- .../bcftools/annotate/tests/vcf.config | 6 +- .../annotate/tests/vcf_gz_index.config | 4 + .../annotate/tests/vcf_gz_index_csi.config | 4 + .../annotate/tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bcftools/concat/environment.yml | 6 +- modules/nf-core/bcftools/concat/main.nf | 37 +- modules/nf-core/bcftools/concat/meta.yml | 81 ++- .../bcftools/concat/tests/main.nf.test | 253 ++++++- .../bcftools/concat/tests/main.nf.test.snap | 342 +++++++++- .../bcftools/concat/tests/vcf_gz_index.config | 4 + .../concat/tests/vcf_gz_index_csi.config | 4 + .../concat/tests/vcf_gz_index_tbi.config | 4 + .../bcftools/pluginscatter/environment.yml | 6 +- .../nf-core/bcftools/pluginscatter/main.nf | 24 +- .../nf-core/bcftools/pluginscatter/meta.yml | 121 ++-- .../bcftools/pluginscatter/tests/main.nf.test | 415 ++++++++++++ .../pluginscatter/tests/main.nf.test.snap | 623 ++++++++++++++++++ .../pluginscatter/tests/nextflow.config | 3 + .../bcftools/pluginscatter/tests/tags.yml | 2 + .../pluginscatter/tests/vcf_gz_index.config | 4 + .../tests/vcf_gz_index_csi.config | 4 + .../tests/vcf_gz_index_tbi.config | 4 + modules/nf-core/bcftools/sort/environment.yml | 6 +- modules/nf-core/bcftools/sort/main.nf | 17 +- modules/nf-core/bcftools/sort/meta.yml | 65 +- .../nf-core/bcftools/sort/tests/main.nf.test | 174 ++++- .../bcftools/sort/tests/main.nf.test.snap | 298 ++++++++- .../bcftools/sort/tests/vcf_gz_index.config | 4 + .../sort/tests/vcf_gz_index_csi.config | 4 + .../sort/tests/vcf_gz_index_tbi.config | 4 + .../nf-core/bedtools/merge/environment.yml | 4 +- modules/nf-core/bedtools/merge/meta.yml | 46 +- .../nf-core/bedtools/merge/tests/main.nf.test | 2 +- modules/nf-core/bedtools/sort/environment.yml | 4 +- modules/nf-core/bedtools/sort/meta.yml | 53 +- .../ensemblvep/download/environment.yml | 6 +- modules/nf-core/ensemblvep/download/main.nf | 4 +- modules/nf-core/ensemblvep/download/meta.yml | 56 +- .../ensemblvep/download/tests/main.nf.test | 4 +- .../download/tests/main.nf.test.snap | 452 ++++++------- .../ensemblvep/download/tests/nextflow.config | 2 +- .../nf-core/ensemblvep/vep/environment.yml | 6 +- modules/nf-core/ensemblvep/vep/main.nf | 31 +- modules/nf-core/ensemblvep/vep/meta.yml | 157 +++-- .../nf-core/ensemblvep/vep/tests/main.nf.test | 17 +- .../ensemblvep/vep/tests/main.nf.test.snap | 22 +- .../ensemblvep/vep/tests/nextflow.config | 2 +- modules/nf-core/fastqc/environment.yml | 2 + .../nf-core/gatk4/applybqsr/environment.yml | 8 +- modules/nf-core/gatk4/applybqsr/main.nf | 17 +- modules/nf-core/gatk4/applybqsr/meta.yml | 101 +-- .../gatk4/applybqsr/tests/main.nf.test | 59 ++ .../gatk4/applybqsr/tests/main.nf.test.snap | 114 +++- .../gatk4/baserecalibrator/environment.yml | 8 +- .../nf-core/gatk4/baserecalibrator/main.nf | 14 +- .../nf-core/gatk4/baserecalibrator/meta.yml | 124 ++-- .../gatk4/baserecalibrator/tests/main.nf.test | 180 +++-- .../baserecalibrator/tests/main.nf.test.snap | 155 ++++- .../gatk4/bedtointervallist/environment.yml | 8 +- .../nf-core/gatk4/bedtointervallist/main.nf | 6 +- .../nf-core/gatk4/bedtointervallist/meta.yml | 59 +- .../bedtointervallist/tests/main.nf.test.snap | 10 +- .../gatk4/combinegvcfs/environment.yml | 8 +- modules/nf-core/gatk4/combinegvcfs/main.nf | 15 +- modules/nf-core/gatk4/combinegvcfs/meta.yml | 78 ++- .../gatk4/combinegvcfs/tests/main.nf.test | 31 +- .../combinegvcfs/tests/main.nf.test.snap | 43 +- .../createsequencedictionary/environment.yml | 8 +- .../gatk4/createsequencedictionary/main.nf | 6 +- .../gatk4/createsequencedictionary/meta.yml | 37 +- .../tests/main.nf.test.snap | 20 +- .../gatk4/haplotypecaller/environment.yml | 8 +- modules/nf-core/gatk4/haplotypecaller/main.nf | 7 +- .../nf-core/gatk4/haplotypecaller/meta.yml | 178 ++--- .../gatk4/haplotypecaller/tests/main.nf.test | 86 +-- .../haplotypecaller/tests/main.nf.test.snap | 96 +-- .../gatk4/indexfeaturefile/environment.yml | 8 +- .../nf-core/gatk4/indexfeaturefile/main.nf | 4 +- .../nf-core/gatk4/indexfeaturefile/meta.yml | 43 +- .../gatk4/indexfeaturefile/tests/main.nf.test | 8 +- .../indexfeaturefile/tests/main.nf.test.snap | 36 +- .../gatk4/intervallisttools/environment.yml | 8 +- .../nf-core/gatk4/intervallisttools/main.nf | 6 +- .../nf-core/gatk4/intervallisttools/meta.yml | 51 +- .../intervallisttools/tests/main.nf.test.snap | 20 +- .../nf-core/gatk4/mergevcfs/environment.yml | 8 +- modules/nf-core/gatk4/mergevcfs/main.nf | 6 +- modules/nf-core/gatk4/mergevcfs/meta.yml | 66 +- .../gatk4/mergevcfs/tests/main.nf.test | 3 + .../gatk4/mergevcfs/tests/main.nf.test.snap | 27 +- .../gatk4/splitncigarreads/environment.yml | 8 +- .../nf-core/gatk4/splitncigarreads/main.nf | 19 +- .../nf-core/gatk4/splitncigarreads/meta.yml | 105 +-- .../gatk4/splitncigarreads/tests/main.nf.test | 42 +- .../splitncigarreads/tests/main.nf.test.snap | 33 +- .../gatk4/variantfiltration/environment.yml | 8 +- .../nf-core/gatk4/variantfiltration/main.nf | 6 +- .../nf-core/gatk4/variantfiltration/meta.yml | 110 ++-- .../variantfiltration/tests/main.nf.test.snap | 16 +- modules/nf-core/gffread/environment.yml | 4 +- modules/nf-core/gffread/meta.yml | 84 ++- modules/nf-core/gffread/tests/main.nf.test | 3 +- modules/nf-core/gunzip/environment.yml | 11 +- modules/nf-core/gunzip/main.nf | 31 +- modules/nf-core/gunzip/meta.yml | 38 +- modules/nf-core/gunzip/tests/main.nf.test | 85 +++ .../nf-core/gunzip/tests/main.nf.test.snap | 109 ++- modules/nf-core/gunzip/tests/nextflow.config | 5 + modules/nf-core/mosdepth/environment.yml | 6 +- modules/nf-core/mosdepth/main.nf | 4 +- modules/nf-core/mosdepth/meta.yml | 214 ++++-- modules/nf-core/mosdepth/tests/main.nf.test | 50 +- .../nf-core/mosdepth/tests/main.nf.test.snap | 132 ++-- .../picard/markduplicates/environment.yml | 2 + .../nf-core/samtools/faidx/environment.yml | 10 +- modules/nf-core/samtools/faidx/main.nf | 4 +- modules/nf-core/samtools/faidx/meta.yml | 85 ++- .../samtools/faidx/tests/main.nf.test.snap | 50 +- .../nf-core/samtools/merge/environment.yml | 8 +- modules/nf-core/samtools/merge/main.nf | 4 +- modules/nf-core/samtools/merge/meta.yml | 117 ++-- .../samtools/merge/tests/main.nf.test.snap | 32 +- .../nf-core/snpeff/download/environment.yml | 4 +- modules/nf-core/snpeff/download/main.nf | 9 +- modules/nf-core/snpeff/download/meta.yml | 44 +- .../snpeff/download/tests/main.nf.test | 51 ++ .../snpeff/download/tests/main.nf.test.snap | 100 +++ modules/nf-core/snpeff/snpeff/environment.yml | 4 +- modules/nf-core/snpeff/snpeff/meta.yml | 96 ++- .../nf-core/snpeff/snpeff/tests/main.nf.test | 5 +- .../snpeff/snpeff/tests/nextflow.config | 3 +- modules/nf-core/star/align/environment.yml | 2 + modules/nf-core/star/align/main.nf | 4 +- .../star/genomegenerate/environment.yml | 11 +- modules/nf-core/star/genomegenerate/main.nf | 4 +- modules/nf-core/star/genomegenerate/meta.yml | 57 +- .../star/genomegenerate/tests/main.nf.test | 39 +- .../genomegenerate/tests/main.nf.test.snap | 186 ++++-- .../nf-core/tabix/bgziptabix/environment.yml | 7 +- modules/nf-core/tabix/bgziptabix/main.nf | 11 +- modules/nf-core/tabix/bgziptabix/meta.yml | 70 +- .../tabix/bgziptabix/tests/main.nf.test | 35 +- .../tabix/bgziptabix/tests/main.nf.test.snap | 117 +++- modules/nf-core/tabix/tabix/environment.yml | 7 +- modules/nf-core/tabix/tabix/main.nf | 11 +- modules/nf-core/tabix/tabix/meta.yml | 55 +- .../nf-core/tabix/tabix/tests/main.nf.test | 44 +- .../tabix/tabix/tests/main.nf.test.snap | 111 ++-- modules/nf-core/untar/environment.yml | 11 +- modules/nf-core/untar/main.nf | 61 +- modules/nf-core/untar/meta.yml | 46 +- modules/nf-core/untar/tests/main.nf.test | 44 +- modules/nf-core/untar/tests/main.nf.test.snap | 152 ++++- .../nf-core/vcf_annotate_ensemblvep/main.nf | 2 +- .../nf-core/vcf_annotate_ensemblvep/meta.yml | 2 +- 163 files changed, 6621 insertions(+), 2280 deletions(-) create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/tags.yml create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config create mode 100644 modules/nf-core/gunzip/tests/nextflow.config create mode 100644 modules/nf-core/snpeff/download/tests/main.nf.test create mode 100644 modules/nf-core/snpeff/download/tests/main.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index bcee8917..584d5a61 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -63,14 +63,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Dependency | Old version | New version | | ---------- | ----------- | ----------- | -| bcftools | 1.17 | 1.18 | +| bcftools | 1.17 | 1.20 | | bedtools | 2.31.0 | 2.31.1 | | fastqc | 0.11.9 | 0.12.1 | -| mosdepth | 0.3.3 | 0.3.6 | +| gatk | 4.2.6.1 | 4.6.1.0 | +| mosdepth | 0.3.3 | 0.3.10 | | multiqc | 1.15 | 1.18 | | picard | 3.1.0 | 3.3.0 | | samtools | 1.17 | 1.21 | | star | 2.7.10a | 2.7.11b | +| vep | 111.0 | 113.0 | ## [1.0.0] nfcore/rnavar - 2022/06/20 diff --git a/modules.json b/modules.json index 37894473..efc246a5 100755 --- a/modules.json +++ b/modules.json @@ -7,32 +7,32 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "bcftools/concat": { "branch": "master", - "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bcftools/pluginscatter": { "branch": "master", - "git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bcftools/sort": { "branch": "master", - "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["vcf_annotate_ensemblvep", "vcf_annotate_snpeff"] }, "bedtools/merge": { "branch": "master", - "git_sha": "a5377837fe9013bde89de8689829e83e84086536", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", - "git_sha": "571a5feac4c9ce0a8df0bc15b94230e7f3e8db47", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "cat/fastq": { @@ -42,87 +42,87 @@ }, "ensemblvep/download": { "branch": "master", - "git_sha": "3db4f8488315cd7d7cf3fcb64251f6603210e831", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", - "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "fastqc": { "branch": "master", - "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/applybqsr": { "branch": "master", - "git_sha": "af273ea6618c50e82c372abe18b0a225e84fe6f7", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/baserecalibrator": { "branch": "master", - "git_sha": "8a223e11d4e6deb36484e01891eae9c1cacb5f5d", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "d3f215802f696f7993f25c759781d2db91232015", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/combinegvcfs": { "branch": "master", - "git_sha": "fe3d7aac1b62efe4fd05cc9629d192e9cdfc3ccb", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/indexfeaturefile": { "branch": "master", - "git_sha": "108e1f5bafc045ac19890852a41e8d95ae12aa67", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "afb604624abcc2fc67a43d70a2de369a50d16105", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/mergevcfs": { "branch": "master", - "git_sha": "194fca815cf594646e638fa5476acbcc296f1850", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/splitncigarreads": { "branch": "master", - "git_sha": "1e15ad71d9022293985dd02e24186e5e496a0b3c", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gatk4/variantfiltration": { "branch": "master", - "git_sha": "00409369b2aff69bded4f0a9e7a80e17d933b426", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gffread": { "branch": "master", - "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "3a5fef109d113b4997c9822198664ca5f2716208", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "e0616fba0919adb190bfe070d17fb12d76ba3a26", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "multiqc": { @@ -132,7 +132,7 @@ }, "picard/markduplicates": { "branch": "master", - "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["bam_markduplicates_picard"] }, "samtools/convert": { @@ -142,7 +142,7 @@ }, "samtools/faidx": { "branch": "master", - "git_sha": "f153f1f10e1083c49935565844cccb7453021682", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/flagstat": { @@ -162,7 +162,7 @@ }, "samtools/merge": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/sort": { @@ -177,22 +177,22 @@ }, "snpeff/download": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "2f3db6f45147ebbb56b371536e31bdf622b5bfee", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "star/align": { "branch": "master", - "git_sha": "59f52afcd8eabf15e8713095207272624171c65a", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["fastq_align_star", "modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] }, "star/indexversion": { @@ -202,12 +202,12 @@ }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "09d3c8c29b31a2dfd610305b10550f0e1dbcd4a9", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules", "vcf_annotate_snpeff"] }, "tabix/tabix": { "branch": "master", - "git_sha": "9502adb23c0b97ed8e616bbbdfa73b4585aec9a1", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules", "vcf_annotate_ensemblvep"] }, "umitools/extract": { @@ -217,7 +217,7 @@ }, "untar": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", "installed_by": ["modules"] } } @@ -261,7 +261,7 @@ }, "vcf_annotate_ensemblvep": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", + "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e", "installed_by": ["subworkflows"] }, "vcf_annotate_snpeff": { diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index e0abc8d2..b276efd9 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,7 +1,7 @@ -name: bcftools_annotate +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index 64e7ec76..b6b73309 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -4,14 +4,18 @@ process BCFTOOLS_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: - tuple val(meta), path(input), path(index), path(annotations), path(annotations_index), path(header_lines) + tuple val(meta), path(input), path(index), path(annotations), path(annotations_index) + path(header_lines) + path(rename_chrs) output: tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -22,17 +26,23 @@ process BCFTOOLS_ANNOTATE { def prefix = task.ext.prefix ?: "${meta.id}" def header_file = header_lines ? "--header-lines ${header_lines}" : '' def annotations_file = annotations ? "--annotations ${annotations}" : '' + def rename_chrs_file = rename_chrs ? "--rename-chrs ${rename_chrs}" : '' def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index_command = !index ? "bcftools index $input" : '' + if ("$input" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ + $index_command + bcftools \\ annotate \\ $args \\ $annotations_file \\ + $rename_chrs_file \\ $header_file \\ --output ${prefix}.${extension} \\ --threads $task.cpus \\ @@ -52,10 +62,16 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" - + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" + """ ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index f3aa463b..fd2c91c7 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -13,41 +13,67 @@ tools: documentation: https://samtools.github.io/bcftools/bcftools.html#annotate doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Query VCF or BCF file, can be either uncompressed or compressed - - index: - type: file - description: Index of the query VCF or BCF file - - annotations: - type: file - description: Bgzip-compressed file with annotations - - annotations_index: - type: file - description: Index of the annotations file - - header_lines: - type: file - description: Contains lines to append to the output VCF header + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Query VCF or BCF file, can be either uncompressed or compressed + - index: + type: file + description: Index of the query VCF or BCF file + - annotations: + type: file + description: Bgzip-compressed file with annotations + - annotations_index: + type: file + description: Index of the annotations file + - - header_lines: + type: file + description: Contains lines to append to the output VCF header + - - rename_chrs: + type: file + description: Rename annotations according to this file containing "old_name new_name\n" pairs separated by whitespaces, each on a separate line. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed annotated VCF file - pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Compressed annotated VCF file + pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/annotate/tests/bcf.config b/modules/nf-core/bcftools/annotate/tests/bcf.config index b8496b33..79d26779 100644 --- a/modules/nf-core/bcftools/annotate/tests/bcf.config +++ b/modules/nf-core/bcftools/annotate/tests/bcf.config @@ -1,6 +1,4 @@ process { - withName: 'BCFTOOLS_ANNOTATE' { - ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type u" - ext.prefix = { "${meta.id}_ann" } - } -} \ No newline at end of file + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type u" + ext.prefix = { "${meta.id}_ann" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test b/modules/nf-core/bcftools/annotate/tests/main.nf.test index 9abf9475..fd6d2cd3 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test @@ -9,20 +9,22 @@ nextflow_process { tag "bcftools" tag "bcftools/annotate" - test("sarscov2 - [vcf, tbi, vcf2, tbi2, []] - vcf_output") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output") { config "./vcf.config" when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] + input[1] = [] + input[2] = [] """ } } @@ -33,34 +35,202 @@ nextflow_process { { assert snapshot( process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, process.out.versions - ).match("vcf") } + ).match() } ) } } + test("sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output") { - test("sarscov2 - [vcf, [], [], [], header] - bcf_output") { + config "./vcf.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match() } + ) + } + + } + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], header, [] - bcf_output") { config "./bcf.config" when { process { """ - vcf = Channel.of([ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), [], - [], - [] - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = Channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, + process.out.versions + ).match("bcf") } + ) + } - header = Channel.of( - '##INFO=', - '##INFO=' - ) - .collectFile(name:"headers.vcf", newLine:true) + } + + test("sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index") { - input[0] = vcf.combine(header) + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = Channel.of( + '##INFO=', + '##INFO=' + ).collectFile(name:"headers.vcf", newLine:true) + input[2] = Channel.of('MT192765.1 renamed').collectFile(name:"rename.txt", newLine:true) """ } } @@ -68,16 +238,17 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).LinesGzip.contains("##contig=")}, { assert snapshot( process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }}, process.out.versions - ).match("bcf") } + ).match() } ) } } - test("sarscov2 - [vcf, tbi, vcf2, tbi2, []] - stub") { + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub") { config "./vcf.config" options "-stub" @@ -85,13 +256,107 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [] + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()}, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) ] + input[1] = [] + input[2] = [] """ } } @@ -99,10 +364,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match("stub") } + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } ) } } -} +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap index 72b06878..16828b6c 100644 --- a/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/annotate/tests/main.nf.test.snap @@ -1,4 +1,37 @@ { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:02:05.809043894" + }, "bcf": { "content": [ [ @@ -11,16 +44,16 @@ ] ], [ - "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-03T09:21:58.526449656" + "timestamp": "2024-06-12T16:39:33.331888" }, - "vcf": { + "sarscov2 - [vcf, [], annotation, annotation_tbi], [], [] - vcf_output": { "content": [ [ [ @@ -32,16 +65,37 @@ ] ], [ - "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-02T16:47:47.127427579" + "timestamp": "2024-11-06T14:01:32.326248064" }, - "stub": { + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_output": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:01:17.821142466" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -54,7 +108,31 @@ ] ], "1": [ - "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "vcf": [ [ @@ -66,14 +144,266 @@ ] ], "versions": [ - "versions.yml:md5,ea2b798edb5c1c0d46938f313a97a901" + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:03:12.574479421" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:02:38.89910979" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:02:49.803045339" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:03:00.654715777" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T14:01:45.446114465" + }, + "sarscov2 - [vcf, [], annotation, annotation_tbi], header, rename_chrs - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-06T13:58:14.280394724" + }, + "sarscov2 - [vcf, tbi, annotation, annotation_tbi], [], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + "versions.yml:md5,ea53f98610d42597cf384ff1fa3eb204" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-02T16:43:43.707474961" + "timestamp": "2024-11-06T14:01:55.70445216" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/annotate/tests/vcf.config b/modules/nf-core/bcftools/annotate/tests/vcf.config index cb809f61..611868d5 100644 --- a/modules/nf-core/bcftools/annotate/tests/vcf.config +++ b/modules/nf-core/bcftools/annotate/tests/vcf.config @@ -1,6 +1,4 @@ process { - withName: 'BCFTOOLS_ANNOTATE' { - ext.prefix = { "${meta.id}_vcf" } - ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type z" - } + ext.args = "-x ID,INFO/DP,FORMAT/DP --output-type z" + ext.prefix = { "${meta.id}_vcf" } } diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config new file mode 100644 index 00000000..2fd9a225 --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..512c1dfb --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index=csi --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..7feb5ebb --- /dev/null +++ b/modules/nf-core/bcftools/annotate/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.args = "--output-type z --write-index=tbi --no-version" + ext.prefix = { "${meta.id}_vcf" } +} diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index ff0200df..b276efd9 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,7 +1,7 @@ -name: bcftools_concat +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index d64640b3..8a0328cf 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -4,15 +4,17 @@ process BCFTOOLS_CONCAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcfs), path(tbi) output: - tuple val(meta), path("*.gz"), emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.${extension}") , emit: vcf + tuple val(meta), path("${prefix}.${extension}.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.${extension}.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,9 +22,18 @@ process BCFTOOLS_CONCAT { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name } + def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") || tbi_names.contains(vcf.name + ".csi") ? "" : "tabix ${vcf}" }.join("\n ") + extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" """ + ${create_input_index} + bcftools concat \\ - --output ${prefix}.vcf.gz \\ + --output ${prefix}.${extension} \\ $args \\ --threads $task.cpus \\ ${vcfs} @@ -34,9 +45,23 @@ process BCFTOOLS_CONCAT { """ stub: + def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" + extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" + """ - echo "" | gzip > ${prefix}.vcf.gz + ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index 91cb54d5..3d12673a 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -13,36 +13,65 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbi: - type: list - description: | - List containing 2 or more index files (optional) - e.g. [ 'file1.tbi', 'file2.tbi' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbi: + type: list + description: | + List containing 2 or more index files (optional) + e.g. [ 'file1.tbi', 'file2.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF concatenated output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}.tbi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}.csi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index d5d9f787..cb4642b2 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -9,22 +9,23 @@ nextflow_process { tag "bcftools" tag "bcftools/concat" - config "./nextflow.config" - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") { + + config "./nextflow.config" when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) ] ] """ @@ -40,16 +41,130 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], []]") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { + + config "./vcf_gz_index.config" when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + + test("homo_sapiens - [[vcf1, vcf2], []]") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [] ] @@ -66,21 +181,23 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + config "./nextflow.config" options "-stub" + when { process { """ - input[0] = [ + input[0] = [ [ id:'test3' ], // meta map [ - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ], [ - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) ] ] """ @@ -96,4 +213,104 @@ nextflow_process { } -} + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test3' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 90d3fc06..4f6cf8ab 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,5 +1,212 @@ { - "sarscov2 - [[vcf1, vcf2], []]": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T11:03:36.575719606" + }, + "homo_sapiens - [[vcf1, vcf2], []]": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-27T13:59:01.079183608" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-27T13:53:58.83709764" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T11:04:11.178539482" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T11:03:44.618596639" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ { "0": [ @@ -7,32 +214,75 @@ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3.vcf:md5,5f6796c3ae109a1a5b87353954693f5a" ] ], "1": [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3.vcf:md5,5f6796c3ae109a1a5b87353954693f5a" ] ], "versions": [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-27T13:52:50.457367833" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-03T13:22:49.766749302" + "timestamp": "2024-09-26T11:03:21.607274757" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -40,32 +290,54 @@ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], "vcf": [ [ { "id": "test3" }, - "test3.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-03T13:22:41.119912312" + "timestamp": "2024-09-26T11:04:27.332133878" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -73,29 +345,51 @@ { "id": "test3" }, - "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + + ], + "2": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ], + "csi": [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + ], "vcf": [ [ { "id": "test3" }, - "test3.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "test3_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ - "versions.yml:md5,24ae05eb858733b40fbd3f89743a6d09" + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-03T13:22:59.90466392" + "timestamp": "2024-09-26T11:04:19.745768656" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/concat/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 42e97daa..b276efd9 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -1,7 +1,7 @@ -name: bcftools_pluginscatter +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginscatter/main.nf b/modules/nf-core/bcftools/pluginscatter/main.nf index 9f52e947..b3b6691d 100644 --- a/modules/nf-core/bcftools/pluginscatter/main.nf +++ b/modules/nf-core/bcftools/pluginscatter/main.nf @@ -4,8 +4,8 @@ process BCFTOOLS_PLUGINSCATTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf), path(tbi) @@ -17,6 +17,8 @@ process BCFTOOLS_PLUGINSCATTER { output: tuple val(meta), path("*{vcf,vcf.gz,bcf,bcf.gz}") , emit: scatter + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -57,11 +59,23 @@ process BCFTOOLS_PLUGINSCATTER { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index_1 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}0.${extension}.${index}" : "" + def create_index_2 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}1.${extension}.${index}" : "" + def create_index_3 = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}2.${extension}.${index}" : "" """ - touch ${prefix}1.${extension} - touch ${prefix}2.${extension} - touch ${prefix}3.${extension} + ${create_cmd} ${prefix}0.${extension} + ${create_cmd} ${prefix}1.${extension} + ${create_cmd} ${prefix}2.${extension} + + ${create_index_1} + ${create_index_2} + ${create_index_3} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/pluginscatter/meta.yml b/modules/nf-core/bcftools/pluginscatter/meta.yml index 1a716ead..5a31dacc 100644 --- a/modules/nf-core/bcftools/pluginscatter/meta.yml +++ b/modules/nf-core/bcftools/pluginscatter/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bcftools_pluginscatter" description: Split VCF by chunks or regions, creating multiple VCFs. @@ -15,57 +14,81 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The input VCF to scatter - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - type: file - description: Optional index of the input VCF - pattern: "*.tbi" - - sites_per_chunk: - type: integer - description: | - How many variants should be in each output file - Either this or `scatter` or `scatter_file` have to be given - - scatter: - type: string - description: | - A comma delimited list of regions to scatter into - Either this or `sites_per_chunk` or `scatter_file` have to be given - - scatter_file: - type: file - description: | - A file containing a region on each line with an optional second column containing the filename - Either this or `sites_per_chunk` or `scatter` have to be given - - regions: - type: file - description: Optional file containing the regions to work on - pattern: "*.bed" - - targets: - type: file - description: Optional file containing the regions to work on (but streams instead of index-jumping) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The input VCF to scatter + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: Optional index of the input VCF + pattern: "*.tbi" + - - sites_per_chunk: + type: integer + description: | + How many variants should be in each output file + Either this or `scatter` or `scatter_file` have to be given + - - scatter: + type: string + description: | + A comma delimited list of regions to scatter into + Either this or `sites_per_chunk` or `scatter_file` have to be given + - - scatter_file: + type: file + description: | + A file containing a region on each line with an optional second column containing the filename + Either this or `sites_per_chunk` or `scatter` have to be given + - - regions: + type: file + description: Optional file containing the regions to work on + pattern: "*.bed" + - - targets: + type: file + description: Optional file containing the regions to work on (but streams instead + of index-jumping) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scatter: - type: file - description: The resulting files of the scattering - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: The resulting files of the scattering + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test new file mode 100644 index 00000000..ce66336e --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test @@ -0,0 +1,415 @@ +nextflow_process { + + name "Test Process BCFTOOLS_PLUGINSCATTER" + script "../main.nf" + process "BCFTOOLS_PLUGINSCATTER" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/pluginscatter" + + test("homo_sapiens - sites per chunk") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index") }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index_csi") }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.csi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { meta, files -> files.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match("vcf_gz_index_tbi") }, + { assert process.out.tbi[0][1][0] =~ ".*/test_vcf0.vcf.gz.tbi" } + ) + } + + } + + test("homo_sapiens - scatter") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = "chr21" + input[3] = [] + input[4] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter file") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = Channel.of("chr21:6000000-41743940\tfile1", "chr21:41743941-46661900\tfile2") + .collectFile(name:"scatter.tsv", newLine:true) + input[4] = [] + input[5] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = "chr21" + input[3] = [] + input[4] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - scatter file - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = Channel.of("chr21:6000000-41743940\tfile1", "chr21:41743941-46661900\tfile2") + .collectFile(name:"scatter.tsv", newLine:true) + input[4] = [] + input[5] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1][0] =~ ".*/test_vcf0.vcf.gz.csi" } + ) + } + + } + + test("homo_sapiens - sites per chunk - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = 100 + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1][0] =~ ".*/test_vcf0.vcf.gz.tbi" } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap new file mode 100644 index 00000000..3168f91b --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap @@ -0,0 +1,623 @@ +{ + "homo_sapiens - 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sites per chunk - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:10:12.470969127" + }, + "homo_sapiens - scatter file": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "testfile1.vcf:md5,68e3660b6d619163692edad8ba7dd179", + "testfile2.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "testfile1.vcf:md5,68e3660b6d619163692edad8ba7dd179", + "testfile2.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:40:25.33705743" + }, + "homo_sapiens - scatter file - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:09:41.478631999" + }, + "homo_sapiens - sites per chunk - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:09:59.976006697" + }, + "vcf_gz_index_tbi": { + "content": [ + [ + + ], + [ + + ], + [ + [ + "test_vcf0.vcf.gz.tbi", + "test_vcf1.vcf.gz.tbi", + "test_vcf2.vcf.gz.tbi", + "test_vcf3.vcf.gz.tbi", + "test_vcf4.vcf.gz.tbi", + "test_vcf5.vcf.gz.tbi", + "test_vcf6.vcf.gz.tbi", + "test_vcf7.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-06T10:27:48.127273006" + }, + "homo_sapiens - sites per chunk - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf1.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_vcf2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "tbi": [ + [ + { + "id": "test" + }, + [ + "test_vcf0.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf1.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_vcf2.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:10:37.027506409" + }, + "vcf_gz_index": { + "content": [ + [ + + ], + [ + [ + "test_vcf0.vcf.gz.csi", + "test_vcf1.vcf.gz.csi", + "test_vcf2.vcf.gz.csi", + "test_vcf3.vcf.gz.csi", + "test_vcf4.vcf.gz.csi", + "test_vcf5.vcf.gz.csi", + "test_vcf6.vcf.gz.csi", + "test_vcf7.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-06T10:24:46.201810185" + }, + "vcf_gz_index_csi": { + "content": [ + [ + + ], + [ + [ + "test_vcf0.vcf.gz.csi", + "test_vcf1.vcf.gz.csi", + "test_vcf2.vcf.gz.csi", + "test_vcf3.vcf.gz.csi", + "test_vcf4.vcf.gz.csi", + "test_vcf5.vcf.gz.csi", + "test_vcf6.vcf.gz.csi", + "test_vcf7.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-06T10:27:20.636624541" + }, + "homo_sapiens - scatter": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "testchr21.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + "testchr21.vcf:md5,68e3660b6d619163692edad8ba7dd179" + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T14:40:12.621284696" + }, + "homo_sapiens - sites per chunk - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ], + "csi": [ + + ], + "scatter": [ + [ + { + "id": "test" + }, + [ + "test0.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test1.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + "test2.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "tbi": [ + + ], + "versions": [ + "versions.yml:md5,9a7bd26da80241e2116a237c7704eabf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T15:08:56.987822348" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config b/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config new file mode 100644 index 00000000..aa8d093b --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = '--no-version' +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/tags.yml b/modules/nf-core/bcftools/pluginscatter/tests/tags.yml new file mode 100644 index 00000000..60cebd43 --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/pluginscatter: + - "modules/nf-core/bcftools/pluginscatter/**" diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config new file mode 100644 index 00000000..7dd696ee --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..aebffb6f --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" +} diff --git a/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..b192ae7d --- /dev/null +++ b/modules/nf-core/bcftools/pluginscatter/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" +} diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 89cf911d..b276efd9 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,7 +1,7 @@ -name: bcftools_sort +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::bcftools=1.18 + - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/sort/main.nf b/modules/nf-core/bcftools/sort/main.nf index 246148d6..7d4c9b8e 100644 --- a/modules/nf-core/bcftools/sort/main.nf +++ b/modules/nf-core/bcftools/sort/main.nf @@ -4,15 +4,17 @@ process BCFTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0': - 'biocontainers/bcftools:1.18--h8b25389_0' }" + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_0': + 'biocontainers/bcftools:1.20--h8b25389_0' }" input: tuple val(meta), path(vcf) output: - tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf - path "versions.yml" , emit: versions + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -49,9 +51,16 @@ process BCFTOOLS_SORT { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + """ ${create_cmd} ${prefix}.${extension} + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index 84747c6d..f7a6eff1 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -12,30 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF/BCF file to be sorted - pattern: "*.{vcf.gz,vcf,bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file to be sorted + pattern: "*.{vcf.gz,vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Sorted VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Sorted VCF file + pattern: "*.{vcf.gz}" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test b/modules/nf-core/bcftools/sort/tests/main.nf.test index 8a496dda..b9bdd76a 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] """ } @@ -30,6 +30,96 @@ nextflow_process { } + test("sarscov2 - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + test("sarscov2 - vcf - stub") { options "-stub" when { @@ -37,7 +127,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ] """ } @@ -51,4 +141,82 @@ nextflow_process { } } -} + + test("sarscov2 - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap index 6200cc42..f38272cb 100644 --- a/modules/nf-core/bcftools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/sort/tests/main.nf.test.snap @@ -1,4 +1,59 @@ { + "sarscov2 - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:06:05.201680777" + }, "vcf": { "content": [ { @@ -11,7 +66,19 @@ ] ], "1": [ - "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -22,15 +89,187 @@ ] ], "versions": [ - "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:04:43.889971134" + }, + "sarscov2 - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:04:55.385964497" + }, + "sarscov2 - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:06.662818922" + }, + "sarscov2 - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:40.012912381" + }, + "sarscov2 - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-02T16:55:21.237927554" + "timestamp": "2024-06-05T12:05:52.405673587" }, "sarscov2 - vcf - stub": { "content": [ @@ -44,7 +283,19 @@ ] ], "1": [ - "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ], + "csi": [ + + ], + "tbi": [ + ], "vcf": [ [ @@ -55,14 +306,45 @@ ] ], "versions": [ - "versions.yml:md5,622bd32d4ff0fac3360cd534ae0f0168" + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-05T12:05:29.117946461" + }, + "sarscov2 - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + [ + + ], + [ + [ + { + "id": "test" + }, + "test_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,2c9f26ca356ef71199c3a7d1742974cb" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" }, - "timestamp": "2024-05-03T12:32:50.506309198" + "timestamp": "2024-06-05T12:05:17.217274984" } } \ No newline at end of file diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config new file mode 100644 index 00000000..aacd1346 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config new file mode 100644 index 00000000..640eb0ba --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_csi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi" +} diff --git a/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config new file mode 100644 index 00000000..589a50c6 --- /dev/null +++ b/modules/nf-core/bcftools/sort/tests/vcf_gz_index_tbi.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi" +} diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml index 99707878..45c307b0 100644 --- a/modules/nf-core/bedtools/merge/environment.yml +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -1,7 +1,7 @@ -name: bedtools_merge +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index d7463e3d..6da54205 100644 --- a/modules/nf-core/bedtools/merge/meta.yml +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -1,5 +1,6 @@ name: bedtools_merge -description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +description: combines overlapping or “book-ended” features in an interval file into + a single feature which spans all of the combined features. keywords: - bed - merge @@ -11,30 +12,33 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Overlapped bed file with combined features - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/merge/tests/main.nf.test b/modules/nf-core/bedtools/merge/tests/main.nf.test index 95dba8e5..2959d6b9 100644 --- a/modules/nf-core/bedtools/merge/tests/main.nf.test +++ b/modules/nf-core/bedtools/merge/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] """ } diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml index 87b2e425..45c307b0 100644 --- a/modules/nf-core/bedtools/sort/environment.yml +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -1,7 +1,7 @@ -name: bedtools_sort +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 7c915f5f..313698f1 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -11,35 +11,38 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BED/BEDGRAPH - pattern: "*.{bed|bedGraph}" - - genome_file: - type: file - description: | - Optional reference genome 2 column file that defines the expected chromosome order. - pattern: "*.{fai,txt,chromsizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" + - - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order. + pattern: "*.{fai,txt,chromsizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: Sorted output file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Sorted output file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index 2ea8642f..cac59e88 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -1,7 +1,7 @@ -name: ensemblvep_download +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::ensembl-vep=111.0 + - bioconda::ensembl-vep=113.0 diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf index f9e025a5..0664a2df 100644 --- a/modules/nf-core/ensemblvep/download/main.nf +++ b/modules/nf-core/ensemblvep/download/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_DOWNLOAD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" input: tuple val(meta), val(assembly), val(species), val(cache_version) diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index a4277ad7..8da9621c 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_download -description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. +description: Ensembl Variant Effect Predictor (VEP). The cache downloading options + are controlled through `task.ext.args`. keywords: - annotation - cache @@ -12,33 +13,40 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: string - description: | - Genome assembly - - species: - type: string - description: | - Specie - - cache_version: - type: string - description: | - cache version + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: string + description: | + Genome assembly + - species: + type: string + description: | + Specie + - cache_version: + type: string + description: | + cache version output: - cache: - type: file - description: cache - pattern: "*" + - meta: + type: file + description: cache + pattern: "*" + - prefix: + type: file + description: cache + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test index 760c9d56..a5585995 100644 --- a/modules/nf-core/ensemblvep/download/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"111_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -41,7 +41,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"111_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap index 6ea596fb..706bd28f 100644 --- a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap @@ -5,282 +5,282 @@ "0": [ [ { - 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"chr_synonyms.txt:md5,8a6fce00cc7817ec727c49b7954f10bc", - "info.txt:md5,33ccb74a030a9a345051628c337cb8af" + "chr_synonyms.txt:md5,d390f0bcc6fec9786bc66b75f2d4390b", + "info.txt:md5,249c88c7a71464e048cca0c4b2a21198" ] ] ] ] ], "versions": [ - "versions.yml:md5,954fd177c394ba167d575a6aac47390b" + "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-15T17:20:01.921038" + "timestamp": "2024-10-21T09:09:48.574969389" }, "celegans - download - stub": { "content": [ @@ -288,7 +288,7 @@ "0": [ [ { - "id": "111_WBcel235" + "id": "113_WBcel235" }, [ @@ -296,12 +296,12 @@ ] ], "1": [ - "versions.yml:md5,954fd177c394ba167d575a6aac47390b" + "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9" ], "cache": [ [ { - "id": "111_WBcel235" + "id": "113_WBcel235" }, [ @@ -309,14 +309,14 @@ ] ], "versions": [ - "versions.yml:md5,954fd177c394ba167d575a6aac47390b" + "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-15T18:09:54.909036" + "timestamp": "2024-10-21T09:10:03.728940123" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config index 882bce41..0a4ae1a6 100644 --- a/modules/nf-core/ensemblvep/download/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config @@ -1,5 +1,5 @@ params { - vep_cache_version = "111" + vep_cache_version = "113" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 91457c05..cac59e88 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,7 +1,7 @@ -name: ensemblvep_vep +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::ensembl-vep=111.0 + - bioconda::ensembl-vep=113.0 diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf index e82471aa..7bd74fc4 100644 --- a/modules/nf-core/ensemblvep/vep/main.nf +++ b/modules/nf-core/ensemblvep/vep/main.nf @@ -4,8 +4,8 @@ process ENSEMBLVEP_VEP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ensembl-vep:111.0--pl5321h2a3209d_0' : - 'biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0' }" + 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' : + 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }" input: tuple val(meta), path(vcf), path(custom_extra_files) @@ -17,22 +17,25 @@ process ENSEMBLVEP_VEP { path extra_files output: - tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf - tuple val(meta), path("*.tab.gz") , optional:true, emit: tab - tuple val(meta), path("*.json.gz") , optional:true, emit: json - path "*.summary.html" , optional:true, emit: report - path "versions.yml" , emit: versions + tuple val(meta), path("*.vcf.gz") , optional:true, emit: vcf + tuple val(meta), path("*.vcf.gz.tbi") , optional:true, emit: tbi + tuple val(meta), path("*.tab.gz") , optional:true, emit: tab + tuple val(meta), path("*.json.gz") , optional:true, emit: json + path "*.html" , optional:true, emit: report + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf' def compress_cmd = args.contains("--compress_output") ? '' : '--compress_output bgzip' def prefix = task.ext.prefix ?: "${meta.id}" def dir_cache = cache ? "\${PWD}/${cache}" : "/.vep" def reference = fasta ? "--fasta $fasta" : "" + def create_index = file_extension == "vcf" ? "tabix ${args2} ${prefix}.${file_extension}.gz" : "" """ vep \\ -i $vcf \\ @@ -47,24 +50,28 @@ process ENSEMBLVEP_VEP { --dir_cache $dir_cache \\ --fork $task.cpus + ${create_index} cat <<-END_VERSIONS > versions.yml "${task.process}": ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" + def file_extension = args.contains("--vcf") ? 'vcf' : args.contains("--json")? 'json' : args.contains("--tab")? 'tab' : 'vcf' + def create_index = file_extension == "vcf" ? "touch ${prefix}.${file_extension}.gz.tbi" : "" """ - echo "" | gzip > ${prefix}.vcf.gz - echo "" | gzip > ${prefix}.tab.gz - echo "" | gzip > ${prefix}.json.gz - touch ${prefix}.summary.html + echo "" | gzip > ${prefix}.${file_extension}.gz + ${create_index} + touch ${prefix}_summary.html cat <<-END_VERSIONS > versions.yml "${task.process}": ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//') + tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index d8ff8d14..cbb194fd 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_vep -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled + through `task.ext.args`. keywords: - annotation - vcf @@ -13,75 +14,105 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) - - genome: - type: string - description: | - which genome to annotate with - - species: - type: string - description: | - which species to annotate with - - cache_version: - type: integer - description: | - which version of the cache to annotate with - - cache: - type: file - description: | - path to VEP cache (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" - - extra_files: - type: file - description: | - path to file(s) needed for plugins (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) + - - genome: + type: string + description: | + which genome to annotate with + - - species: + type: string + description: | + which species to annotate with + - - cache_version: + type: integer + description: | + which version of the cache to annotate with + - - cache: + type: file + description: | + path to VEP cache (optional) + - - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" + - - extra_files: + type: file + description: | + path to file(s) needed for plugins (optional) output: - vcf: - type: file - description: | - annotated vcf (optional) - pattern: "*.ann.vcf.gz" + - meta: + type: map + description: | + Map with sample information + - "*.vcf.gz": + type: file + description: | + annotated vcf (optional) + pattern: "*.vcf.gz" + - tbi: + - meta: + type: map + description: | + Map with sample information + - "*.vcf.gz.tbi": + type: file + description: | + annotated vcf index (optional) + pattern: "*.vcf.gz.tbi" - tab: - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" + - meta: + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + - "*.tab.gz": + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" - json: - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" + - meta: + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + - "*.json.gz": + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" - report: - type: file - description: VEP report file - pattern: "*.html" + - "*.html": + type: file + description: VEP report file + pattern: "*.html" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test index 4aff84a3..e5b20af7 100644 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test @@ -11,7 +11,7 @@ nextflow_process { tag "ensemblvep/vep" tag "ensemblvep/download" - test("test_ensemblvep_vep_fasta_vcf") { + test("test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)") { config "./vcf.config" setup { @@ -21,7 +21,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"111_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -55,8 +55,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match() }, - { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.2") } + { assert snapshot( + process.out.versions, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + file(process.out.tbi.get(0).get(1)).name + ).match() } ) } @@ -72,7 +75,7 @@ nextflow_process { process { """ input[0] = Channel.of([ - [id:"111_WBcel235"], + [id:"113_WBcel235"], params.vep_genome, params.vep_species, params.vep_cache_version @@ -107,8 +110,8 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out.versions).match() }, - { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v111.0") } + { assert path(process.out.tab.get(0).get(1)).linesGzip.contains("## ENSEMBL VARIANT EFFECT PREDICTOR v113.0") } ) } } -} +} \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap index f937b299..2597a476 100644 --- a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap +++ b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap @@ -2,25 +2,27 @@ "test_ensemblvep_vep_fasta_tab_gz": { "content": [ [ - "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba" + "versions.yml:md5,534306f30b29b830c409da4b0a26bd20" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-15T17:35:20.694114" + "timestamp": "2025-01-24T10:03:33.681292738" }, - "test_ensemblvep_vep_fasta_vcf": { + "test_ensemblvep_vep_fasta_vcf - stub (not really but linting complains otherwise)": { "content": [ [ - "versions.yml:md5,bd2ba1b4741a7d0a224160b50859f4ba" - ] + "versions.yml:md5,534306f30b29b830c409da4b0a26bd20" + ], + "d41d8cd98f00b204e9800998ecf8427e", + "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nf-test": "0.9.1", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-15T17:34:41.093843" + "timestamp": "2025-01-24T10:15:45.231110684" } } \ No newline at end of file diff --git a/modules/nf-core/ensemblvep/vep/tests/nextflow.config b/modules/nf-core/ensemblvep/vep/tests/nextflow.config index 882bce41..0a4ae1a6 100644 --- a/modules/nf-core/ensemblvep/vep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/vep/tests/nextflow.config @@ -1,5 +1,5 @@ params { - vep_cache_version = "111" + vep_cache_version = "113" vep_genome = "WBcel235" vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c76..f9f54ee9 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 80c811e6..b562b72c 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_applybqsr +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 78db9d7f..5267454e 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -4,8 +4,8 @@ process GATK4_APPLYBQSR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) @@ -48,4 +48,17 @@ process GATK4_APPLYBQSR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def input_extension = input.getExtension() + def output_extension = input_extension == 'bam' ? 'bam' : 'cram' + """ + touch ${prefix}.${output_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml index ab9efea3..65d9c9e9 100644 --- a/modules/nf-core/gatk4/applybqsr/meta.yml +++ b/modules/nf-core/gatk4/applybqsr/meta.yml @@ -16,56 +16,65 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - bqsr_table: - type: file - description: Recalibration table from gatk4_baserecalibrator - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - bqsr_table: + type: file + description: Recalibration table from gatk4_baserecalibrator + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Recalibrated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Recalibrated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Recalibrated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Recalibrated CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test index 3d9c6204..acb41ce1 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test @@ -92,4 +92,63 @@ nextflow_process { } } + test("sarscov2 - cram - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + [] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + } diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index a387039d..427cbddb 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -1,4 +1,43 @@ { + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,91928754768510a59bde637403ee6a94" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "versions": [ + "versions.yml:md5,91928754768510a59bde637403ee6a94" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T10:32:45.888751339" + }, "sarscov2 - bam - intervals": { "content": [ { @@ -7,48 +46,48 @@ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,096d269e17f4ae53f765013479240db8" + "test.bam:md5,51259943bca01c92b20fb5b7ac09a246" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:48.144461" + "timestamp": "2024-10-31T10:31:59.340916681" }, "sarscov2 - cram": { "content": [ [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:22:09.308602" + "timestamp": "2024-10-31T10:32:16.162569909" }, "test.cram": { "content": [ @@ -60,6 +99,45 @@ }, "timestamp": "2023-12-09T03:10:46.70859771" }, + "sarscov2 - cram - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,91928754768510a59bde637403ee6a94" + ], + "bam": [ + + ], + "cram": [ + [ + { + "id": "test" + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,91928754768510a59bde637403ee6a94" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T10:32:34.223186142" + }, "sarscov2 - bam": { "content": [ { @@ -68,35 +146,35 @@ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "1": [ ], "2": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ], "bam": [ [ { "id": "test" }, - "test.bam:md5,022271b9ce0a07579282a2a5c1186513" + "test.bam:md5,213acb451007a0098a6a6a360fa68d72" ] ], "cram": [ ], "versions": [ - "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + "versions.yml:md5,91928754768510a59bde637403ee6a94" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:21:28.719225" + "timestamp": "2024-10-31T10:31:44.601557038" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 365e5c63..b562b72c 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_baserecalibrator +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/baserecalibrator/main.nf b/modules/nf-core/gatk4/baserecalibrator/main.nf index 1a299862..493533c7 100644 --- a/modules/nf-core/gatk4/baserecalibrator/main.nf +++ b/modules/nf-core/gatk4/baserecalibrator/main.nf @@ -4,16 +4,16 @@ process GATK4_BASERECALIBRATOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals) - path fasta - path fai - path dict - path known_sites - path known_sites_tbi + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(known_sites) + tuple val(meta6), path(known_sites_tbi) output: tuple val(meta), path("*.table"), emit: table diff --git a/modules/nf-core/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml index 8252b8c2..c3caeb80 100644 --- a/modules/nf-core/gatk4/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4/baserecalibrator/meta.yml @@ -16,57 +16,85 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Recalibration table from BaseRecalibrator - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Recalibration table from BaseRecalibrator + pattern: "*.{table}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test index fbd91bea..97c1c1ec 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test @@ -13,18 +13,17 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) - + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -35,26 +34,23 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } test("sarscov2 - bam - intervals") { when { process { """ - - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) - + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -72,25 +68,23 @@ nextflow_process { when { process { """ - - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) - input[4] = [ + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) - ] - input[5] = [ + ]) + input[5] = Channel.of([ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) - ] - + ]) """ } } @@ -101,7 +95,34 @@ nextflow_process { { assert snapshot(process.out).match() } ) } + } + + test("homo_sapiens - cram") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + [] + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)]) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } } test("sarscov2 - bam - stub") { @@ -110,17 +131,46 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map - [], - [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] - ] - input[1] = [] - input[2] = [] - input[3] = [] - input[4] = [] - input[5] = [] + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - bam - intervals - stub") { + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -134,22 +184,58 @@ nextflow_process { } - test("homo_sapiens - cram ") { + test("sarscov2 - bam - multiple sites - stub") { + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ]) + input[5] = Channel.of([ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - cram - stub") { + options "-stub" when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) - input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) - input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) + ]) + input[1] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)]) + input[2] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)]) + input[3] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)]) + input[4] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true)]) + input[5] = Channel.of([[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true)]) """ } } @@ -160,7 +246,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap index 8291304b..efdf46b3 100644 --- a/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/baserecalibrator/tests/main.nf.test.snap @@ -1,4 +1,37 @@ { + "homo_sapiens - cram": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + ] + ], + "1": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + ] + ], + "versions": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-23T15:37:29.36262858" + }, "sarscov2 - bam - stub": { "content": [ { @@ -11,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -22,15 +55,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:16:00.04396" + "timestamp": "2024-10-31T10:36:20.634357503" }, "sarscov2 - bam - intervals": { "content": [ @@ -44,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -55,15 +88,15 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:17.899391" + "timestamp": "2024-10-31T10:35:55.223087741" }, "sarscov2 - bam - multiple sites": { "content": [ @@ -77,7 +110,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -88,17 +121,17 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-13T16:15:47.770383" + "timestamp": "2024-10-31T10:36:10.08523788" }, - "homo_sapiens - cram ": { + "homo_sapiens - cram - stub": { "content": [ { "0": [ @@ -106,30 +139,30 @@ { "id": "test" }, - "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ { "id": "test" }, - "test.table:md5,35d89a3811aa31711fc9815b6b80e6ec" + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-13T16:16:42.135898" + "timestamp": "2025-01-23T15:38:23.045092592" }, "sarscov2 - bam": { "content": [ @@ -143,7 +176,7 @@ ] ], "1": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ], "table": [ [ @@ -154,14 +187,80 @@ ] ], "versions": [ - "versions.yml:md5,4ff697a3a05bb4d30701e6750c246ed2" + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T10:35:41.89476551" + }, + "sarscov2 - bam - intervals - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-01-23T15:37:56.722728282" + }, + "sarscov2 - bam - multiple sites - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" + ], + "table": [ + [ + { + "id": "test" + }, + "test.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1150a8b62c614926eeedda9d4bc8f651" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-02-13T16:14:57.629443" + "timestamp": "2025-01-23T15:38:09.797767675" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index d6fbe2e7..b562b72c 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_bedtointervallist +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 68863d67..89960e04 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -1,11 +1,11 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bed) diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 187da885..25348e16 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -15,34 +15,45 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bed: - type: file - description: Input bed file - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bed: + type: file + description: Input bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary + pattern: "*.dict" output: - interval_list: - type: file - description: gatk interval list file - pattern: "*.interval_list" + - meta: + type: file + description: gatk interval list file + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: gatk interval list file + pattern: "*.interval_list" + - _list: + type: file + description: gatk interval list file + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap index 48c322fd..6936cf97 100644 --- a/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/bedtointervallist/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,29a18c36f27584eb5a5f2f5457088b3b" + "versions.yml:md5,6b3aa4d49cc3ba433ecf92e31f155d00" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-19T14:20:12.168775" + "timestamp": "2024-10-31T10:37:25.720782902" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index e4510f97..b562b72c 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_combinegvcfs +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index df8ade11..1528ac73 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_COMBINEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(vcf_idx) @@ -45,4 +45,15 @@ process GATK4_COMBINEGVCFS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.combined.g.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/combinegvcfs/meta.yml b/modules/nf-core/gatk4/combinegvcfs/meta.yml index f13ddde7..c4fd646c 100644 --- a/modules/nf-core/gatk4/combinegvcfs/meta.yml +++ b/modules/nf-core/gatk4/combinegvcfs/meta.yml @@ -1,5 +1,6 @@ name: gatk4_combinegvcfs -description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file +description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample + gVCF file keywords: - gvcf - gatk4 @@ -8,47 +9,58 @@ keywords: - short variant discovery tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: Compressed VCF files - pattern: "*.vcf.gz" - - vcf_idx: - type: file - description: VCF Index file - pattern: "*.vcf.gz.idx" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: FASTA index file - pattern: "*.fasta.fai" - - dict: - type: file - description: FASTA dictionary file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: Compressed VCF files + pattern: "*.vcf.gz" + - vcf_idx: + type: file + description: VCF Index file + pattern: "*.vcf.gz.idx" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: FASTA index file + pattern: "*.fasta.fai" + - - dict: + type: file + description: FASTA dictionary file + pattern: "*.dict" output: - combined_gvcf: - type: file - description: Compressed Combined GVCF file - pattern: "*.combined.g.vcf.gz" + - meta: + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" + - "*.combined.g.vcf.gz": + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test index 56f54d0f..df2d5b4e 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test @@ -13,10 +13,10 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) ] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -35,4 +35,31 @@ nextflow_process { ) } } + + test("test_gatk4_combinegvcfs - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap index 1f04b8bd..00aea2bd 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap @@ -1,4 +1,39 @@ { + "test_gatk4_combinegvcfs - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.combined.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" + ], + "combined_gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.combined.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" + ] + } + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.10.0" + }, + "timestamp": "2024-10-31T10:47:56.847188152" + }, "test_gatk4_combinegvcfs": { "content": [ [ @@ -134,13 +169,13 @@ "chr22\t4608\t.\tA\t\t.\t.\tEND=40001\tGT:DP:GQ:MIN_DP:PL\t./.:0:0:0:0,0,0" ], [ - "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + "versions.yml:md5,aca96fc758ea3451abf185e1470788b5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-03-20T15:41:25.316932" + "timestamp": "2024-10-31T10:47:45.34645647" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 78822ad0..b562b72c 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_createsequencedictionary +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b..998622a0 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -1,11 +1,11 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index f9d70be0..7b5156bb 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -15,25 +15,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fasta,fa}" output: - dict: - type: file - description: gatk dictionary file - pattern: "*.{dict}" + - meta: + type: file + description: gatk dictionary file + pattern: "*.{dict}" + - "*.dict": + type: file + description: gatk dictionary file + pattern: "*.{dict}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap index 16735f95..e8a600fd 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T10:16:16.34453" + "timestamp": "2024-10-31T10:51:56.155954077" }, "sarscov2 - fasta": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ], "dict": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,e60dd34a71fc2029d81dc67ccb5d6be6" + "versions.yml:md5,e993b2c99f7f6b0fcd8428de15c61439" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-16T13:58:25.822068" + "timestamp": "2024-10-31T10:51:45.562993875" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index d4e8d360..b562b72c 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_haplotypecaller +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 3043ee07..1ef76789 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -1,11 +1,11 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) @@ -44,6 +44,7 @@ process GATK4_HAPLOTYPECALLER { --input $input \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ + --native-pair-hmm-threads ${task.cpus} \\ $dbsnp_command \\ $interval_command \\ $dragstr_command \\ diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 703b99a0..9d4a05e9 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -14,92 +14,108 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - dragstr_model: - type: file - description: Text file containing the DragSTR model of the used BAM/CRAM file (optional) - pattern: "*.txt" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test_dbsnp' ] - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - meta6: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test_dbsnp' ] - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - dragstr_model: + type: file + description: Text file containing the DragSTR model of the used BAM/CRAM file + (optional) + pattern: "*.txt" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test_dbsnp' ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - meta6: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test_dbsnp' ] + - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - bam: - type: file - description: Assembled haplotypes and locally realigned reads - pattern: "*.realigned.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.realigned.bam": + type: file + description: Assembled haplotypes and locally realigned reads + pattern: "*.realigned.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test index a124bff5..18d35f49 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test @@ -17,14 +17,14 @@ nextflow_process { """ input[0] = [ [ id:'test_bam' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] input[4] = [ [], [] ] input[5] = [ [], [] ] @@ -35,9 +35,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_bam_input") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_bam_input") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -50,14 +53,14 @@ nextflow_process { """ input[0] = [ [ id:'test_cram' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] input[4] = [ [], [] ] input[5] = [ [], [] ] """ @@ -67,9 +70,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -82,16 +88,16 @@ nextflow_process { """ input[0] = [ [ id:'test_cram_sites' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], [] ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] - input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ] """ } } @@ -99,9 +105,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_input_with_sites") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_input_with_sites") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } @@ -114,16 +123,16 @@ nextflow_process { """ input[0] = [ [ id:'test_cram_sites_dragstr' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt', checkIfExists: true) ] - input[1] = [ [ id:'test_fa' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'test_fai' ], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'test_dict' ], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) ] - input[4] = [ [ id:'test_sites' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true) ] - input[5] = [ [ id:'test_sites_tbi' ], file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true) ] + input[1] = [ [ id:'test_fa' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'test_fai' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'test_dict' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) ] + input[4] = [ [ id:'test_sites' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz', checkIfExists: true) ] + input[5] = [ [ id:'test_sites_tbi' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi', checkIfExists: true) ] """ } } @@ -131,9 +140,12 @@ nextflow_process { then { assertAll( { assert process.success }, - // { assert snapshot(process.out).match() }, // Unstable hashes - { assert snapshot(file(process.out.vcf.get(0).get(1)).name).match("gatk_hc_vcf_cram_dragstr_input_with_sites") }, - { assert snapshot(file(process.out.tbi.get(0).get(1)).name).match("gatk_hc_vcf_tbi_cram_dragstr_input_with_sites") }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap index 375025ee..e3ba2bdf 100644 --- a/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap @@ -1,82 +1,58 @@ { - "gatk_hc_vcf_cram_dragstr_input_with_sites": { + "homo_sapiens - [cram, crai] - fasta - fai - dict": { "content": [ - "test_cram_sites_dragstr.vcf.gz" + "test_cram.vcf.gz", + "test_cram.vcf.gz.tbi", + [ + "versions.yml:md5,2528212fed975c92514cf6641379e878" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-20T13:24:45.142682" + "timestamp": "2024-10-31T11:20:32.392608448" }, - "gatk_hc_vcf_bam_input": { + "homo_sapiens - [cram, crai] - fasta - fai - dict - sites - sites_tbi": { "content": [ - "test_bam.vcf.gz" + "test_cram_sites.vcf.gz", + "test_cram_sites.vcf.gz.tbi", + [ + "versions.yml:md5,2528212fed975c92514cf6641379e878" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-20T13:23:19.203837" + "timestamp": "2024-10-31T11:20:49.012555768" }, - "gatk_hc_vcf_cram_input": { + "homo_sapiens - [bam, bai] - fasta - fai - dict": { "content": [ - "test_cram.vcf.gz" + "test_bam.vcf.gz", + "test_bam.vcf.gz.tbi", + [ + "versions.yml:md5,2528212fed975c92514cf6641379e878" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-20T13:23:48.434615" + "timestamp": "2024-10-31T11:20:09.342159899" }, - "gatk_hc_vcf_cram_input_with_sites": { + "homo_sapiens - [cram, crai, dragstr_model] - fasta - fai - dict - sites - sites_tbi": { "content": [ - "test_cram_sites.vcf.gz" + "test_cram_sites_dragstr.vcf.gz", + "test_cram_sites_dragstr.vcf.gz.tbi", + [ + "versions.yml:md5,2528212fed975c92514cf6641379e878" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-20T13:24:17.147745" - }, - "gatk_hc_vcf_tbi_bam_input": { - "content": [ - "test_bam.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:23:19.23048" - }, - "gatk_hc_vcf_tbi_cram_input": { - "content": [ - "test_cram.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:23:48.45958" - }, - "gatk_hc_vcf_tbi_cram_dragstr_input_with_sites": { - "content": [ - "test_cram_sites_dragstr.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:24:45.154818" - }, - "gatk_hc_vcf_tbi_cram_input_with_sites": { - "content": [ - "test_cram_sites.vcf.gz.tbi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-20T13:24:17.158138" + "timestamp": "2024-10-31T11:21:06.551678783" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index dccdb15e..b562b72c 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_indexfeaturefile +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/indexfeaturefile/main.nf b/modules/nf-core/gatk4/indexfeaturefile/main.nf index b1a2698c..6993537f 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/main.nf +++ b/modules/nf-core/gatk4/indexfeaturefile/main.nf @@ -4,8 +4,8 @@ process GATK4_INDEXFEATUREFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(feature_file) diff --git a/modules/nf-core/gatk4/indexfeaturefile/meta.yml b/modules/nf-core/gatk4/indexfeaturefile/meta.yml index 575c6038..cfc717d2 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/meta.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - feature_file: - type: file - description: VCF/BED file - pattern: "*.{vcf,vcf.gz,bed,bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - feature_file: + type: file + description: VCF/BED file + pattern: "*.{vcf,vcf.gz,bed,bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Index for VCF/BED file - pattern: "*.{tbi,idx}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tbi,idx}": + type: file + description: Index for VCF/BED file + pattern: "*.{tbi,idx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@santiagorevale" maintainers: diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test index ee99a541..994606f1 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] """ } @@ -40,7 +40,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed.gz', checkIfExists: true) ] """ } @@ -63,7 +63,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true) ] """ } @@ -86,7 +86,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) ] """ } diff --git a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap index fc193336..788b9290 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/indexfeaturefile/tests/main.nf.test.snap @@ -12,14 +12,14 @@ "test_gatk4_indexfeaturefile_vcf": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:20.602472" + "timestamp": "2024-10-31T11:22:21.619530121" }, "geneome.bed.idx": { "content": [ @@ -53,7 +53,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -64,15 +64,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:03.058351" + "timestamp": "2024-10-31T11:22:06.537858152" }, "test_gatk4_indexfeaturefile_vcf_gz": { "content": [ @@ -86,7 +86,7 @@ ] ], "1": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ], "index": [ [ @@ -97,15 +97,15 @@ ] ], "versions": [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:57:51.861697" + "timestamp": "2024-10-31T11:22:37.41693965" }, "test.genome.vcf.idx": { "content": [ @@ -120,13 +120,13 @@ "test_gatk4_indexfeaturefile_bed": { "content": [ [ - "versions.yml:md5,e01e4575236d930ace929eec9c4c80dd" + "versions.yml:md5,3a4023239bad8505fdf37002915f8a7f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T18:56:46.885162" + "timestamp": "2024-10-31T11:21:52.805375486" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index a4026f98..b562b72c 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_intervallisttools +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 400fa038..bf20d4c9 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -1,11 +1,11 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(intervals) diff --git a/modules/nf-core/gatk4/intervallisttools/meta.yml b/modules/nf-core/gatk4/intervallisttools/meta.yml index 748dccfc..8ee15a29 100644 --- a/modules/nf-core/gatk4/intervallisttools/meta.yml +++ b/modules/nf-core/gatk4/intervallisttools/meta.yml @@ -1,5 +1,6 @@ name: gatk4_intervallisttools -description: Splits the interval list file into unique, equally-sized interval files and place it under a directory +description: Splits the interval list file into unique, equally-sized interval files + and place it under a directory keywords: - bed - gatk4 @@ -15,30 +16,36 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - interval_list: - type: file - description: Interval list file - pattern: "*.interval_list" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: Interval file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Interval list files - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_split/*/*.interval_list": + type: file + description: Interval list files + pattern: "*.interval_list" + - _list: + type: file + description: Interval list files + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@praveenraj2018" maintainers: diff --git a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap index 7718ed00..3be7acaa 100644 --- a/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/intervallisttools/tests/main.nf.test.snap @@ -16,7 +16,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -32,15 +32,15 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T21:26:22.252885" + "timestamp": "2024-10-31T10:37:46.848386632" }, "test_gatk4_intervallisttools -stub": { "content": [ @@ -59,7 +59,7 @@ ] ], "1": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ], "interval_list": [ [ @@ -75,14 +75,14 @@ ] ], "versions": [ - "versions.yml:md5,ff682cc9ad70d65a80280df57b316b03" + "versions.yml:md5,a2a074f61ecf1e0a21d1aeefd139125f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:15:11.772344" + "timestamp": "2024-10-31T10:38:00.631338482" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index efd9faa2..b562b72c 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_mergevcfs +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf index 9e8d4391..1752f48a 100644 --- a/modules/nf-core/gatk4/mergevcfs/main.nf +++ b/modules/nf-core/gatk4/mergevcfs/main.nf @@ -1,11 +1,11 @@ process GATK4_MERGEVCFS { tag "$meta.id" - label 'process_medium' + label 'process_low' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml index 996053fc..b4f61d78 100644 --- a/modules/nf-core/gatk4/mergevcfs/meta.yml +++ b/modules/nf-core/gatk4/mergevcfs/meta.yml @@ -14,38 +14,50 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: Two or more VCF files - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - dict: - type: file - description: Optional Sequence Dictionary as input - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: Two or more VCF files + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: + type: file + description: Optional Sequence Dictionary as input + pattern: "*.dict" output: - vcf: - type: file - description: merged vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: merged vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: merged vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: index files for the merged vcf files - pattern: "*.tbi" + - meta: + type: file + description: index files for the merged vcf files + pattern: "*.tbi" + - "*.tbi": + type: file + description: index files for the merged vcf files + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test index 77ace10a..343fff68 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test @@ -24,6 +24,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs") @@ -48,6 +49,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict") @@ -75,6 +77,7 @@ nextflow_process { { assert process.success }, { assert snapshot( + process.out.versions, file(process.out.vcf.get(0).get(1)).name, file(process.out.tbi.get(0).get(1)).name ).match("test_gatk4_mergevcfs_no_dict_stub") diff --git a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap index 62cceed5..5fab6dca 100644 --- a/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/mergevcfs/tests/main.nf.test.snap @@ -1,35 +1,44 @@ { "test_gatk4_mergevcfs_no_dict_stub": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:57:40.784590995" + "timestamp": "2024-11-07T08:29:25.813956308" }, "test_gatk4_mergevcfs": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:56:42.178255913" + "timestamp": "2024-11-07T08:28:42.580265083" }, "test_gatk4_mergevcfs_no_dict": { "content": [ + [ + "versions.yml:md5,829a91432cc945f3227b1355587d25e0" + ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-14T14:57:11.404322124" + "timestamp": "2024-11-07T08:29:12.795329336" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 834d2486..b562b72c 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_splitncigarreads +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/splitncigarreads/main.nf b/modules/nf-core/gatk4/splitncigarreads/main.nf index e2c287a0..40bfee1b 100644 --- a/modules/nf-core/gatk4/splitncigarreads/main.nf +++ b/modules/nf-core/gatk4/splitncigarreads/main.nf @@ -1,11 +1,11 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(bam), path(bai), path(intervals) @@ -46,4 +46,17 @@ process GATK4_SPLITNCIGARREADS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + } diff --git a/modules/nf-core/gatk4/splitncigarreads/meta.yml b/modules/nf-core/gatk4/splitncigarreads/meta.yml index f8132746..6b05bef1 100644 --- a/modules/nf-core/gatk4/splitncigarreads/meta.yml +++ b/modules/nf-core/gatk4/splitncigarreads/meta.yml @@ -14,59 +14,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: list - description: BAM/SAM/CRAM file containing reads - pattern: "*.{bam,sam,cram}" - - bai: - type: list - description: BAI/SAI/CRAI index file (optional) - pattern: "*.{bai,sai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: list + description: BAM/SAM/CRAM file containing reads + pattern: "*.{bam,sam,cram}" + - bai: + type: list + description: BAI/SAI/CRAI index file (optional) + pattern: "*.{bai,sai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - bam: - type: file - description: Output file with split reads (BAM/SAM/CRAM) - pattern: "*.{bam,sam,cram}" + - meta: + type: file + description: Output file with split reads (BAM/SAM/CRAM) + pattern: "*.{bam,sam,cram}" + - "*.bam": + type: file + description: Output file with split reads (BAM/SAM/CRAM) + pattern: "*.{bam,sam,cram}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test index b4910126..7a5eee09 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test @@ -14,10 +14,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), []] - input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), []] + input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -25,7 +25,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads") } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() + } ) } @@ -36,10 +40,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists:true), file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)] - input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)] + input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -47,7 +51,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_intervals") } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() + } ) } @@ -60,10 +68,10 @@ nextflow_process { when { process { """ - input[0] = [ [ id:'test' ], file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), [], []] - input[1] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] - input[2] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] - input[3] = [ [ id:'reference' ], file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), [], []] + input[1] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [ id:'reference' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] """ } } @@ -71,7 +79,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.bam.get(0).get(1)).name).match("test_gatk4_splitncigarreads_stub") } + { assert snapshot( + file(process.out.bam[0][1]).name, + process.out.versions + ).match() + } ) } diff --git a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap index 3e581ceb..5c2fee14 100644 --- a/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/splitncigarreads/tests/main.nf.test.snap @@ -1,32 +1,41 @@ { "test_gatk4_splitncigarreads_intervals": { "content": [ - "test.bam" + "test.bam", + [ + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T08:26:10.91960579" + "timestamp": "2024-10-31T12:06:43.83765238" }, "test_gatk4_splitncigarreads_stub": { "content": [ - "test.bam" + "test.bam", + [ + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T08:26:32.322712467" + "timestamp": "2024-11-07T10:35:24.483631375" }, "test_gatk4_splitncigarreads": { "content": [ - "test.bam" + "test.bam", + [ + "versions.yml:md5,7ddd35e618d7a827231e7dc94f7a7b4e" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-02-15T08:25:53.532205456" + "timestamp": "2024-10-31T12:06:15.200052646" } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 0812b6f2..b562b72c 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -1,7 +1,9 @@ -name: gatk4_variantfiltration +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gatk4=4.5.0.0 + # renovate: datasource=conda depName=bioconda/gatk4 + - bioconda::gatk4=4.6.1.0 + - bioconda::gcnvkernel=0.9 diff --git a/modules/nf-core/gatk4/variantfiltration/main.nf b/modules/nf-core/gatk4/variantfiltration/main.nf index 388c60ab..5bf0e353 100644 --- a/modules/nf-core/gatk4/variantfiltration/main.nf +++ b/modules/nf-core/gatk4/variantfiltration/main.nf @@ -1,11 +1,11 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" - label 'process_medium' + label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b28daf5d9bb2f0d129dcad1b7410e0dd8a9b087aaf3ec7ced929b1f57624ad98/data': + 'community.wave.seqera.io/library/gatk4_gcnvkernel:e48d414933d188cd' }" input: tuple val(meta), path(vcf), path(tbi) diff --git a/modules/nf-core/gatk4/variantfiltration/meta.yml b/modules/nf-core/gatk4/variantfiltration/meta.yml index 11915a94..8e23e205 100644 --- a/modules/nf-core/gatk4/variantfiltration/meta.yml +++ b/modules/nf-core/gatk4/variantfiltration/meta.yml @@ -15,60 +15,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: List of VCF(.gz) files - pattern: "*.{vcf,vcf.gz}" - - vcf_tbi: - type: list - description: List of VCF file indexes - pattern: "*.{idx,tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of fastea file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: List of VCF(.gz) files + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: list + description: List of VCF file indexes + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of fastea file + pattern: "*.dict" output: - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap index 36c03f7c..29cb3cdc 100644 --- a/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/variantfiltration/tests/main.nf.test.snap @@ -2,29 +2,29 @@ "test_gatk4_variantfiltration_gz_input": { "content": [ [ - "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" + "versions.yml:md5,ad4241d2454ae3611dd8e7383b3109ff" ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:43:27.609784" + "timestamp": "2024-10-31T12:10:17.964554959" }, "test_gatk4_variantfiltration_vcf_input": { "content": [ [ - "versions.yml:md5,96943659275ba62de1f0d283a2f6e97b" + "versions.yml:md5,ad4241d2454ae3611dd8e7383b3109ff" ], "test.vcf.gz", "test.vcf.gz.tbi" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.2" + "nf-test": "0.9.1", + "nextflow": "24.10.0" }, - "timestamp": "2024-05-22T22:42:55.316294" + "timestamp": "2024-10-31T12:10:04.6172075" } } \ No newline at end of file diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index c6df58ad..46c5faec 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -1,7 +1,7 @@ -name: gffread +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index c0602820..bebe7f57 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -1,53 +1,73 @@ name: gffread -description: Validate, filter, convert and perform various other operations on GFF files +description: Validate, filter, convert and perform various other operations on GFF + files keywords: - gff - conversion - validation tools: - gffread: - description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more. + description: GFF/GTF utility providing format conversions, region filtering, FASTA + sequence extraction and more. homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] + identifier: biotools:gffread input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - gff: + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" + - - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - gtf: - type: file - description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present - pattern: "*.{gtf}" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gtf": + type: file + description: GTF file resulting from the conversion of the GFF input file if + '-T' argument is present + pattern: "*.{gtf}" - gffread_gff: - type: file - description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gff3": + type: file + description: GFF3 file resulting from the conversion of the GFF input file if + '-T' argument is absent + pattern: "*.gff3" - gffread_fasta: - type: file - description: Fasta file produced when either of '-w', '-x', '-y' parameters is present - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.fasta": + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters + is present + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test index 4cd13dcd..d039f367 100644 --- a/modules/nf-core/gffread/tests/main.nf.test +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -23,6 +23,7 @@ nextflow_process { file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.gff3", checkIfExists: true) ] input[1] = [] + """ } } @@ -220,4 +221,4 @@ nextflow_process { } -} +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index 25910b34..9b926b1f 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,7 +1,12 @@ -name: gunzip +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - conda-forge::sed=4.7 + - conda-forge::coreutils=9.5 + - conda-forge::grep=3.11 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 468a6f28..3ffc8e92 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -1,34 +1,37 @@ process GUNZIP { - tag "$archive" + tag "${archive}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: tuple val(meta), path(archive) output: - tuple val(meta), path("$gunzip"), emit: gunzip - path "versions.yml" , emit: versions + tuple val(meta), path("${gunzip}"), emit: gunzip + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - gunzip = archive.toString() - '.gz' + def extension = (archive.toString() - '.gz').tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".${extension}" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".${extension}" """ # Not calling gunzip itself because it creates files # with the original group ownership rather than the # default one for that user / the work directory gzip \\ -cd \\ - $args \\ - $archive \\ - > $gunzip + ${args} \\ + ${archive} \\ + > ${gunzip} cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -37,9 +40,13 @@ process GUNZIP { """ stub: - gunzip = archive.toString() - '.gz' + def args = task.ext.args ?: '' + def extension = (archive.toString() - '.gz').tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".${extension}" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".${extension}" """ - touch $gunzip + touch ${gunzip} cat <<-END_VERSIONS > versions.yml "${task.process}": gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 231034f2..69d31024 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - ${gunzip}: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" @@ -37,3 +44,4 @@ maintainers: - "@joseespinosa" - "@drpatelh" - "@jfy133" + - "@gallvp" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test index 6406008e..776211ad 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -33,4 +33,89 @@ nextflow_process { } + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + } diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap index 720fd9ff..a0f0e67e 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test.snap +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -1,4 +1,70 @@ { + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-13T11:48:22.080222697" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-13T11:48:14.593020264" + }, "Should run without failures": { "content": [ { @@ -11,7 +77,7 @@ ] ], "1": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" ], "gunzip": [ [ @@ -22,10 +88,47 @@ ] ], "versions": [ - "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-13T11:48:01.295397925" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d327e4a19a6d5c5e974136cef8999d8c" ] } ], - "timestamp": "2023-10-17T15:35:37.690477896" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-13T11:48:07.414271387" } } \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config new file mode 100644 index 00000000..dec77642 --- /dev/null +++ b/modules/nf-core/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index bcb9d64a..f871e054 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,8 +1,8 @@ -name: mosdepth +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - - mosdepth=0.3.8 + - mosdepth=0.3.10 diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf index 6f4a8383..3bf945f9 100644 --- a/modules/nf-core/mosdepth/main.nf +++ b/modules/nf-core/mosdepth/main.nf @@ -4,8 +4,8 @@ process MOSDEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.8--hd299d5a_0' : - 'biocontainers/mosdepth:0.3.8--hd299d5a_0'}" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.10--h4e814b3_1' : + 'biocontainers/mosdepth:0.3.10--h4e814b3_1'}" input: tuple val(meta), path(bam), path(bai), path(bed) diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index 9caaf2cd..dc783c90 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -12,91 +12,161 @@ tools: documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 licence: ["MIT"] + identifier: biotools:mosdepth input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index for BAM/CRAM file - pattern: "*.{bai,crai}" - - bed: - type: file - description: BED file with intersected intervals - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index for BAM/CRAM file + pattern: "*.{bai,crai}" + - bed: + type: file + description: BED file with intersected intervals + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - global_txt: - type: file - description: Text file with global cumulative coverage distribution - pattern: "*.{global.dist.txt}" - - regions_txt: - type: file - description: Text file with region cumulative coverage distribution - pattern: "*.{region.dist.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.global.dist.txt": + type: file + description: Text file with global cumulative coverage distribution + pattern: "*.{global.dist.txt}" - summary_txt: - type: file - description: Text file with summary mean depths per chromosome and regions - pattern: "*.{summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.txt": + type: file + description: Text file with summary mean depths per chromosome and regions + pattern: "*.{summary.txt}" + - regions_txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.region.dist.txt": + type: file + description: Text file with region cumulative coverage distribution + pattern: "*.{region.dist.txt}" + - per_base_d4: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.d4": + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" - per_base_bed: - type: file - description: BED file with per-base coverage - pattern: "*.{per-base.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz": + type: file + description: BED file with per-base coverage + pattern: "*.{per-base.bed.gz}" - per_base_csi: - type: file - description: Index file for BED file with per-base coverage - pattern: "*.{per-base.bed.gz.csi}" - - per_base_d4: - type: file - description: D4 file with per-base coverage - pattern: "*.{per-base.d4}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz.csi": + type: file + description: Index file for BED file with per-base coverage + pattern: "*.{per-base.bed.gz.csi}" - regions_bed: - type: file - description: BED file with per-region coverage - pattern: "*.{regions.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz": + type: file + description: BED file with per-region coverage + pattern: "*.{regions.bed.gz}" - regions_csi: - type: file - description: Index file for BED file with per-region coverage - pattern: "*.{regions.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz.csi": + type: file + description: Index file for BED file with per-region coverage + pattern: "*.{regions.bed.gz.csi}" - quantized_bed: - type: file - description: BED file with binned coverage - pattern: "*.{quantized.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz": + type: file + description: BED file with binned coverage + pattern: "*.{quantized.bed.gz}" - quantized_csi: - type: file - description: Index file for BED file with binned coverage - pattern: "*.{quantized.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz.csi": + type: file + description: Index file for BED file with binned coverage + pattern: "*.{quantized.bed.gz.csi}" - thresholds_bed: - type: file - description: BED file with the number of bases in each region that are covered at or above each threshold - pattern: "*.{thresholds.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz": + type: file + description: BED file with the number of bases in each region that are covered + at or above each threshold + pattern: "*.{thresholds.bed.gz}" - thresholds_csi: - type: file - description: Index file for BED file with threshold coverage - pattern: "*.{thresholds.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz.csi": + type: file + description: Index file for BED file with threshold coverage + pattern: "*.{thresholds.bed.gz.csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/mosdepth/tests/main.nf.test b/modules/nf-core/mosdepth/tests/main.nf.test index 21eebc1f..0b3c860d 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test +++ b/modules/nf-core/mosdepth/tests/main.nf.test @@ -15,8 +15,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -40,9 +40,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -65,13 +65,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), [] ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -93,13 +93,13 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [ [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] """ } @@ -122,8 +122,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -148,8 +148,8 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), [] ] input[1] = [[],[]] @@ -174,9 +174,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -200,9 +200,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ @@ -225,9 +225,9 @@ nextflow_process { """ input[0] = [ [ id:'test', single_end:true ], - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] input[1] = [[],[]] """ diff --git a/modules/nf-core/mosdepth/tests/main.nf.test.snap b/modules/nf-core/mosdepth/tests/main.nf.test.snap index c604540b..67e16562 100644 --- a/modules/nf-core/mosdepth/tests/main.nf.test.snap +++ b/modules/nf-core/mosdepth/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ] ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -222,15 +222,15 @@ ] ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:33:16.953408231" + "timestamp": "2025-01-17T14:57:12.350279421" }, "homo_sapiens - cram, crai, bed": { "content": [ @@ -260,7 +260,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -289,7 +289,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -307,7 +307,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "8": [ @@ -340,7 +340,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -367,7 +367,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "regions_txt": [ @@ -395,15 +395,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:50.160217828" + "timestamp": "2025-01-17T14:56:12.528228123" }, "homo_sapiens - bam, bai, [] - quantized": { "content": [ @@ -433,7 +433,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ @@ -456,7 +456,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -480,7 +480,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" + "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" ] ], "global_txt": [ @@ -507,7 +507,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -528,7 +528,7 @@ "id": "test", "single_end": true }, - "test.quantized.bed.gz.csi:md5,4f69e6ace50206a2768be66ded3a56f0" + "test.quantized.bed.gz.csi:md5,be9617f551f19a33923f1e886eaefb93" ] ], "regions_bed": [ @@ -556,15 +556,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:33:01.164885111" + "timestamp": "2025-01-17T14:56:38.422491251" }, "homo_sapiens - bam, bai, bed": { "content": [ @@ -594,7 +594,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -623,7 +623,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -641,7 +641,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "8": [ @@ -674,7 +674,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -701,7 +701,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "regions_txt": [ @@ -729,15 +729,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:39.071657456" + "timestamp": "2025-01-17T14:55:43.01015749" }, "homo_sapiens - bam, bai, [] - window": { "content": [ @@ -767,7 +767,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -796,7 +796,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -814,7 +814,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" + "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" ] ], "8": [ @@ -847,7 +847,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -874,7 +874,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,2a30bcb7f5c7632136b3efce24723970" + "test.regions.bed.gz.csi:md5,257d67678136963d9dd904330079609d" ] ], "regions_txt": [ @@ -902,15 +902,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:55.631776118" + "timestamp": "2025-01-17T14:56:27.10647246" }, "homo_sapiens - bam, bai, []": { "content": [ @@ -940,7 +940,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ @@ -963,7 +963,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -1002,7 +1002,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -1039,15 +1039,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:33.642125299" + "timestamp": "2025-01-17T14:55:30.449110281" }, "homo_sapiens - cram, crai, []": { "content": [ @@ -1077,7 +1077,7 @@ ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ @@ -1100,7 +1100,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -1139,7 +1139,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -1176,15 +1176,15 @@ ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:32:44.704920941" + "timestamp": "2025-01-17T14:55:55.244274402" }, "homo_sapiens - bam, bai, bed - thresholds": { "content": [ @@ -1222,11 +1222,11 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" + "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" ] ], "12": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ], "2": [ [ @@ -1255,7 +1255,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "6": [ @@ -1273,7 +1273,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "8": [ @@ -1306,7 +1306,7 @@ "id": "test", "single_end": true }, - "test.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294" + "test.per-base.bed.gz.csi:md5,9e649ac749ff6c6073bef5ab63e8aaa4" ] ], "per_base_d4": [ @@ -1333,7 +1333,7 @@ "id": "test", "single_end": true }, - "test.regions.bed.gz.csi:md5,e7df086f0a36e88ca231e143d43bd3f9" + "test.regions.bed.gz.csi:md5,47669cfe41f3e222e74d81e1b1be191f" ] ], "regions_txt": [ @@ -1369,18 +1369,18 @@ "id": "test", "single_end": true }, - "test.thresholds.bed.gz.csi:md5,219414a0751185adb98d2235d83ea055" + "test.thresholds.bed.gz.csi:md5,912055ee9452229439df6fae95644196" ] ], "versions": [ - "versions.yml:md5,87634e525fb18990cd98fe1080ad72ce" + "versions.yml:md5,333368078626c18a32eeb12299080cc9" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-04-29T13:33:06.737266831" + "timestamp": "2025-01-17T14:56:49.888375978" } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index 1d715d56..8f34e975 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 9c24eb0a..62054fc9 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,10 +1,8 @@ -name: samtools_faidx - +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults - dependencies: - - bioconda::htslib=1.19.1 - - bioconda::samtools=1.19.2 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index cfe7ad95..28c0a81c 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index f3c25de2..6721b2cb 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -14,47 +14,62 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fa: - type: file - description: FASTA file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fasta}": + type: file + description: FASTA file + pattern: "*.{fa}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 3e651ef6..1bbb3ec2 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T16:22:39.412601" + "timestamp": "2024-09-16T07:57:47.450887871" }, "test_samtools_faidx_bgzip": { "content": [ @@ -71,7 +71,7 @@ ] ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -95,15 +95,15 @@ ] ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T16:23:22.427966" + "timestamp": "2024-09-16T07:58:04.804905659" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +124,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -142,15 +142,15 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T16:24:04.107537" + "timestamp": "2024-09-16T07:58:23.831268154" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -171,7 +171,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -189,15 +189,15 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T16:24:45.868463" + "timestamp": "2024-09-16T07:58:35.600243706" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -218,7 +218,7 @@ ], "3": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -236,14 +236,14 @@ ], "versions": [ - "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T16:25:27.550554" + "timestamp": "2024-09-16T07:58:54.705460167" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index fc669b1b..62054fc9 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,8 +1,8 @@ -name: samtools_merge +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::samtools=1.19.2 - - bioconda::htslib=1.19.1 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index a3048c28..34da4c7c 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' : - 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 2e8f3dbb..235aa219 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -15,60 +15,81 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_files: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of the reference file the CRAM was created with (optional) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_files: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of the reference file the CRAM was created with (optional) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file + pattern: "*.{bam}" - cram: - type: file - description: CRAM file - pattern: "*.{cram}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: CRAM file + pattern: "*.{cram}" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa " diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index f7da7699..0a41e01a 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -80,14 +80,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:16:33.782637377" + "timestamp": "2024-09-16T09:16:30.476887194" }, "bams_csi": { "content": [ @@ -124,14 +124,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:16:42.594476052" + "timestamp": "2024-09-16T09:16:52.203823961" }, "bam_cram": { "content": [ @@ -158,14 +158,14 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:16:04.805335656" + "timestamp": "2024-09-16T08:29:57.524363148" }, "crams_bam": { "content": [ @@ -182,14 +182,14 @@ "crams_versions": { "content": [ [ - "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-13T16:16:25.889394689" + "timestamp": "2024-09-16T09:16:06.977096207" }, "bam_csi": { "content": [ diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml index 62f3d5aa..48236b6f 100644 --- a/modules/nf-core/snpeff/download/environment.yml +++ b/modules/nf-core/snpeff/download/environment.yml @@ -1,7 +1,7 @@ -name: snpeff_download +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpeff/download/main.nf b/modules/nf-core/snpeff/download/main.nf index f1fc4cc3..e4225933 100644 --- a/modules/nf-core/snpeff/download/main.nf +++ b/modules/nf-core/snpeff/download/main.nf @@ -8,7 +8,7 @@ process SNPEFF_DOWNLOAD { 'biocontainers/snpeff:5.1--hdfd78af_2' }" input: - tuple val(meta), val(genome), val(cache_version) + tuple val(meta), val(snpeff_db) output: tuple val(meta), path('snpeff_cache'), emit: cache @@ -28,7 +28,7 @@ process SNPEFF_DOWNLOAD { """ snpEff \\ -Xmx${avail_mem}M \\ - download ${genome}.${cache_version} \\ + download ${snpeff_db} \\ -dataDir \${PWD}/snpeff_cache \\ ${args} @@ -41,7 +41,10 @@ process SNPEFF_DOWNLOAD { stub: """ - mkdir ${genome}.${cache_version} + mkdir -p snpeff_cache/${snpeff_db} + + touch snpeff_cache/${snpeff_db}/sequence.I.bin + touch snpeff_cache/${snpeff_db}/sequence.bin cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index f367c696..a3211fc7 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -14,29 +14,35 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] + identifier: biotools:snpeff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - db: - type: string - description: | - which db to annotate with + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fna,fa}" + - cache_version: + type: string + description: Version of the snpEff cache to download output: - cache: - type: file - description: | - snpEff cache + - meta: + type: file + description: | + snpEff cache + - snpeff_cache: + type: file + description: | + snpEff cache - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/snpeff/download/tests/main.nf.test b/modules/nf-core/snpeff/download/tests/main.nf.test new file mode 100644 index 00000000..ef547c6f --- /dev/null +++ b/modules/nf-core/snpeff/download/tests/main.nf.test @@ -0,0 +1,51 @@ + +nextflow_process { + + name "Test Process SNPEFF_DOWNLOAD" + script "../main.nf" + process "SNPEFF_DOWNLOAD" + + tag "modules" + tag "modules_nfcore" + tag "snpeff" + tag "snpeff/download" + + test("test-snpeff-download") { + + when { + process { + """ + input[0] = [ [ id:"WBcel235.105" ], "WBcel235.105" ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-snpeff-download-stub") { + options '-stub' + when { + process { + """ + input[0] = [ [ id:"WBcel235.105" ], "WBcel235.105" ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/snpeff/download/tests/main.nf.test.snap b/modules/nf-core/snpeff/download/tests/main.nf.test.snap new file mode 100644 index 00000000..5bccdd8a --- /dev/null +++ b/modules/nf-core/snpeff/download/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "test-snpeff-download-stub": { + "content": [ + { + "0": [ + [ + { + "id": "WBcel235.105" + }, + [ + [ + "sequence.I.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "sequence.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "1": [ + "versions.yml:md5,5fc7ed9f548eccf5fac9fdefc12ef56e" + ], + "cache": [ + [ + { + "id": "WBcel235.105" + }, + [ + [ + "sequence.I.bin:md5,d41d8cd98f00b204e9800998ecf8427e", + "sequence.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ] + ], + "versions": [ + "versions.yml:md5,5fc7ed9f548eccf5fac9fdefc12ef56e" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-19T12:48:45.183665736" + }, + "test-snpeff-download": { + "content": [ + { + "0": [ + [ + { + "id": "WBcel235.105" + }, + [ + [ + "sequence.I.bin:md5,2fd1694bd91cf7952cbad8cfed161e53", + "sequence.II.bin:md5,bacedbdea89508e108223767fa260a4c", + "sequence.III.bin:md5,444118a9fb9d0a03c37e86094d8e52a9", + "sequence.IV.bin:md5,ff756628faa0b71cd65495668c3d82b5", + "sequence.V.bin:md5,d6ad5476162ac45829f719dd4ee3f4e7", + "sequence.X.bin:md5,b79bec6cc8f96b8373dac56bab5d0a6c", + "sequence.bin:md5,ec2bc2ae81755ab90fcf1848bc7ce41f", + "snpEffectPredictor.bin:md5,1d99251d0405f0a42913ed8b5b2c2fa7" + ] + ] + ] + ], + "1": [ + "versions.yml:md5,5fc7ed9f548eccf5fac9fdefc12ef56e" + ], + "cache": [ + [ + { + "id": "WBcel235.105" + }, + [ + [ + "sequence.I.bin:md5,2fd1694bd91cf7952cbad8cfed161e53", + "sequence.II.bin:md5,bacedbdea89508e108223767fa260a4c", + "sequence.III.bin:md5,444118a9fb9d0a03c37e86094d8e52a9", + "sequence.IV.bin:md5,ff756628faa0b71cd65495668c3d82b5", + "sequence.V.bin:md5,d6ad5476162ac45829f719dd4ee3f4e7", + "sequence.X.bin:md5,b79bec6cc8f96b8373dac56bab5d0a6c", + "sequence.bin:md5,ec2bc2ae81755ab90fcf1848bc7ce41f", + "snpEffectPredictor.bin:md5,1d99251d0405f0a42913ed8b5b2c2fa7" + ] + ] + ] + ], + "versions": [ + "versions.yml:md5,5fc7ed9f548eccf5fac9fdefc12ef56e" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-29T14:27:47.123555" + } +} \ No newline at end of file diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml index b492e6a8..48236b6f 100644 --- a/modules/nf-core/snpeff/snpeff/environment.yml +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -1,7 +1,7 @@ -name: snpeff_snpeff +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 7559c3de..ef3d495a 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -14,46 +14,76 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] + identifier: biotools:snpeff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - db: - type: string - description: | - which db to annotate with - - cache: - type: file - description: | - path to snpEff cache (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - - db: + type: string + description: | + which db to annotate with + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cache: + type: file + description: | + path to snpEff cache (optional) output: - vcf: - type: file - description: | - annotated vcf - pattern: "*.ann.vcf" + - meta: + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" + - "*.ann.vcf": + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" - report: - type: file - description: snpEff report csv file - pattern: "*.csv" + - meta: + type: file + description: snpEff report csv file + pattern: "*.csv" + - "*.csv": + type: file + description: snpEff report csv file + pattern: "*.csv" - summary_html: - type: file - description: snpEff summary statistics in html file - pattern: "*.html" + - meta: + type: file + description: snpEff summary statistics in html file + pattern: "*.html" + - "*.html": + type: file + description: snpEff summary statistics in html file + pattern: "*.html" - genes_txt: - type: file - description: txt (tab separated) file having counts of the number of variants affecting each transcript and gene - pattern: "*.genes.txt" + - meta: + type: file + description: txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + pattern: "*.genes.txt" + - "*.genes.txt": + type: file + description: txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + pattern: "*.genes.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test index dd37f275..2be0b7d7 100644 --- a/modules/nf-core/snpeff/snpeff/tests/main.nf.test +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -6,6 +6,7 @@ nextflow_process { config "./nextflow.config" tag "modules" tag "modules_nfcore" + tag "modules_snpeff" tag "snpeff" tag "snpeff/download" tag "snpeff/snpeff" @@ -17,7 +18,7 @@ nextflow_process { script "../../download/main.nf" process { """ - input[0] = Channel.of([[id:params.snpeff_genome + '.' + params.snpeff_cache_version], params.snpeff_genome, params.snpeff_cache_version]) + input[0] = Channel.of([[id:params.snpeff_db], params.snpeff_db]) """ } } @@ -30,7 +31,7 @@ nextflow_process { [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]) - input[1] = params.snpeff_genome + '.' + params.snpeff_cache_version + input[1] = params.snpeff_db input[2] = SNPEFF_DOWNLOAD.out.cache """ } diff --git a/modules/nf-core/snpeff/snpeff/tests/nextflow.config b/modules/nf-core/snpeff/snpeff/tests/nextflow.config index d31ebf6b..a950a047 100644 --- a/modules/nf-core/snpeff/snpeff/tests/nextflow.config +++ b/modules/nf-core/snpeff/snpeff/tests/nextflow.config @@ -1,4 +1,3 @@ params { - snpeff_cache_version = "105" - snpeff_genome = "WBcel235" + snpeff_db = "WBcel235.105" } diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 9ed1940f..91e37ae1 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,3 +1,5 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index b435f60c..22a52184 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,8 +4,8 @@ process STAR_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/101ea47973178f85ff66a34de6a7462aaf99d947d3924c27ce8a2d5a63009065/data' : - 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d/data' : + 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 791f255e..91e37ae1 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,10 +1,11 @@ -name: star_genomegenerate +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults + dependencies: - - bioconda::samtools=1.18 - - bioconda::htslib=1.18 - - bioconda::star=2.7.10a + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 + - bioconda::star=2.7.11b - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index b8855715..4eb95654 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -4,8 +4,8 @@ process STAR_GENOMEGENERATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/26/268b4c9c6cbf8fa6606c9b7fd4fafce18bf2c931d1a809a0ce51b105ec06c89d/data' : + 'community.wave.seqera.io/library/htslib_samtools_star_gawk:ae438e9a604351a4' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 1061e1b8..33c1f65f 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -14,37 +14,40 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the reference genome - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the reference genome + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: directory - description: Folder containing the star index files - pattern: "star" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - star: + type: directory + description: Folder containing the star index files + pattern: "star" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test index c17c8ba4..4d619c47 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -28,15 +28,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_index") }, - { assert snapshot(process.out.versions).match("fasta_gtf_versions") } + { assert snapshot( + file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(), + process.out.versions) + .match() } ) } } - test("fasta_gtf_stub") { - - options '-stub' + test("fasta") { when { process { @@ -45,10 +45,7 @@ nextflow_process { [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = Channel.of([ - [ id:'test_gtf' ], - [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] - ]) + input[1] = Channel.of([ [], [] ]) """ } } @@ -56,13 +53,17 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_gtf_stub_index") }, - { assert snapshot(process.out.versions).match("fasta_gtf_stub_versions") } + { assert snapshot( + file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString(), + process.out.versions + ).match() } ) } } - test("fasta") { + test("fasta_gtf_stub") { + + options '-stub' when { process { @@ -71,7 +72,10 @@ nextflow_process { [ id:'test_fasta' ], [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] ]) - input[1] = Channel.of([ [], [] ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) """ } } @@ -79,11 +83,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_index") }, - { assert snapshot(process.out.versions).match("fasta_versions") } + { assert snapshot(process.out).match() } ) } - } test("fasta_stub") { @@ -105,11 +107,8 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("fasta_stub_index") }, - { assert snapshot(process.out.versions).match("fasta_stub_versions") } + { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap index 5653d6e6..b79da991 100644 --- a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -1,90 +1,148 @@ { - "fasta_gtf_versions": { + "fasta_gtf": { "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]", [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,0c6c5fab50cc8601f9072268a2f49aad" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-01T15:54:31.798555" + "timestamp": "2024-12-11T16:29:40.748676908" }, - "fasta_stub_versions": { + "fasta_gtf_stub": { "content": [ - [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:55:07.521209" - }, - "fasta_gtf_stub_index": { - "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:54:46.478098" - }, - "fasta_gtf_stub_versions": { - "content": [ - [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" - ] + { + "0": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,0c6c5fab50cc8601f9072268a2f49aad" + ], + "index": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonGeTrInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "exonInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "geneInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbInfo.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.fromGTF.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "sjdbList.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptInfo.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,0c6c5fab50cc8601f9072268a2f49aad" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-01T15:54:46.491657" + "timestamp": "2024-12-11T16:30:11.024076742" }, - "fasta_index": { + "fasta_stub": { "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + { + "0": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,0c6c5fab50cc8601f9072268a2f49aad" + ], + "index": [ + [ + { + "id": "test_fasta" + }, + [ + "Genome:md5,d41d8cd98f00b204e9800998ecf8427e", + "Log.out:md5,d41d8cd98f00b204e9800998ecf8427e", + "SA:md5,d41d8cd98f00b204e9800998ecf8427e", + "SAindex:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrName.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrNameLength.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "chrStart.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genomeParameters.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,0c6c5fab50cc8601f9072268a2f49aad" + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-01T15:54:57.552329" + "timestamp": "2024-12-11T16:30:22.674364031" }, - "fasta_versions": { + "fasta": { "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]", [ - "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + "versions.yml:md5,0c6c5fab50cc8601f9072268a2f49aad" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:54:57.560541" - }, - "fasta_gtf_index": { - "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-01T15:54:31.786814" - }, - "fasta_stub_index": { - "content": [ - "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-02-01T15:55:07.517472" + "timestamp": "2024-12-11T16:29:57.958812354" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index c4235872..fe48f542 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,8 +1,9 @@ -name: tabix_bgziptabix +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults + dependencies: + - bioconda::htslib=1.20 - bioconda::tabix=1.11 - - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index bcdcf2a6..22f37a77 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : - 'biocontainers/htslib:1.19.1--h81da01d_1' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(input) @@ -24,7 +24,7 @@ process TABIX_BGZIPTABIX { def prefix = task.ext.prefix ?: "${meta.id}" """ bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz - tabix $args2 ${prefix}.${input.getExtension()}.gz + tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -34,10 +34,11 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" + def args2 = task.ext.args2 ?: '' + def index = args2.contains("-C ") || args2.contains("--csi") ? "csi" : "tbi" """ echo "" | gzip > ${prefix}.${input.getExtension()}.gz - touch ${prefix}.${input.getExtension()}.gz.tbi - touch ${prefix}.${input.getExtension()}.gz.csi + touch ${prefix}.${input.getExtension()}.gz.${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 438aba4d..806fbc12 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -13,38 +13,50 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file - pattern: "*.{bed,gff,sam,vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Sorted tab-delimited genome file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gz: - type: file - description: Output compressed file - pattern: "*.{gz}" - - tbi: - type: file - description: tabix index file - pattern: "*.{gz.tbi}" - - csi: - type: file - description: tabix alternate index file - pattern: "*.{gz.csi}" + - gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.tbi": + type: file + description: tabix index file + pattern: "*.tbi" + - gz_csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.csi": + type: file + description: csi index file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@DLBPointon" diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test index 87ea2c84..4d4130dc 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'tbi_test' ], - [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] ] """ } @@ -43,7 +43,7 @@ nextflow_process { """ input[0] = [ [ id:'csi_test' ], - [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] ] """ } @@ -72,7 +72,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], - [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] ] """ } @@ -91,4 +91,33 @@ nextflow_process { } + test("sarscov2_bed_tbi_stub") { + config "./tabix_tbi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_stub") + } + ) + } + + } + } diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap index fcecb2e4..fb87799b 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -8,14 +8,14 @@ "id": "tbi_test" }, "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4" + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" ] ], "1": [ ], "2": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ], "gz_csi": [ @@ -26,15 +26,19 @@ "id": "tbi_test" }, "tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4" + "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c" ] ], "versions": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ] } ], - "timestamp": "2024-02-19T14:50:51.513838" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:16.053817543" }, "sarscov2_bed_csi": { "content": [ @@ -48,11 +52,11 @@ "id": "csi_test" }, "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43" + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" ] ], "2": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ], "gz_csi": [ [ @@ -60,48 +64,109 @@ "id": "csi_test" }, "csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74", - "csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43" + "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5" ] ], "gz_tbi": [ ], "versions": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ] } ], - "timestamp": "2024-02-19T14:51:00.513777" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T11:29:27.667745444" }, "csi_test": { "content": [ "csi_test.bed.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:51:00.548801" }, + "sarscov2_bed_tbi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.533169949" + }, "csi_stub": { "content": [ "test.bed.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:51:09.218454" }, + "tbi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.550930179" + }, "tbi_test": { "content": [ "tbi_test.bed.gz" ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, "timestamp": "2024-02-19T14:50:51.579654" }, "sarscov2_bed_csi_stub": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ [ @@ -113,7 +178,7 @@ ] ], "2": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ], "gz_csi": [ [ @@ -125,19 +190,17 @@ ] ], "gz_tbi": [ - [ - { - "id": "test" - }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ - "versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc" + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" ] } ], - "timestamp": "2024-02-19T14:51:09.164254" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:44:19.786135972" } } \ No newline at end of file diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 76b45e16..fe48f542 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,8 +1,9 @@ -name: tabix_tabix +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults + dependencies: + - bioconda::htslib=1.20 - bioconda::tabix=1.11 - - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf index 1737141d..13acd670 100644 --- a/modules/nf-core/tabix/tabix/main.nf +++ b/modules/nf-core/tabix/tabix/main.nf @@ -4,8 +4,8 @@ process TABIX_TABIX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' : - 'biocontainers/htslib:1.19.1--h81da01d_1' }" + 'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' : + 'biocontainers/htslib:1.20--h5efdd21_2' }" input: tuple val(meta), path(tab) @@ -21,7 +21,10 @@ process TABIX_TABIX { script: def args = task.ext.args ?: '' """ - tabix $args $tab + tabix \\ + --threads $task.cpus \\ + $args \\ + $tab cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -33,8 +36,8 @@ process TABIX_TABIX { """ touch ${tab}.tbi touch ${tab}.csi - cat <<-END_VERSIONS > versions.yml + cat <<-END_VERSIONS > versions.yml "${task.process}": tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//') END_VERSIONS diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index ae5b4f43..7864832d 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -11,34 +11,43 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file compressed with bgzip - pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tab: + type: file + description: TAB-delimited genome position file compressed with bgzip + pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: tabix index file + pattern: "*.{tbi}" - csi: - type: file - description: coordinate sorted index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: coordinate sorted index file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test index 3a150c70..102b0d7b 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'tbi_bed' ], - [ file(params.test_data['sarscov2']['genome']['test_bed_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ] ] """ } @@ -25,11 +25,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_bed") - } + process.out, + file(process.out.tbi[0][1]).name + ).match() } ) } } @@ -41,7 +40,7 @@ nextflow_process { """ input[0] = [ [ id:'tbi_gff' ], - [ file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ] ] """ } @@ -50,11 +49,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_gff") - } + process.out, + file(process.out.tbi[0][1]).name).match() } ) } @@ -67,7 +64,7 @@ nextflow_process { """ input[0] = [ [ id:'tbi_vcf' ], - [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] ] """ } @@ -76,11 +73,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.tbi[0][1]).name - ).match("tbi_vcf") - } + process.out, + file(process.out.tbi[0][1]).name + ).match() } ) } @@ -93,7 +89,7 @@ nextflow_process { """ input[0] = [ [ id:'vcf_csi' ], - [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] ] """ } @@ -102,11 +98,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.csi[0][1]).name - ).match("vcf_csi") - } + process.out, + file(process.out.csi[0][1]).name + ).match() } ) } @@ -120,7 +115,7 @@ nextflow_process { """ input[0] = [ [ id:'vcf_csi_stub' ], - [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ] ] """ } @@ -129,11 +124,10 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, { assert snapshot( - file(process.out.csi[0][1]).name - ).match("vcf_csi_stub") - } + process.out, + file(process.out.csi[0][1]).name + ).match() } ) } diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap index 034e38b6..c2b9ed0b 100644 --- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap @@ -1,16 +1,4 @@ { - "vcf_csi_stub": { - "content": [ - "test.vcf.gz.csi" - ], - "timestamp": "2024-03-04T14:51:59.788002" - }, - "tbi_gff": { - "content": [ - "genome.gff3.gz.tbi" - ], - "timestamp": "2024-02-19T14:53:37.420216" - }, "sarscov2_gff_tbi": { "content": [ { @@ -19,14 +7,14 @@ { "id": "tbi_gff" }, - "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178" + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" ] ], "1": [ ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ @@ -36,15 +24,20 @@ { "id": "tbi_gff" }, - "genome.gff3.gz.tbi:md5,53fc683fd217aae47ef10d23c52a9178" + "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926" ] ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "genome.gff3.gz.tbi" ], - "timestamp": "2024-02-19T14:53:37.388157" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:25.653807564" }, "sarscov2_bedgz_tbi": { "content": [ @@ -54,14 +47,14 @@ { "id": "tbi_bed" }, - "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8" + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" ] ], "1": [ ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ @@ -71,27 +64,20 @@ { "id": "tbi_bed" }, - "test.bed.gz.tbi:md5,0f17d85e7f0a042b2aa367b70df224f8" + "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d" ] ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } - ], - "timestamp": "2024-02-19T14:53:28.879408" - }, - "tbi_vcf": { - "content": [ - "test.vcf.gz.tbi" - ], - "timestamp": "2024-02-19T14:53:46.402522" - }, - "vcf_csi": { - "content": [ - "test.vcf.gz.csi" + }, + "test.bed.gz.tbi" ], - "timestamp": "2024-02-19T14:53:54.921189" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:09.754082161" }, "sarscov2_vcf_tbi": { "content": [ @@ -101,14 +87,14 @@ { "id": "tbi_vcf" }, - "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf" + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" ] ], "1": [ ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ @@ -118,15 +104,20 @@ { "id": "tbi_vcf" }, - "test.vcf.gz.tbi:md5,897f3f378a811b90e6dee56ce08d2bcf" + "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e" ] ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "test.vcf.gz.tbi" ], - "timestamp": "2024-02-19T14:53:46.370358" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:40.042648294" }, "sarscov2_vcf_csi_stub": { "content": [ @@ -148,7 +139,7 @@ ] ], "2": [ - "versions.yml:md5,3d45df6d80883bad358631069a2940fd" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ [ @@ -167,11 +158,16 @@ ] ], "versions": [ - "versions.yml:md5,3d45df6d80883bad358631069a2940fd" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } + }, + "test.vcf.gz.csi" ], - "timestamp": "2024-03-04T14:51:59.766184" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:07:08.700367261" }, "sarscov2_vcf_csi": { "content": [ @@ -184,34 +180,33 @@ { "id": "vcf_csi" }, - "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03" + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" ] ], "2": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ], "csi": [ [ { "id": "vcf_csi" }, - "test.vcf.gz.csi:md5,0731ad6f40104d2bbb1a2cc478ef8f03" + "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b" ] ], "tbi": [ ], "versions": [ - "versions.yml:md5,f4feeda7fdd4b567102f7f8e5d7037a3" + "versions.yml:md5,07064637fb8a217174052be8e40234e2" ] - } - ], - "timestamp": "2024-02-19T14:53:54.886876" - }, - "tbi_bed": { - "content": [ - "test.bed.gz.tbi" + }, + "test.vcf.gz.csi" ], - "timestamp": "2024-02-19T14:53:28.947628" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-19T12:06:55.362067748" } } \ No newline at end of file diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb10..9b926b1f 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,11 +1,12 @@ -name: untar - +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults - dependencies: + - conda-forge::coreutils=9.5 - conda-forge::grep=3.11 - - conda-forge::sed=4.7 + - conda-forge::gzip=1.13 + - conda-forge::lbzip2=2.5 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8a75bb95..e712ebe6 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -1,46 +1,46 @@ process UNTAR { - tag "$archive" + tag "${archive}" label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data' + : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}" input: tuple val(meta), path(archive) output: - tuple val(meta), path("$prefix"), emit: untar - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}"), emit: untar + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) + prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) """ - mkdir $prefix + mkdir ${prefix} ## Ensures --strip-components only applied when top level of tar contents is a directory ## If just files or multiple directories, place all in prefix if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then tar \\ - -C $prefix --strip-components 1 \\ + -C ${prefix} --strip-components 1 \\ -xavf \\ - $args \\ - $archive \\ - $args2 + ${args} \\ + ${archive} \\ + ${args2} else tar \\ - -C $prefix \\ + -C ${prefix} \\ -xavf \\ - $args \\ - $archive \\ - $args2 + ${args} \\ + ${archive} \\ + ${args2} fi cat <<-END_VERSIONS > versions.yml @@ -50,10 +50,31 @@ process UNTAR { """ stub: - prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) + prefix = task.ext.prefix ?: (meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ - mkdir $prefix - touch ${prefix}/file.txt + mkdir ${prefix} + ## Dry-run untaring the archive to get the files and place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch \${i} + else + mkdir -p \${i} + fi + done + else + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch ${prefix}/\${i} + else + mkdir -p ${prefix}/\${i} + fi + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f..3a37bb35 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,36 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*/" + - ${prefix}: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 2a7c97bf..c957517a 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -6,6 +6,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "untar" + test("test_untar") { when { @@ -19,10 +20,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar") }, + { assert snapshot(process.out).match() }, ) } - } test("test_untar_onlyfiles") { @@ -38,10 +38,48 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + { assert snapshot(process.out).match() }, ) } + } + + test("test_untar - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } } + test("test_untar_onlyfiles - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 64550292..ceb91b79 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,42 +1,158 @@ { "test_untar_onlyfiles": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:28.231047" + }, + "test_untar_onlyfiles - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:41.320643" + "timestamp": "2024-07-10T12:04:45.773103" + }, + "test_untar - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:36.777441" }, "test_untar": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:33.795172" + "timestamp": "2024-07-10T12:04:19.377674" } } \ No newline at end of file diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf index 291eddc1..d9c9e834 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf @@ -7,7 +7,7 @@ include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' workflow VCF_ANNOTATE_ENSEMBLVEP { take: - ch_vcf // channel: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optionnal)]] + ch_vcf // channel: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)]] ch_fasta // channel: [ val(meta2), path(fasta) ] (optional) val_genome // value: genome to use val_species // value: species to use diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml b/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml index 15d42da2..12677c68 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/meta.yml @@ -12,7 +12,7 @@ input: - ch_vcf: description: | vcf file to annotate - Structure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optionnal)] ] + Structure: [ val(meta), path(vcf), [path(custom_file1), path(custom_file2)... (optional)] ] - ch_fasta: description: | Reference genome fasta file (optional) From 5427d17571167a9883b977e1b3ac24d68475d1cf Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 16:13:01 +0100 Subject: [PATCH 243/275] fix workflow --- workflows/rnavar.nf | 23 +++++++++++++++++------ 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 01b3096b..65cb86b0 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -218,18 +218,29 @@ workflow RNAVAR { if (!params.skip_baserecalibration) { // known_sites is made by grouping both the dbsnp and the known indels ressources // they can either or both be optional - def known_sites = dbsnp.map { _meta, dbsnp_ -> dbsnp_ }.concat(known_indels).collect() - def known_sites_tbi = dbsnp_tbi.map { _meta, tbi -> tbi }.concat(known_indels_tbi).collect() + def known_sites = dbsnp + .map { _meta, dbsnp_ -> dbsnp_ } + .concat(known_indels) + .collect() + .map { files -> + [ [id:'known_sites'], files ] + } + def known_sites_tbi = dbsnp_tbi + .map { _meta, tbi -> tbi } + .concat(known_indels_tbi) + .collect() + .map { files -> + [ [id:'known_sites'], files ] + } def interval_list_recalib = interval_list.map{ _meta, bed -> [bed] }.flatten() def splitncigar_bam_bai_interval = splitncigar_bam_bai.combine(interval_list_recalib) - .map{ meta, bam, bai, interval -> [ meta, bam, bai, interval] } GATK4_BASERECALIBRATOR( splitncigar_bam_bai_interval, - fasta.map{ _meta, fasta_ -> [fasta_] }, - fasta_fai.map { _meta, fai -> fai }, - dict.map{ _meta, dict_ -> [dict_] }, + fasta, + fasta_fai, + dict, known_sites, known_sites_tbi ) From 5a0a69826414c6b0f462e197f294c6b4abc7657d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 16:47:03 +0100 Subject: [PATCH 244/275] fix snpeff download input --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index a4017512..55d6ecbe 100644 --- a/main.nf +++ b/main.nf @@ -145,7 +145,7 @@ workflow NFCORE_RNAVAR { if (params.download_cache) { // Assuming that even if the cache is provided, if the user specify download_cache, rnavar will download the cache ensemblvep_info = Channel.of([ [ id:"${params.vep_cache_version}_${params.vep_genome}" ], params.vep_genome, params.vep_species, params.vep_cache_version ]) - snpeff_info = Channel.of([ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], params.snpeff_genome, params.snpeff_db ]) + snpeff_info = Channel.of([ [ id:"${params.snpeff_genome}.${params.snpeff_db}" ], "${params.snpeff_genome}.${params.snpeff_db}" ]) DOWNLOAD_CACHE_SNPEFF_VEP(ensemblvep_info, snpeff_info) snpeff_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.snpeff_cache vep_cache = DOWNLOAD_CACHE_SNPEFF_VEP.out.ensemblvep_cache.map{ _meta, cache -> [ cache ] } From 5466f3c5ed131c6e2d3ff3320265e07cb6395350 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 17:25:00 +0100 Subject: [PATCH 245/275] fix order when no star index has been given --- subworkflows/local/prepare_genome/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index d28f6001..67ab101e 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -155,8 +155,8 @@ workflow PREPARE_GENOME { // def star_index_input = star_index.branch { _meta, index -> - tarzipped: index.name.endsWith(".tar.gz") no_index: !index + tarzipped: index.name.endsWith(".tar.gz") index: true } From 804e0e41b994de34421af4627546b7638a45223f Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Mon, 3 Mar 2025 16:47:49 +0000 Subject: [PATCH 246/275] update snapshots --- tests/all_inputs.nf.test.snap | 22 +++---- tests/annotation.nf.test.snap | 80 ++++++++++++----------- tests/bam_csi.nf.test.snap | 20 +++--- tests/bam_input.nf.test.snap | 22 +++---- tests/cram_input.nf.test.snap | 22 +++---- tests/default.nf.test.snap | 22 +++---- tests/extract_umi.nf.test.snap | 22 +++---- tests/removeduplicates.nf.test.snap | 22 +++---- tests/skip_baserecalibration.nf.test.snap | 18 ++--- 9 files changed, 126 insertions(+), 124 deletions(-) diff --git a/tests/all_inputs.nf.test.snap b/tests/all_inputs.nf.test.snap index 119a135f..1f7b4aa9 100644 --- a/tests/all_inputs.nf.test.snap +++ b/tests/all_inputs.nf.test.snap @@ -4,7 +4,7 @@ 79, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 @@ -13,25 +13,25 @@ "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -46,7 +46,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -60,7 +60,7 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -127,6 +127,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:33:31.371268626" + "timestamp": "2025-03-03T15:55:25.193517846" } } \ No newline at end of file diff --git a/tests/annotation.nf.test.snap b/tests/annotation.nf.test.snap index 0a8a49cd..00df0987 100644 --- a/tests/annotation.nf.test.snap +++ b/tests/annotation.nf.test.snap @@ -4,37 +4,38 @@ 47, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 }, "ENSEMBLVEP_VEP": { - "ensemblvep": 111.0 + "ensemblvep": 113.0, + "tabix": 1.21 }, "FASTQC": { "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -49,7 +50,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -66,13 +67,13 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "TABIX_BGZIPTABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "TABIX_TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -259,44 +260,45 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:46:27.75077738" + "timestamp": "2025-03-03T16:12:01.018371164" }, "Run with profile test | annotation with vep": { "content": [ 44, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 }, "ENSEMBLVEP_VEP": { - "ensemblvep": 111.0 + "ensemblvep": 113.0, + "tabix": 1.21 }, "FASTQC": { "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -311,7 +313,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -325,10 +327,10 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "TABIX_TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -502,14 +504,14 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:41:21.446868258" + "timestamp": "2025-03-03T16:07:16.86368092" }, "Run with profile test | annotation with snpeff": { "content": [ 44, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 @@ -518,25 +520,25 @@ "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -551,7 +553,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -568,10 +570,10 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "TABIX_BGZIPTABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -641,6 +643,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:36:52.683033566" + "timestamp": "2025-03-03T16:01:07.177008312" } } \ No newline at end of file diff --git a/tests/bam_csi.nf.test.snap b/tests/bam_csi.nf.test.snap index f47f216b..dfb10cc5 100644 --- a/tests/bam_csi.nf.test.snap +++ b/tests/bam_csi.nf.test.snap @@ -4,7 +4,7 @@ 40, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 @@ -13,22 +13,22 @@ "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -43,7 +43,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -57,7 +57,7 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -102,6 +102,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:51:12.605457529" + "timestamp": "2025-03-03T16:16:20.863243018" } } \ No newline at end of file diff --git a/tests/bam_input.nf.test.snap b/tests/bam_input.nf.test.snap index 5e2994fd..a76b9141 100644 --- a/tests/bam_input.nf.test.snap +++ b/tests/bam_input.nf.test.snap @@ -4,40 +4,40 @@ 28, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "SAMTOOLS_INDEX": { "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { "samtools": 1.21 }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -73,6 +73,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:54:12.491719133" + "timestamp": "2025-03-03T16:20:09.300905173" } } \ No newline at end of file diff --git a/tests/cram_input.nf.test.snap b/tests/cram_input.nf.test.snap index d5926438..5178e7ba 100644 --- a/tests/cram_input.nf.test.snap +++ b/tests/cram_input.nf.test.snap @@ -4,40 +4,40 @@ 28, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "SAMTOOLS_INDEX": { "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_STATS": { "samtools": 1.21 }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -73,6 +73,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T13:57:55.375924294" + "timestamp": "2025-03-03T16:24:41.041611867" } } \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1f225707..6e769465 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -4,7 +4,7 @@ 41, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 @@ -13,25 +13,25 @@ "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -46,7 +46,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -60,7 +60,7 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -107,6 +107,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T14:01:49.031861331" + "timestamp": "2025-03-03T16:29:48.290653989" } } \ No newline at end of file diff --git a/tests/extract_umi.nf.test.snap b/tests/extract_umi.nf.test.snap index 0ecf7a8e..5d3f29d8 100644 --- a/tests/extract_umi.nf.test.snap +++ b/tests/extract_umi.nf.test.snap @@ -4,31 +4,31 @@ 41, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "FASTQC": { "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -43,7 +43,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -57,7 +57,7 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "UMITOOLS_EXTRACT": { "umitools": "1.1.5" @@ -110,6 +110,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-03-03T13:25:38.180578622" + "timestamp": "2025-03-03T16:34:10.154536954" } } \ No newline at end of file diff --git a/tests/removeduplicates.nf.test.snap b/tests/removeduplicates.nf.test.snap index 388fbac2..8909d557 100644 --- a/tests/removeduplicates.nf.test.snap +++ b/tests/removeduplicates.nf.test.snap @@ -4,7 +4,7 @@ 41, { "APPLYBQSR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "CAT_FASTQ": { "cat": 9.5 @@ -13,25 +13,25 @@ "fastqc": "0.12.1" }, "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -46,7 +46,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -60,7 +60,7 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -107,6 +107,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T14:05:08.874427283" + "timestamp": "2025-03-03T16:38:55.840118536" } } \ No newline at end of file diff --git a/tests/skip_baserecalibration.nf.test.snap b/tests/skip_baserecalibration.nf.test.snap index d7e07a4e..e9bfaac4 100644 --- a/tests/skip_baserecalibration.nf.test.snap +++ b/tests/skip_baserecalibration.nf.test.snap @@ -10,22 +10,22 @@ "fastqc": "0.12.1" }, "GATK4_BEDTOINTERVALLIST": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_HAPLOTYPECALLER": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_INTERVALLISTTOOLS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_MERGEVCFS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_SPLITNCIGARREADS": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "GATK4_VARIANTFILTRATION": { - "gatk4": "4.5.0.0" + "gatk4": "4.6.1.0" }, "PICARD_MARKDUPLICATES": { "picard": "3.3.0" @@ -40,7 +40,7 @@ "samtools": 1.21 }, "SAMTOOLS_MERGE": { - "samtools": "1.19.2" + "samtools": 1.21 }, "SAMTOOLS_SORT": { "samtools": 1.21 @@ -54,7 +54,7 @@ "gawk": "5.1.0" }, "TABIX": { - "tabix": "1.19.1" + "tabix": 1.2 }, "Workflow": { "nf-core/rnavar": "v2.0.0dev" @@ -99,6 +99,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-28T14:08:15.055621292" + "timestamp": "2025-03-03T16:43:53.820362584" } } \ No newline at end of file From 0ef259056487dcb81dd8430aa905ee053020bf25 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Mon, 3 Mar 2025 17:59:42 +0100 Subject: [PATCH 247/275] bump changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 584d5a61..a36350c1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#161](https://github.com/nf-core/rnavar/pull/161) - Template update for nf-core/tools v3.2.0 - [#167](https://github.com/nf-core/rnavar/pull/167) - Removed the strandedness field from the samplesheet as it wasn't used in the pipeline. - [#172](https://github.com/nf-core/rnavar/pull/172) - Added support for TSV, JSON and YAML samplesheets +- [#182](https://github.com/nf-core/rnavar/pull/182) - Bumped all modules to the latest version (as of 03/03/2025) ### Fixed From e84ea35bba98c7b2d46d635b72dfb60961ed5fcd Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 09:51:02 +0100 Subject: [PATCH 248/275] fixed dbsnp and known_indels error handling --- main.nf | 4 ++++ workflows/rnavar.nf | 22 ++++++++++++---------- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/main.nf b/main.nf index 55d6ecbe..0f986b48 100644 --- a/main.nf +++ b/main.nf @@ -71,6 +71,10 @@ workflow NFCORE_RNAVAR { error("Expected --umitools_bc_pattern when --extract_umi is specified.") } + if(!params.skip_baserecalibration && !params.dbsnp && !params.known_indels) { + error("Known sites are required for performing base recalibration. Supply them with either --dbsnp and/or --known_sites or disable base recalibration with --skip_baserecalibration") + } + // Initialize fasta file with meta map: ch_fasta_raw = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty() diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index 65cb86b0..a4d433a2 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -219,19 +219,21 @@ workflow RNAVAR { // known_sites is made by grouping both the dbsnp and the known indels ressources // they can either or both be optional def known_sites = dbsnp - .map { _meta, dbsnp_ -> dbsnp_ } - .concat(known_indels) - .collect() - .map { files -> - [ [id:'known_sites'], files ] + .combine(known_indels) + .map { _meta, dbsnp_, known_indels_=[] -> + def file_list = [dbsnp_] + file_list.add(known_indels_) + return [[id:"known_sites"], file_list.flatten().findAll { entry -> entry != [] }] } - def known_sites_tbi = dbsnp_tbi - .map { _meta, tbi -> tbi } - .concat(known_indels_tbi) .collect() - .map { files -> - [ [id:'known_sites'], files ] + def known_sites_tbi = dbsnp_tbi + .combine(known_indels_tbi) + .map { _meta, dbsnp_, known_indels_=[] -> + def file_list = [dbsnp_] + file_list.add(known_indels_) + return [[id:"known_sites"], file_list.flatten().findAll { entry -> entry != [] }] } + .collect() def interval_list_recalib = interval_list.map{ _meta, bed -> [bed] }.flatten() def splitncigar_bam_bai_interval = splitncigar_bam_bai.combine(interval_list_recalib) From 9149f72b6d7b0f14a695e9fb496bc885db7a22d4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 09:53:39 +0100 Subject: [PATCH 249/275] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index a36350c1..d2843245 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -59,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#173](https://github.com/nf-core/rnavar/pull/173) - Added STAR index version control, the pipeline will now automatically detect a wrong STAR index version an create the correct index instead. - [#175](https://github.com/nf-core/rnavar/pull/175) - Fixed the handling of GFF files so they are now correctly being used. - [#177](https://github.com/nf-core/rnavar/pull/177) - Added a check and filter step for unknown regions in the exon BED. You can disable this check with `--skip_exon_bed_check`. +- [#184](https://github.com/nf-core/rnavar/pull/184) - Added an early error when --dbsnp and/or --known_indels were missing and base recalibration wasn't turned off. ### Dependencies From 346a6a772726263de54deb32c2e5de34d924c72e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 19:01:22 +0100 Subject: [PATCH 250/275] update modules.config --- conf/modules.config | 67 +++++++++++++++---------------- conf/modules/annotate.config | 4 +- conf/modules/prepare_cache.config | 4 +- 3 files changed, 37 insertions(+), 38 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index eac39d86..783c7f3b 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -24,7 +24,7 @@ process { process { - withName: CAT_FASTQ { + withName: 'NFCORE_RNAVAR:.*:CAT_FASTQ' { publishDir = [ path: { "${params.outdir}/fastq" }, mode: params.publish_dir_mode, @@ -33,23 +33,23 @@ process { ] } - withName: STAR_GENOMEGENERATE { + withName: 'NFCORE_RNAVAR:.*:STAR_GENOMEGENERATE' { ext.args = params.read_length ? "--sjdbOverhang ${params.read_length - 1}" : '' } - withName: STAR_INDEXVERSION { + withName: 'NFCORE_RNAVAR:.*:STAR_INDEXVERSION' { publishDir = [ enabled: false ] } - withName: '.*PREPARE_GENOME:UNTAR' { + withName: 'NFCORE_RNAVAR:.*:PREPARE_GENOME:UNTAR' { publishDir = [ enabled: false ] } - withName: REMOVE_UNKNOWN_REGIONS { + withName: 'NFCORE_RNAVAR:.*:REMOVE_UNKNOWN_REGIONS' { ext.prefix = { "${meta.id}.exon" } publishDir = [ path: { "${params.outdir}/genome" }, @@ -59,7 +59,7 @@ process { ] } - withName: 'STAR_GENOMEGENERATE' { + withName: 'NFCORE_RNAVAR:.*:STAR_GENOMEGENERATE' { publishDir = [ path: { "${params.outdir}/genome/index" }, mode: params.publish_dir_mode, @@ -68,7 +68,7 @@ process { ] } - withName: GFFREAD { + withName: 'NFCORE_RNAVAR:.*:GFFREAD' { ext.args = '--keep-exon-attrs -F -T' publishDir = [ path: { "${params.outdir}/genome" }, @@ -78,7 +78,7 @@ process { ] } - withName: GTF2BED { + withName: 'NFCORE_RNAVAR:.*:GTF2BED' { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -87,8 +87,7 @@ process { ] } - - withName: SAMTOOLS_FAIDX { + withName: 'NFCORE_RNAVAR:.*:SAMTOOLS_FAIDX' { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -97,7 +96,7 @@ process { ] } - withName: GATK4_CREATESEQUENCEDICTIONARY { + withName: 'NFCORE_RNAVAR:.*:GATK4_CREATESEQUENCEDICTIONARY' { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -111,7 +110,7 @@ process { process { - withName: MULTIQC { + withName: 'NFCORE_RNAVAR:.*:MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/reports"}, @@ -121,7 +120,7 @@ process { ] } - withName: FASTQC { + withName: 'NFCORE_RNAVAR:.*:FASTQC' { ext.args = '--quiet' publishDir = [ enabled: false @@ -133,7 +132,7 @@ process { process { // UMITOOLS_EXTRACT - withName: UMITOOLS_EXTRACT { + withName: 'NFCORE_RNAVAR:.*:UMITOOLS_EXTRACT' { ext.args = { [ params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '', params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '', @@ -144,7 +143,7 @@ process { // ALIGN_STAR - withName: STAR_ALIGN { + withName: 'NFCORE_RNAVAR:.*:STAR_ALIGN' { ext.args = { [ '--outSAMtype BAM SortedByCoordinate', '--readFilesCommand zcat', @@ -182,7 +181,7 @@ process { process { - withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { + withName: 'NFCORE_RNAVAR:.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { ext.prefix = {"${meta.id}.aligned"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, @@ -192,7 +191,7 @@ process { ] } - withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR:.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.aligned"} publishDir = [ @@ -203,11 +202,11 @@ process { ] } - withName: GATK4_BEDTOINTERVALLIST { + withName: 'NFCORE_RNAVAR:.*:GATK4_BEDTOINTERVALLIST' { publishDir = [ enabled: false ] } - withName: GATK4_INTERVALLISTTOOLS { + withName: 'NFCORE_RNAVAR:.*:GATK4_INTERVALLISTTOOLS' { ext.args = [ '--SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW', '--UNIQUE true', @@ -217,7 +216,7 @@ process { publishDir = [ enabled: false ] } - withName: 'PICARD_MARKDUPLICATES' { + withName: 'NFCORE_RNAVAR:.*:PICARD_MARKDUPLICATES' { ext.args = [ '--ASSUME_SORTED true', '--VALIDATION_STRINGENCY LENIENT', @@ -240,7 +239,7 @@ process { ] } - withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR:.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.md"} publishDir = [ @@ -251,20 +250,20 @@ process { ] } - withName: '.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { + withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { ext.args = '--create-output-bam-index false' ext.prefix = { "${meta.id}.splitncigarreads" } } - withName: '.*:SPLITNCIGAR:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' } - withName: '.*:SPLITNCIGAR:.*' { + withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:.*' { publishDir = [ enabled: false ] } - withName: 'SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' { + withName: 'NFCORE_RNAVAR:.*:SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' { publishDir = [ path: { "${params.outdir}/reports/stats/${meta.id}" }, mode: params.publish_dir_mode, @@ -278,12 +277,12 @@ process { // BASE RECALIBRATION PROCESS process { - withName: GATK4_BASERECALIBRATOR { + withName: 'NFCORE_RNAVAR:.*:GATK4_BASERECALIBRATOR' { ext.args = '--use-original-qualities' publishDir = [ enabled: false ] } - withName: '.*:RECALIBRATE:APPLYBQSR' { + withName: 'NFCORE_RNAVAR:.*:RECALIBRATE:APPLYBQSR' { ext.args = [ '--use-original-qualities', '--add-output-sam-program-record' @@ -297,7 +296,7 @@ process { ] } - withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR:.*:RECALIBRATE:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.recal"} publishDir = [ @@ -314,7 +313,7 @@ process { process { - withName: GATK4_HAPLOTYPECALLER { + withName: 'NFCORE_RNAVAR:.*:GATK4_HAPLOTYPECALLER' { ext.args = [ '--dont-use-soft-clipped-bases', '--create-output-variant-index true', @@ -324,7 +323,7 @@ process { publishDir = [ enabled: false ] } - withName: GATK4_MERGEVCFS { + withName: 'NFCORE_RNAVAR:.*:GATK4_MERGEVCFS' { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, @@ -332,7 +331,7 @@ process { pattern: "*.{vcf.gz}" ] } - withName: GATK4_COMBINEGVCFS { + withName: 'NFCORE_RNAVAR:.*:GATK4_COMBINEGVCFS' { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, @@ -341,7 +340,7 @@ process { ] } - withName: TABIX_TABIX { + withName: 'NFCORE_RNAVAR:.*:TABIX_TABIX' { ext.args = params.bam_csi_index ? '--csi' : '' ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ @@ -351,7 +350,7 @@ process { ] } - withName: GATK4_VARIANTFILTRATION { + withName: 'NFCORE_RNAVAR:.*:GATK4_VARIANTFILTRATION' { ext.prefix = {"${meta.id}.haplotypecaller.filtered"} ext.args = [ params.gatk_vf_window_size ? "--cluster-window-size $params.gatk_vf_window_size" : '', @@ -366,7 +365,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:RNAVAR:GATK4_BEDTOINTERVALLIST' { + withName: 'NFCORE_RNAVAR:.*:GATK4_BEDTOINTERVALLIST' { ext.args = '--DROP_MISSING_CONTIGS TRUE' } } diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 0704a6ca..08167a92 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -16,7 +16,7 @@ process { // SNPEFF - withName: 'SNPEFF_SNPEFF' { + withName: 'NFCORE_RNAVAR:.*:SNPEFF_SNPEFF' { ext.args = { '-nodownload -canon -v' } ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' } publishDir = [ @@ -30,7 +30,7 @@ process { } // VEP - withName: 'ENSEMBLVEP_VEP' { + withName: 'NFCORE_RNAVAR:.*:ENSEMBLVEP_VEP' { ext.args = { [ "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html", (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', diff --git a/conf/modules/prepare_cache.config b/conf/modules/prepare_cache.config index 7329d0ab..0fa0684e 100644 --- a/conf/modules/prepare_cache.config +++ b/conf/modules/prepare_cache.config @@ -16,7 +16,7 @@ process { // SNPEFF - withName: 'SNPEFF_DOWNLOAD' { + withName: 'NFCORE_RNAVAR:.*:SNPEFF_DOWNLOAD' { ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge')) } publishDir = [ mode: params.publish_dir_mode, @@ -25,7 +25,7 @@ process { } // VEP - withName: 'ENSEMBLVEP_DOWNLOAD' { + withName: 'NFCORE_RNAVAR:.*:ENSEMBLVEP_DOWNLOAD' { ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge')) } ext.args = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' } publishDir = [ From d48306bb02a1f73198d28062ae8f642c60b617c5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 11:07:27 +0100 Subject: [PATCH 251/275] WIP --- conf/modules.config | 66 +++++++++++++++---------------- conf/modules/annotate.config | 6 +-- conf/modules/prepare_cache.config | 4 +- 3 files changed, 38 insertions(+), 38 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 783c7f3b..b8e07e27 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -24,7 +24,7 @@ process { process { - withName: 'NFCORE_RNAVAR:.*:CAT_FASTQ' { + withName: 'NFCORE_RNAVAR.*CAT_FASTQ' { publishDir = [ path: { "${params.outdir}/fastq" }, mode: params.publish_dir_mode, @@ -33,23 +33,23 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:STAR_GENOMEGENERATE' { + withName: 'NFCORE_RNAVAR.*STAR_GENOMEGENERATE' { ext.args = params.read_length ? "--sjdbOverhang ${params.read_length - 1}" : '' } - withName: 'NFCORE_RNAVAR:.*:STAR_INDEXVERSION' { + withName: 'NFCORE_RNAVAR.*STAR_INDEXVERSION' { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:PREPARE_GENOME:UNTAR' { + withName: 'NFCORE_RNAVAR.*PREPARE_GENOME:UNTAR' { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:REMOVE_UNKNOWN_REGIONS' { + withName: 'NFCORE_RNAVAR.*REMOVE_UNKNOWN_REGIONS' { ext.prefix = { "${meta.id}.exon" } publishDir = [ path: { "${params.outdir}/genome" }, @@ -59,7 +59,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:STAR_GENOMEGENERATE' { + withName: 'NFCORE_RNAVAR.*STAR_GENOMEGENERATE' { publishDir = [ path: { "${params.outdir}/genome/index" }, mode: params.publish_dir_mode, @@ -68,7 +68,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:GFFREAD' { + withName: 'NFCORE_RNAVAR.*GFFREAD' { ext.args = '--keep-exon-attrs -F -T' publishDir = [ path: { "${params.outdir}/genome" }, @@ -78,7 +78,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:GTF2BED' { + withName: 'NFCORE_RNAVAR.*GTF2BED' { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -87,7 +87,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:SAMTOOLS_FAIDX' { + withName: 'NFCORE_RNAVAR.*SAMTOOLS_FAIDX' { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -96,7 +96,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_CREATESEQUENCEDICTIONARY' { + withName: 'NFCORE_RNAVAR.*GATK4_CREATESEQUENCEDICTIONARY' { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -110,7 +110,7 @@ process { process { - withName: 'NFCORE_RNAVAR:.*:MULTIQC' { + withName: 'NFCORE_RNAVAR.*MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/reports"}, @@ -120,7 +120,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:FASTQC' { + withName: 'NFCORE_RNAVAR.*FASTQC' { ext.args = '--quiet' publishDir = [ enabled: false @@ -132,7 +132,7 @@ process { process { // UMITOOLS_EXTRACT - withName: 'NFCORE_RNAVAR:.*:UMITOOLS_EXTRACT' { + withName: 'NFCORE_RNAVAR.*UMITOOLS_EXTRACT' { ext.args = { [ params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '', params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '', @@ -143,7 +143,7 @@ process { // ALIGN_STAR - withName: 'NFCORE_RNAVAR:.*:STAR_ALIGN' { + withName: 'NFCORE_RNAVAR.*STAR_ALIGN' { ext.args = { [ '--outSAMtype BAM SortedByCoordinate', '--readFilesCommand zcat', @@ -181,7 +181,7 @@ process { process { - withName: 'NFCORE_RNAVAR:.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { + withName: 'NFCORE_RNAVAR.*ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { ext.prefix = {"${meta.id}.aligned"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, @@ -191,7 +191,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR.*ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.aligned"} publishDir = [ @@ -202,11 +202,11 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_BEDTOINTERVALLIST' { + withName: 'NFCORE_RNAVAR.*GATK4_BEDTOINTERVALLIST' { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_INTERVALLISTTOOLS' { + withName: 'NFCORE_RNAVAR.*GATK4_INTERVALLISTTOOLS' { ext.args = [ '--SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW', '--UNIQUE true', @@ -216,7 +216,7 @@ process { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:PICARD_MARKDUPLICATES' { + withName: 'NFCORE_RNAVAR.*PICARD_MARKDUPLICATES' { ext.args = [ '--ASSUME_SORTED true', '--VALIDATION_STRINGENCY LENIENT', @@ -239,7 +239,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR.*BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.md"} publishDir = [ @@ -250,20 +250,20 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { + withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { ext.args = '--create-output-bam-index false' ext.prefix = { "${meta.id}.splitncigarreads" } } - withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' } - withName: 'NFCORE_RNAVAR:.*:SPLITNCIGAR:.*' { + withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:*' { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' { + withName: 'NFCORE_RNAVAR.*SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' { publishDir = [ path: { "${params.outdir}/reports/stats/${meta.id}" }, mode: params.publish_dir_mode, @@ -277,12 +277,12 @@ process { // BASE RECALIBRATION PROCESS process { - withName: 'NFCORE_RNAVAR:.*:GATK4_BASERECALIBRATOR' { + withName: 'NFCORE_RNAVAR.*GATK4_BASERECALIBRATOR' { ext.args = '--use-original-qualities' publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:RECALIBRATE:APPLYBQSR' { + withName: 'NFCORE_RNAVAR.*RECALIBRATE:APPLYBQSR' { ext.args = [ '--use-original-qualities', '--add-output-sam-program-record' @@ -296,7 +296,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:RECALIBRATE:SAMTOOLS_INDEX' { + withName: 'NFCORE_RNAVAR.*RECALIBRATE:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.recal"} publishDir = [ @@ -313,7 +313,7 @@ process { process { - withName: 'NFCORE_RNAVAR:.*:GATK4_HAPLOTYPECALLER' { + withName: 'NFCORE_RNAVAR.*GATK4_HAPLOTYPECALLER' { ext.args = [ '--dont-use-soft-clipped-bases', '--create-output-variant-index true', @@ -323,7 +323,7 @@ process { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_MERGEVCFS' { + withName: 'NFCORE_RNAVAR.*GATK4_MERGEVCFS' { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, @@ -331,7 +331,7 @@ process { pattern: "*.{vcf.gz}" ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_COMBINEGVCFS' { + withName: 'NFCORE_RNAVAR.*GATK4_COMBINEGVCFS' { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, @@ -340,7 +340,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:TABIX_TABIX' { + withName: 'NFCORE_RNAVAR.*TABIX_TABIX' { ext.args = params.bam_csi_index ? '--csi' : '' ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ @@ -350,7 +350,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_VARIANTFILTRATION' { + withName: 'NFCORE_RNAVAR.*GATK4_VARIANTFILTRATION' { ext.prefix = {"${meta.id}.haplotypecaller.filtered"} ext.args = [ params.gatk_vf_window_size ? "--cluster-window-size $params.gatk_vf_window_size" : '', @@ -365,7 +365,7 @@ process { ] } - withName: 'NFCORE_RNAVAR:.*:GATK4_BEDTOINTERVALLIST' { + withName: 'NFCORE_RNAVAR.*GATK4_BEDTOINTERVALLIST' { ext.args = '--DROP_MISSING_CONTIGS TRUE' } } diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 08167a92..603b551c 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -16,7 +16,7 @@ process { // SNPEFF - withName: 'NFCORE_RNAVAR:.*:SNPEFF_SNPEFF' { + withName: 'NFCORE_RNAVAR.*SNPEFF_SNPEFF' { ext.args = { '-nodownload -canon -v' } ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' } publishDir = [ @@ -30,7 +30,7 @@ process { } // VEP - withName: 'NFCORE_RNAVAR:.*:ENSEMBLVEP_VEP' { + withName: 'NFCORE_RNAVAR.*ENSEMBLVEP_VEP' { ext.args = { [ "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html", (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', @@ -85,7 +85,7 @@ process { } // ALL ANNOTATION TOOLS - withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' { + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL.*(TABIX_BGZIPTABIX|TABIX_TABIX)' { ext.prefix = { input.name - '.vcf' } publishDir = [ mode: params.publish_dir_mode, diff --git a/conf/modules/prepare_cache.config b/conf/modules/prepare_cache.config index 0fa0684e..88cd4b1c 100644 --- a/conf/modules/prepare_cache.config +++ b/conf/modules/prepare_cache.config @@ -16,7 +16,7 @@ process { // SNPEFF - withName: 'NFCORE_RNAVAR:.*:SNPEFF_DOWNLOAD' { + withName: 'NFCORE_RNAVAR.*SNPEFF_DOWNLOAD' { ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge')) } publishDir = [ mode: params.publish_dir_mode, @@ -25,7 +25,7 @@ process { } // VEP - withName: 'NFCORE_RNAVAR:.*:ENSEMBLVEP_DOWNLOAD' { + withName: 'NFCORE_RNAVAR.*ENSEMBLVEP_DOWNLOAD' { ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge')) } ext.args = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' } publishDir = [ From 379e79c6d7c8921a7ef95b3f430759383dd4edc4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 11:17:15 +0100 Subject: [PATCH 252/275] keep config the same --- conf/modules.config | 67 ++++++++++++++++--------------- conf/modules/annotate.config | 6 +-- conf/modules/prepare_cache.config | 4 +- 3 files changed, 39 insertions(+), 38 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b8e07e27..eac39d86 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -24,7 +24,7 @@ process { process { - withName: 'NFCORE_RNAVAR.*CAT_FASTQ' { + withName: CAT_FASTQ { publishDir = [ path: { "${params.outdir}/fastq" }, mode: params.publish_dir_mode, @@ -33,23 +33,23 @@ process { ] } - withName: 'NFCORE_RNAVAR.*STAR_GENOMEGENERATE' { + withName: STAR_GENOMEGENERATE { ext.args = params.read_length ? "--sjdbOverhang ${params.read_length - 1}" : '' } - withName: 'NFCORE_RNAVAR.*STAR_INDEXVERSION' { + withName: STAR_INDEXVERSION { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*PREPARE_GENOME:UNTAR' { + withName: '.*PREPARE_GENOME:UNTAR' { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*REMOVE_UNKNOWN_REGIONS' { + withName: REMOVE_UNKNOWN_REGIONS { ext.prefix = { "${meta.id}.exon" } publishDir = [ path: { "${params.outdir}/genome" }, @@ -59,7 +59,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*STAR_GENOMEGENERATE' { + withName: 'STAR_GENOMEGENERATE' { publishDir = [ path: { "${params.outdir}/genome/index" }, mode: params.publish_dir_mode, @@ -68,7 +68,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*GFFREAD' { + withName: GFFREAD { ext.args = '--keep-exon-attrs -F -T' publishDir = [ path: { "${params.outdir}/genome" }, @@ -78,7 +78,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*GTF2BED' { + withName: GTF2BED { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -87,7 +87,8 @@ process { ] } - withName: 'NFCORE_RNAVAR.*SAMTOOLS_FAIDX' { + + withName: SAMTOOLS_FAIDX { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -96,7 +97,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*GATK4_CREATESEQUENCEDICTIONARY' { + withName: GATK4_CREATESEQUENCEDICTIONARY { publishDir = [ path: { "${params.outdir}/genome" }, mode: params.publish_dir_mode, @@ -110,7 +111,7 @@ process { process { - withName: 'NFCORE_RNAVAR.*MULTIQC' { + withName: MULTIQC { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/reports"}, @@ -120,7 +121,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*FASTQC' { + withName: FASTQC { ext.args = '--quiet' publishDir = [ enabled: false @@ -132,7 +133,7 @@ process { process { // UMITOOLS_EXTRACT - withName: 'NFCORE_RNAVAR.*UMITOOLS_EXTRACT' { + withName: UMITOOLS_EXTRACT { ext.args = { [ params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '', params.umitools_bc_pattern ? "--bc-pattern='${params.umitools_bc_pattern}'" : '', @@ -143,7 +144,7 @@ process { // ALIGN_STAR - withName: 'NFCORE_RNAVAR.*STAR_ALIGN' { + withName: STAR_ALIGN { ext.args = { [ '--outSAMtype BAM SortedByCoordinate', '--readFilesCommand zcat', @@ -181,7 +182,7 @@ process { process { - withName: 'NFCORE_RNAVAR.*ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { + withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT' { ext.prefix = {"${meta.id}.aligned"} publishDir = [ path: { "${params.outdir}/preprocessing/${meta.id}" }, @@ -191,7 +192,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { + withName: '.*:ALIGN_STAR:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.aligned"} publishDir = [ @@ -202,11 +203,11 @@ process { ] } - withName: 'NFCORE_RNAVAR.*GATK4_BEDTOINTERVALLIST' { + withName: GATK4_BEDTOINTERVALLIST { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*GATK4_INTERVALLISTTOOLS' { + withName: GATK4_INTERVALLISTTOOLS { ext.args = [ '--SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW', '--UNIQUE true', @@ -216,7 +217,7 @@ process { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*PICARD_MARKDUPLICATES' { + withName: 'PICARD_MARKDUPLICATES' { ext.args = [ '--ASSUME_SORTED true', '--VALIDATION_STRINGENCY LENIENT', @@ -239,7 +240,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { + withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.md"} publishDir = [ @@ -250,20 +251,20 @@ process { ] } - withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { + withName: '.*:SPLITNCIGAR:GATK4_SPLITNCIGARREADS' { ext.args = '--create-output-bam-index false' ext.prefix = { "${meta.id}.splitncigarreads" } } - withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:SAMTOOLS_INDEX' { + withName: '.*:SPLITNCIGAR:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' } - withName: 'NFCORE_RNAVAR.*SPLITNCIGAR:*' { + withName: '.*:SPLITNCIGAR:.*' { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' { + withName: 'SAMTOOLS_STATS|SAMTOOLS_FLAGSTAT|SAMTOOLS_IDXSTATS' { publishDir = [ path: { "${params.outdir}/reports/stats/${meta.id}" }, mode: params.publish_dir_mode, @@ -277,12 +278,12 @@ process { // BASE RECALIBRATION PROCESS process { - withName: 'NFCORE_RNAVAR.*GATK4_BASERECALIBRATOR' { + withName: GATK4_BASERECALIBRATOR { ext.args = '--use-original-qualities' publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*RECALIBRATE:APPLYBQSR' { + withName: '.*:RECALIBRATE:APPLYBQSR' { ext.args = [ '--use-original-qualities', '--add-output-sam-program-record' @@ -296,7 +297,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*RECALIBRATE:SAMTOOLS_INDEX' { + withName: '.*:RECALIBRATE:SAMTOOLS_INDEX' { ext.args = params.bam_csi_index ? '-c' : '' ext.prefix = {"${meta.id}.recal"} publishDir = [ @@ -313,7 +314,7 @@ process { process { - withName: 'NFCORE_RNAVAR.*GATK4_HAPLOTYPECALLER' { + withName: GATK4_HAPLOTYPECALLER { ext.args = [ '--dont-use-soft-clipped-bases', '--create-output-variant-index true', @@ -323,7 +324,7 @@ process { publishDir = [ enabled: false ] } - withName: 'NFCORE_RNAVAR.*GATK4_MERGEVCFS' { + withName: GATK4_MERGEVCFS { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, @@ -331,7 +332,7 @@ process { pattern: "*.{vcf.gz}" ] } - withName: 'NFCORE_RNAVAR.*GATK4_COMBINEGVCFS' { + withName: GATK4_COMBINEGVCFS { ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ path: { "${params.outdir}/variant_calling/${meta.id}" }, @@ -340,7 +341,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*TABIX_TABIX' { + withName: TABIX_TABIX { ext.args = params.bam_csi_index ? '--csi' : '' ext.prefix = {"${meta.id}.haplotypecaller"} publishDir = [ @@ -350,7 +351,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*GATK4_VARIANTFILTRATION' { + withName: GATK4_VARIANTFILTRATION { ext.prefix = {"${meta.id}.haplotypecaller.filtered"} ext.args = [ params.gatk_vf_window_size ? "--cluster-window-size $params.gatk_vf_window_size" : '', @@ -365,7 +366,7 @@ process { ] } - withName: 'NFCORE_RNAVAR.*GATK4_BEDTOINTERVALLIST' { + withName: 'NFCORE_RNAVAR:RNAVAR:GATK4_BEDTOINTERVALLIST' { ext.args = '--DROP_MISSING_CONTIGS TRUE' } } diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 603b551c..0704a6ca 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -16,7 +16,7 @@ process { // SNPEFF - withName: 'NFCORE_RNAVAR.*SNPEFF_SNPEFF' { + withName: 'SNPEFF_SNPEFF' { ext.args = { '-nodownload -canon -v' } ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' } publishDir = [ @@ -30,7 +30,7 @@ process { } // VEP - withName: 'NFCORE_RNAVAR.*ENSEMBLVEP_VEP' { + withName: 'ENSEMBLVEP_VEP' { ext.args = { [ "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html", (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', @@ -85,7 +85,7 @@ process { } // ALL ANNOTATION TOOLS - withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL.*(TABIX_BGZIPTABIX|TABIX_TABIX)' { + withName: 'NFCORE_RNAVAR:RNAVAR:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' { ext.prefix = { input.name - '.vcf' } publishDir = [ mode: params.publish_dir_mode, diff --git a/conf/modules/prepare_cache.config b/conf/modules/prepare_cache.config index 88cd4b1c..7329d0ab 100644 --- a/conf/modules/prepare_cache.config +++ b/conf/modules/prepare_cache.config @@ -16,7 +16,7 @@ process { // SNPEFF - withName: 'NFCORE_RNAVAR.*SNPEFF_DOWNLOAD' { + withName: 'SNPEFF_DOWNLOAD' { ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('snpeff') || params.annotate_tools.split(',').contains('merge')) } publishDir = [ mode: params.publish_dir_mode, @@ -25,7 +25,7 @@ process { } // VEP - withName: 'NFCORE_RNAVAR.*ENSEMBLVEP_DOWNLOAD' { + withName: 'ENSEMBLVEP_DOWNLOAD' { ext.when = { params.annotate_tools && (params.annotate_tools.split(',').contains('vep') || params.annotate_tools.split(',').contains('merge')) } ext.args = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' } publishDir = [ From 3c338d589db879dd855bed0b6822eca1a908a85e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 11:19:11 +0100 Subject: [PATCH 253/275] properly ignore tests --- nf-test.config | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nf-test.config b/nf-test.config index b7213127..e2c877ef 100644 --- a/nf-test.config +++ b/nf-test.config @@ -8,6 +8,9 @@ config { // location of an optional nextflow.config file specific for executing tests configFile "tests/nextflow.config" + // ignore tests coming from the nf-core/modules repo + ignore 'modules/nf-core/*', 'subworkflows/nf-core/*' + // run all test with defined profile(s) from the main nextflow.config profile "test" From d956911fe0bf3d939ccd0a7dfa080b050832839c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 11:22:26 +0100 Subject: [PATCH 254/275] properly ignore tests --- nf-test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-test.config b/nf-test.config index e2c877ef..4ba00ef2 100644 --- a/nf-test.config +++ b/nf-test.config @@ -9,7 +9,7 @@ config { configFile "tests/nextflow.config" // ignore tests coming from the nf-core/modules repo - ignore 'modules/nf-core/*', 'subworkflows/nf-core/*' + ignore 'modules/nf-core/**/*', 'subworkflows/nf-core/**/*' // run all test with defined profile(s) from the main nextflow.config profile "test" From 9173ddce1c54b29903fa2c61c7029d953e5c9b96 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 11:38:32 +0100 Subject: [PATCH 255/275] update README --- README.md | 52 ++++++++++++++++++++++++++------------------- workflows/rnavar.nf | 2 +- 2 files changed, 31 insertions(+), 23 deletions(-) diff --git a/README.md b/README.md index 34ddd0d5..ff815b0b 100644 --- a/README.md +++ b/README.md @@ -30,32 +30,38 @@ 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html)) 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -3. Align reads to reference genome ([`STAR`](https://github.com/alexdobin/STAR)) -4. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/)) -5. Duplicate read marking ([`GATK4 MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard)) -6. Splits reads that contain Ns in their cigar string ([`GATK4 SplitNCigarReads`](https://gatk.broadinstitute.org/hc/en-us/articles/4409917482651-SplitNCigarReads)) -7. Estimate and correct systematic bias using base quality score recalibration ([`GATK4 BaseRecalibrator`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897206043-BaseRecalibrator), [`GATK4 ApplyBQSR`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897168667-ApplyBQSR)) -8. Convert a BED file to a Picard Interval List ([`GATK4 BedToIntervalList`](https://gatk.broadinstitute.org/hc/en-us/articles/4409924780827-BedToIntervalList-Picard-)) -9. Scatter one interval-list into many interval-files ([`GATK4 IntervalListTools`](https://gatk.broadinstitute.org/hc/en-us/articles/4409917392155-IntervalListTools-Picard-)) -10. Call SNPs and indels ([`GATK4 HaplotypeCaller`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897180827-HaplotypeCaller)) -11. Merge multiple VCF files into one VCF ([`GATK4 MergeVCFs`](https://gatk.broadinstitute.org/hc/en-us/articles/4409924817691-MergeVcfs-Picard-)) -12. Index the VCF ([`Tabix`](http://www.htslib.org/doc/tabix.html)) -13. Filter variant calls based on certain criteria ([`GATK4 VariantFiltration`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897204763-VariantFiltration)) -14. Annotate variants ([`snpEff`](https://pcingola.github.io/SnpEff/se_introduction/), [Ensembl VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)) -15. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/)) +3. (Optionally) Extract UMIs from FASTQ reads ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools)) +4. Align reads to reference genome ([`STAR`](https://github.com/alexdobin/STAR)) +5. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/)) +6. Duplicate read marking ([`Picard MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard)) +7. Scatter one interval-list into many interval-files ([`GATK4 IntervalListTools`](https://gatk.broadinstitute.org/hc/en-us/articles/4409917392155-IntervalListTools-Picard-)) +8. Splits reads that contain Ns in their cigar string ([`GATK4 SplitNCigarReads`](https://gatk.broadinstitute.org/hc/en-us/articles/4409917482651-SplitNCigarReads)) +9. Estimate and correct systematic bias using base quality score recalibration ([`GATK4 BaseRecalibrator`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897206043-BaseRecalibrator), [`GATK4 ApplyBQSR`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897168667-ApplyBQSR)) +10. Convert a BED file to a Picard Interval List ([`GATK4 BedToIntervalList`](https://gatk.broadinstitute.org/hc/en-us/articles/4409924780827-BedToIntervalList-Picard-)) +11. Call SNPs and indels ([`GATK4 HaplotypeCaller`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897180827-HaplotypeCaller)) +12. Merge multiple VCF files into one VCF ([`GATK4 MergeVCFs`](https://gatk.broadinstitute.org/hc/en-us/articles/4409924817691-MergeVcfs-Picard-)) +13. Index the VCF ([`Tabix`](http://www.htslib.org/doc/tabix.html)) +14. Filter variant calls based on certain criteria ([`GATK4 VariantFiltration`](https://gatk.broadinstitute.org/hc/en-us/articles/4409897204763-VariantFiltration)) +15. Annotate variants ([`snpEff`](https://pcingola.github.io/SnpEff/se_introduction/), [Ensembl VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)) +16. Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/)) ### Summary of tools and version used in the pipeline | Tool | Version | | ----------- | ------- | -| FastQC | 0.11.9 | -| STAR | 2.7.9a | -| Samtools | 1.15.1 | -| GATK | 4.2.6.1 | -| Tabix | 1.11 | -| SnpEff | 5.0 | -| Ensembl VEP | 104.3 | -| MultiQC | 1.12 | +| BCFtools | 1.20 | +| BEDtools | 2.31.1 | +| Ensembl VEP | 113.0 | +| FastQC | 0.12.1 | +| GATK | 4.6.1.0 | +| mosdepth | 0.3.10 | +| MultiQC | 1.27 | +| Picard | 3.3.0 | +| Samtools | 1.21 | +| SnpEff | 5.1 | +| STAR | 2.7.11b | +| Tabix | 1.20 | +| UMI-tools | 1.1.5 | ## Usage @@ -95,13 +101,15 @@ For more details about the output files and reports, please refer to the nf-core/rnavar was originally written in Nextflow DSL2 for use at the [Barntumörbanken, Karolinska Institutet](https://ki.se/forskning/barntumorbanken), by Praveen Raj ([@praveenraj2018](https://github.com/praveenraj2018)) and Maxime U Garcia ([@maxulysse](https://github.com/maxulysse)). nf-core/rnavar was originally written by Praveen Raj at [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken). -Maxime U Garcia at [The Swedish Childhood Tumor Biobank (Barntumörbanken)](https://ki.se/forskning/barntumorbanken) helped with development. +Maxime U Garcia at [Seqera](https://seqera.io/) helped with development. +Nicolas Vannieuwkerke at [CMGG](https://www.cmgg.be/en/) helped with development from version 1.2.0 and on. Maintenance is now lead by Maxime U Garcia (now at [Seqera Labs](https://seqera/io)) Main developers: - [Maxime U Garcia](https://github.com/maxulysse) +- [Nicolas Vannieuwkerke](https://github.com/nvnieuwk) We thank the following people for their extensive assistance in the development of this pipeline: diff --git a/workflows/rnavar.nf b/workflows/rnavar.nf index a4d433a2..e00e286f 100644 --- a/workflows/rnavar.nf +++ b/workflows/rnavar.nf @@ -94,7 +94,7 @@ workflow RNAVAR { return [ meta, cram, crai ] } - // MODULE: Prepare the alignment files (convert CRAM -> BAM and index) + // MODULE: Prepare the alignment files (index BAM/CRAM files that are missing an index) PREPARE_ALIGNMENT( parsed_input.cram, parsed_input.bam, From 0343d5a93d9b013c6a5a4d03398e5ad22f2d09fd Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 12:56:40 +0100 Subject: [PATCH 256/275] remove unused file --- test.gff | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 test.gff diff --git a/test.gff b/test.gff deleted file mode 100644 index e69de29b..00000000 From 23e3affba2d9575a38d5ca9710bd54ccba55252f Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 13:18:11 +0100 Subject: [PATCH 257/275] update citations --- CITATIONS.md | 68 ++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 55 insertions(+), 13 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 10a8f371..5b825ec2 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,42 +10,84 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [BCFTools](https://pubmed.ncbi.nlm.nih.gov/21903627/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011 Nov 1;27(21):2987-93. doi: 10.1093/bioinformatics/btr509. PubMed PMID: 21903627; PubMed Central PMCID: PMC3198575. -- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) +- [BEDTools](https://pubmed.ncbi.nlm.nih.gov/20110278/) - > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905. + > Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28. PMID: 20110278; PMCID: PMC2832824. -- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) +- [cat](https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html#cat-invocation) - > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. +- [coreutils](https://www.gnu.org/software/coreutils/) + +- [EnsemblVEP](https://pubmed.ncbi.nlm.nih.gov/27268795/) + + > McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825. + +- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/) > McKenna A, Hanna M, Banks E, et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed Central PMCID: PMC2928508. -- [snpEff](https://pubmed.ncbi.nlm.nih.gov/22728672/) +- [gawk](https://www.gnu.org/software/gawk/) - > Cingolani P, Platts A, Wang le L, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). Apr-Jun 2012;6(2):80-92. doi: 10.4161/fly.19695. PubMed PMID: 22728672; PubMed Central PMCID: PMC3679285. +- [GffRead](https://f1000research.com/articles/9-304/v1) -- [VEP](https://pubmed.ncbi.nlm.nih.gov/27268795/) + > Pertea G and Pertea M. GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]. F1000Research 2020, 9:304 (https://doi.org/10.12688/f1000research.23297.1) - > McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825. +- [grep](https://www.gnu.org/software/grep/) + +- [gzip](https://www.gnu.org/software/gzip/) + +- [Mosdepth](https://academic.oup.com/bioinformatics/article/34/5/867/4583630) + + > Brent S Pedersen, Aaron R Quinlan, Mosdepth: quick coverage calculation for genomes and exomes, Bioinformatics, Volume 34, Issue 5, 01 March 2018, Pages 867–868. doi: 10.1093/bioinformatics/btx699. PubMed PMID: 29096012. PubMed Central PMCID: PMC6030888. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) -> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. -- [Tabix](https://pubmed.ncbi.nlm.nih.gov/21208982/) +- [Picard](https://broadinstitute.github.io/picard/) - > Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719. doi: 10.1093/bioinformatics/btq671. PubMed PMID: 21208982; PubMed Central PMCID: PMC3042176. + > “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute - [R](https://www.R-project.org/) > R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. +- [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) + + > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. + +- [sed](https://www.gnu.org/software/sed/) + +- [snpEff](https://pubmed.ncbi.nlm.nih.gov/22728672/) + + > Cingolani P, Platts A, Wang le L, et al.: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). Apr-Jun 2012;6(2):80-92. doi: 10.4161/fly.19695. PubMed PMID: 22728672; PubMed Central PMCID: PMC3679285. + +- [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) + + > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905. + +- [Tabix](https://pubmed.ncbi.nlm.nih.gov/21208982/) + + > Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718–719. doi: 10.1093/bioinformatics/btq671. PubMed PMID: 21208982; PubMed Central PMCID: PMC3042176. + +- [tar](https://www.gnu.org/software/tar/) + +- [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/) + + > Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PMID: 28100584; PMCID: PMC5340976. + +- [VEP](https://pubmed.ncbi.nlm.nih.gov/27268795/) + + > McLaren W, Gil L, Hunt SE, et al.: The Ensembl Variant Effect Predictor. Genome Biol. 2016 Jun 6;17(1):122. doi: 10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PubMed Central PMCID: PMC4893825. + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) From a85e4cc516841e074c6f826d0e7abf2c09bfecb3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 14:28:06 +0100 Subject: [PATCH 258/275] update usage docs --- docs/usage.md | 61 +++++++++++++++++--------------------------- nextflow_schema.json | 55 ++++++++++++++++++++------------------- 2 files changed, 51 insertions(+), 65 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 77955985..d065bedf 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -90,7 +90,7 @@ CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz #### Full samplesheet -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 4 columns to match those defined in the table below. +The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the `sample` column and one of these: `fastq_1`, `bam` or `cram`. A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. @@ -130,16 +130,16 @@ The minimum reference genome requirements are a FASTA and GTF file, all other fi > **NB:** Compressed reference files are also supported by the pipeline i.e. standard files with the `.gz` extension and indices folders with the `tar.gz` extension. -The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space. You can then either provide the appropriate reference genome files on the command-line via the appropriate parameters (e.g. `--star_index '/path/to/STAR/index/'`) or via a custom config file. +The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space. You can then either provide the appropriate reference genome files on the command-line via the appropriate parameters (e.g. `--star_index '/path/to/STAR/index/'`) or via a parameters file. > **NB:** If you are supplying a pre-built genome index file via `--star_index`, please ensure that the index has been generated with the latest STAR version i.e. v2.7.9a or above. In case if the pipeline found an incompatible index, it will generate a new one using the reference genome which will consume time and memory unnecessarily. - If `--genome` is provided then the FASTA and GTF files (and existing indices) will be automatically obtained from AWS-iGenomes unless these have already been downloaded locally in the path specified by `--igenomes_base`. -- If `--gff` is provided as input then this will be converted to a GTF file, or the latter will be used if both are provided. +- If `--gff` is provided as input then this will be converted to a GTF file. - The `--exon_bed` parameter file is expected to be exon coordinates with at least three columns i.e., in the file. The should be 0-based. If this parameter is not provided, the exon coordinates are extracted from the GTF file and generates a bed file by the process `GTF2BED`. - If `--star_index` is not provided then it will be generated from the reference genome FASTA file using `STAR --runmode genomeGenerate` command. -> **NB:** In case if you are providing a GTF and/or a BED file, please ensure that the chromosomes and contigs in the files are also present in the genome FASTA (and in the .dict) file. Otherwise `GATK BedToIntervalList` module is likely to fail if the chromosomes/contigs do not match with the reference genome data. +> **NB:** In case if you are providing a GTF and/or a BED file, please ensure that the chromosomes and contigs in the files are also present in the genome FASTA (and in the .dict) file. The pipeline automatically checks and filters out contigs unknown to the reference (`--fasta`). This check can be turned off with `--skip_exon_bed_check`. ### Recommendation when using very large genomes @@ -147,26 +147,30 @@ When the pipeline is used on very large genomes having chromosome size greater t > **NB:** When `--bam_csi_index` is used, variant filtration step will be disabled as `GATK VariantFiltration` does not currently support CSI index for the input VCF. It may be incorporated in the future when newer GATK versions support CSI for VCF inputs. +## FASTQ preprocessing + +UMIs (Unique Molecular Identifiers) can be extracted by specifying `--extract_umi`, `--umitools_bc_pattern` and for paired-end reads also `umitools_bc_pattern2`. The pipeline uses [UMI-tools](https://github.com/CGATOxford/UMI-tools) for this preprocessing step. Additionally, the extraction method used can be specified using `--umitools_extract_method` and the UMI separator can be specified using `--umitools_umi_separator`. + ## Alignment options The pipeline uses [STAR](https://github.com/alexdobin/STAR) to map the raw FastQ reads to the reference genome. STAR is fast but requires a lot of memory to run, typically around 38GB for the Human GRCh37 reference genome. By default, STAR runs in `2-pass` mode. For the most sensitive novel junction discovery, it is recommend running STAR in the 2-pass -mode. It does not increase the number of detected novel junctions, but allows to detect more splices reads mapping to novel junctions. The basic idea is to run 1st pass of STAR mapping with the usual parameters, then collect the junctions detected in the first pass, and use them as ”annotated” junctions for the 2nd pass mapping. You can turn off this feature by setting `--star_twopass false` in command line. +mode. It does not increase the number of detected novel junctions, but allows to detect more spliced reads mapping to novel junctions. The basic idea is to run 1st pass of STAR mapping with the usual parameters, then collect the junctions detected in the first pass, and use them as ”annotated” junctions for the 2nd pass mapping. You can turn off this feature by setting `--star_twopass false` in command line. Read length is an important parameter therefore it has to be used carefully. The default is set to 150, but it has to be changed according to the input reads. For example, if the input read length is 2x151bp, then you use `--read_length 151`. The `--read_length` parameter is used while generating an index as well as in the alignment process. In both processes, the pipeline use (read_length - 1) to the STAR parameter `--sjdbOverhang` as recommended in STAR documentation. > **NB:** Read length `--read_length` is an important parameter, therefore it has to set according to the input read length. If you are supplying a pre-built genome index, please make sure that you have used the same (read_length -1) during the genomeGenerate step. -STAR alignment generates a coordinated-sorted BAM file as output. The coordinate-sorting process can be very memory intensive when the input data is deep sequenced or the genome has many highly expressed loci. When the pipeline runs on memory constrained environment, sorting step may fail due to low memory. In such cases you may adjust the limit parameters such as `--star_limitBAMsortRAM`, `--star_outBAMsortingBinsN` and `--star_limitOutSJcollapsed` to increase the sorting memory and genomic bins. Refer the parameter documentation for the default values and adjust as appropriate based on your memory availability. +STAR alignment generates a coordinated-sorted BAM file as output. The coordinate-sorting process can be very memory intensive when the input data is deep sequenced or the genome has many highly expressed loci. When the pipeline runs on memory constrained environment, sorting step may fail due to low memory. In such cases you may adjust the limit parameters such as `--star_max_memory_bamsort`, `--star_bins_bamsort` and `--star_max_collapsed_junc` to increase the sorting memory and genomic bins. Refer the parameter documentation for the default values and adjust as appropriate based on your memory availability. -## Preprocessing options +## Postprocessing of alignment output -Marking duplicate reads is performed using `GATK4 MarkDuplicates` tool. The tool does not remove duplicate reads by default, however you can set `--remove_duplicates true` to remove them. +Marking duplicate reads is performed using `Picard MarkDuplicates` tool. The tool does not remove duplicate reads by default, however you can set `--remove_duplicates` to remove them. GATK best practices has been followed in this pipeline for RNA analysis, hence it uses GATK modules such as `SplitNCigarReads`, `BaseRecalibrator`, `ApplyBQSR`. The `BaseRecalibrator` process requires known variants sites VCF. ExAc, gnomAD, or dbSNP resources can be used as known sites of variation.You can supply the VCF and index files using parameters such as `--dbsnp`, `--dbsnp_tbi`, `--known_indels`, `--known_indels_tbi`. -> **NB:** Base recalibration can be turned off using `--skip_baserecalibration true` option. This is useful when you are analyzing data from non-model organisms where there is no known variant datasets exist. +> **NB:** Base recalibration can be turned off using `--skip_baserecalibration` option. This is useful when you are analyzing data from non-model organisms where there is no known variant datasets exist. `GATK SplitNCigarReads` is very time consuming step, therefore we made an attempt to break the GTF file into multiple chunks (scatters) using `GATK IntervalListTools` to run the process independently on each chunk in a parallel way to speed up the analysis. The default number of splits is set to 25, that means the GTF file is split into 25 smaller files and run `GATK SplitNCigarReads` on each of them in parallel. You can modify the number of splits using parameter `--gatk_interval_scatter_count`. @@ -174,7 +178,7 @@ GATK best practices has been followed in this pipeline for RNA analysis, hence i `GATK HaplotypeCaller` is used for variant calling with default minimum phred-scaled confidence threshold as 20. This value can be changed using paramerter `--gatk_hc_call_conf`. -The pipeline runs a hard-filtering step on the variants by default. It does not filter out any variants, rather it flags i.e. PASS or other flags such as FS, QD, SnpCluster, etc. in FILTER column of the VCF. The following are the default filter criteria, however it can be changed using the respective parameters. +The pipeline runs a soft-filtering step on the variants by default. It does not filter out any variants, rather it flags i.e. PASS or other flags such as FS, QD, SnpCluster, etc. in FILTER column of the VCF. The following are the default filter criteria, however it can be changed using the respective parameters. - `--gatk_vf_cluster_size` is set to 3. It is the number of SNPs which make up a cluster. - `--gatk_vf_window_size` is set to 35. The window size (in bases) in which to evaluate clustered SNPs. @@ -192,9 +196,9 @@ You can skip the variant annotation step using `--skip_variantannotation` parame ### Annotation cache Both `snpEff` and `VEP` enable usage of cache. -If cache is available on the machine where `rnavar` is run, it is possible to run annotation using cache. -You need to specify the cache directory using `--snpeff_cache` and `--vep_cache` in the command lines or within configuration files. -The cache will only be used when `--annotation_cache` and cache directories are specified (either in command lines or in a configuration file). +If the cache is available on the machine where `rnavar` is run, it is possible to run annotation using the cache. +You need to specify the cache directory using `--snpeff_cache` and `--vep_cache` on the command line or within a parameters file. +The cache will only be used when `--annotation_cache` and cache directories are specified (either on the command line or in a parameters file). Example: @@ -205,39 +209,22 @@ nextflow run nf-core/rnavar --input samplesheet.csv --genome GRCh38 -profile doc ### Download annotation cache -A `Nextflow` helper script [link](https://raw.githubusercontent.com/nf-core/sarek/master/download_cache.nf) has been designed to help downloading `snpEff` and `VEP` caches. -Such files are meant to be shared between multiple users, so this script is mainly meant for people administrating servers, clusters and advanced users. - -```bash -nextflow run download_cache.nf --snpeff_cache --snpeff_db --genome -nextflow run download_cache.nf --vep_cache --species --vep_cache_version --genome -``` - -### Using VEP CADD plugin +The [`annotation-cache`](https://github.com/annotation-cache) resource can be used to download `snpEff` and `vep` annotation cache directories. -To enable the use of the `VEP` `CADD` plugin: +#### Install snpEff annotation cache -- Download the `CADD` files -- Specify them (either on the command line, like in the example or in a configuration file) -- use the `--cadd_cache` flag - -Example: +The [`downloadsnpeffcache`](https://github.com/annotation-cache/downloadsnpeffcache) pipeline can be used to download snpEff annotation cache directories. Expected parameters are `--snpeff_db` (e.g. `105`) and `--snpeff_genome` (e.g. `GRCh38`). ```bash -nextflow run nf-core/rnavar --input samplesheet.csv --genome GRCh38 -profile docker --annotate_tools VEP VEP --cadd_cache \ - --cadd_indels \ - --cadd_indels_tbi \ - --cadd_wg_snvs \ - --cadd_wg_snvs_tbi +nextflow run annotation-cache/downloadsnpeffcache --outdir --snpeff_db --snpeff_genome ``` -### Downloading CADD files +#### Install VEP annotation cache -An helper script has been designed to help downloading `CADD` files. -Such files are meant to be share between multiple users, so this script is mainly meant for people administrating servers, clusters and advanced users. +The [`downloadvepcache`](https://github.com/annotation-cache/downloadvepcache) pipeline can be used to download VEP annotation cache directories. Expected parameters are `--vep_species` (e.g. `homo_sapiens`), `--vep_cache_version` (e.g. `110`) and `--vep_genome` (e.g. `GRCh38`). ```bash -nextflow run download_cache.nf --cadd_cache --cadd_version --genome +nextflow run annotation-cache/downloadvepcache --outdir --vep_species --vep_cache_version --vep_genome ``` ## GENERAL NEXTFLOW ARGUMENTS diff --git a/nextflow_schema.json b/nextflow_schema.json index 62d15274..2b02c0a3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -207,6 +207,21 @@ } } }, + "postprocessing": { + "title": "Postprocessing of alignment", + "type": "object", + "description": "Parameters for postprocessing of alignment files.", + "fa_icon": "fas fa-toolbox", + "properties": { + "remove_duplicates": { + "type": "boolean", + "fa_icon": "fas fa-hammer", + "description": "Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.", + "help_text": "Specify true for removing duplicates from BAM file during Picard MarkDuplicates step.", + "hidden": false + } + } + }, "alignment_options": { "title": "Alignment options", "type": "object", @@ -292,16 +307,9 @@ "preprocessing": { "title": "Preprocessing of alignment", "type": "object", - "description": "Parameters for preprocessing analysis.", + "description": "Parameters for preprocessing FASTQ files before alignment.", "fa_icon": "fas fa-toolbox", "properties": { - "remove_duplicates": { - "type": "boolean", - "fa_icon": "fas fa-hammer", - "description": "Specify whether to remove duplicates from the BAM during Picard MarkDuplicates step.", - "help_text": "Specify true for removing duplicates from BAM file during Picard MarkDuplicates step.", - "hidden": false - }, "extract_umi": { "type": "boolean", "fa_icon": "fas fa-hammer", @@ -400,7 +408,6 @@ "type": "boolean", "fa_icon": "fas fa-database", "description": "Enable the use of the VEP dbNSFP plugin.", - "hidden": true, "help_text": "For details, see [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#dbnsfp)." }, "dbnsfp": { @@ -410,8 +417,7 @@ "pattern": "^\\S+\\.gz$", "fa_icon": "fas fa-file", "description": "Path to dbNSFP processed file.", - "help_text": "To be used with `--vep_dbnsfp`.\ndbNSFP files and more information are available at https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#dbnsfp and https://sites.google.com/site/jpopgen/dbNSFP/", - "hidden": true + "help_text": "To be used with `--vep_dbnsfp`.\ndbNSFP files and more information are available at https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#dbnsfp and https://sites.google.com/site/jpopgen/dbNSFP/" }, "dbnsfp_tbi": { "type": "string", @@ -420,36 +426,31 @@ "pattern": "^\\S+\\.tbi$", "fa_icon": "fas fa-file", "description": "Path to dbNSFP tabix indexed file.", - "help_text": "To be used with `--vep_dbnsfp`.", - "hidden": true + "help_text": "To be used with `--vep_dbnsfp`." }, "dbnsfp_consequence": { "type": "string", "fa_icon": "fas fa-arrow-alt-circle-right", "description": "Consequence to annotate with", - "help_text": "To be used with `--vep_dbnsfp`.\nThis params is used to filter/limit outputs to a specific effect of the variant.\nThe set of consequence terms is defined by the Sequence Ontology and an overview of those used in VEP can be found here: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html\nIf one wants to filter using several consequences, then separate those by using '&' (i.e. 'consequence=3_prime_UTR_variant&intron_variant'.", - "hidden": true + "help_text": "To be used with `--vep_dbnsfp`.\nThis params is used to filter/limit outputs to a specific effect of the variant.\nThe set of consequence terms is defined by the Sequence Ontology and an overview of those used in VEP can be found here: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html\nIf one wants to filter using several consequences, then separate those by using '&' (i.e. 'consequence=3_prime_UTR_variant&intron_variant'." }, "dbnsfp_fields": { "type": "string", "fa_icon": "fas fa-border-all", "description": "Fields to annotate with", "default": "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF", - "help_text": "To be used with `--vep_dbnsfp`.\nThis params can be used to retrieve individual values from the dbNSFP file. The values correspond to the name of the columns in the dbNSFP file and are separated by comma.\nThe column names might differ between the different dbNSFP versions. Please check the Readme.txt file, which is provided with the dbNSFP file, to obtain the correct column names. The Readme file contains also a short description of the provided values and the version of the tools used to generate them.\n\nDefault value are explained below:\n\nrs_dbSNP - rs number from dbSNP\nHGVSc_VEP - HGVS coding variant presentation from VEP. Multiple entries separated by ';', corresponds to Ensembl_transcriptid\nHGVSp_VEP - HGVS protein variant presentation from VEP. Multiple entries separated by ';', corresponds to Ensembl_proteinid\n1000Gp3_EAS_AF - Alternative allele frequency in the 1000Gp3 East Asian descendent samples\n1000Gp3_AMR_AF - Alternative allele counts in the 1000Gp3 American descendent samples\nLRT_score - Original LRT two-sided p-value (LRTori), ranges from 0 to 1\nGERP++_RS - Conservation score. The larger the score, the more conserved the site, ranges from -12.3 to 6.17\ngnomAD_exomes_AF - Alternative allele frequency in the whole gnomAD exome samples.", - "hidden": true + "help_text": "To be used with `--vep_dbnsfp`.\nThis params can be used to retrieve individual values from the dbNSFP file. The values correspond to the name of the columns in the dbNSFP file and are separated by comma.\nThe column names might differ between the different dbNSFP versions. Please check the Readme.txt file, which is provided with the dbNSFP file, to obtain the correct column names. The Readme file contains also a short description of the provided values and the version of the tools used to generate them.\n\nDefault value are explained below:\n\nrs_dbSNP - rs number from dbSNP\nHGVSc_VEP - HGVS coding variant presentation from VEP. Multiple entries separated by ';', corresponds to Ensembl_transcriptid\nHGVSp_VEP - HGVS protein variant presentation from VEP. Multiple entries separated by ';', corresponds to Ensembl_proteinid\n1000Gp3_EAS_AF - Alternative allele frequency in the 1000Gp3 East Asian descendent samples\n1000Gp3_AMR_AF - Alternative allele counts in the 1000Gp3 American descendent samples\nLRT_score - Original LRT two-sided p-value (LRTori), ranges from 0 to 1\nGERP++_RS - Conservation score. The larger the score, the more conserved the site, ranges from -12.3 to 6.17\ngnomAD_exomes_AF - Alternative allele frequency in the whole gnomAD exome samples." }, "vep_loftee": { "type": "boolean", "fa_icon": "fas fa-database", "description": "Enable the use of the VEP LOFTEE plugin.", - "hidden": true, "help_text": "For details, see [here](https://github.com/konradjk/loftee)." }, "vep_spliceai": { "type": "boolean", "fa_icon": "fas fa-database", "description": "Enable the use of the VEP SpliceAI plugin.", - "hidden": true, "help_text": "For details, see [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#spliceai)." }, "spliceai_snv": { @@ -459,8 +460,7 @@ "pattern": "^\\S+\\.vcf\\.gz$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores snv file.", - "help_text": "To be used with `--vep_spliceai`.", - "hidden": true + "help_text": "To be used with `--vep_spliceai`." }, "spliceai_snv_tbi": { "type": "string", @@ -469,8 +469,7 @@ "pattern": "^\\S+\\.tbi$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores snv tabix indexed file.", - "help_text": "To be used with `--vep_spliceai`.", - "hidden": true + "help_text": "To be used with `--vep_spliceai`." }, "spliceai_indel": { "type": "string", @@ -479,8 +478,7 @@ "pattern": "^\\S+\\.vcf\\.gz$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores indel file.", - "help_text": "To be used with `--vep_spliceai`.", - "hidden": true + "help_text": "To be used with `--vep_spliceai`." }, "spliceai_indel_tbi": { "type": "string", @@ -489,14 +487,12 @@ "pattern": "^\\S+\\.tbi$", "fa_icon": "fas fa-file", "description": "Path to spliceai raw scores indel tabix indexed file.", - "help_text": "To be used with `--vep_spliceai`.", - "hidden": true + "help_text": "To be used with `--vep_spliceai`." }, "vep_spliceregion": { "type": "boolean", "fa_icon": "fas fa-database", "description": "Enable the use of the VEP SpliceRegion plugin.", - "hidden": true, "help_text": "For details, see [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#spliceregion) and [here](https://www.ensembl.info/2018/10/26/cool-stuff-the-vep-can-do-splice-site-variant-annotation/)." }, "vep_custom_args": { @@ -788,6 +784,9 @@ { "$ref": "#/$defs/pipeline_stage_options" }, + { + "$ref": "#/$defs/postprocessing" + }, { "$ref": "#/$defs/alignment_options" }, From 8a4dbde62c38ca7733594598c4f35c922f090325 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 14:42:55 +0100 Subject: [PATCH 259/275] update output docs --- docs/output.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index b6f44316..d9654b53 100644 --- a/docs/output.md +++ b/docs/output.md @@ -79,6 +79,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d If multiple libraries/runs have been provided for the same sample in the input samplesheet (e.g. to increase sequencing depth) then these will be merged at the very beginning of the pipeline in order to have consistent sample naming throughout the pipeline. Please refer to the [usage documentation](https://nf-co.re/rnavar/usage#samplesheet-input) to see how to specify these samples in the input samplesheet. +### umitools + +
    +Output files + +- `umitools` + - `*.umi_extract.fastq.gz`: For single-end data + - `*.umi_extract_1.fastq.gz`: For paired-end data + - `*.umi_extract_2.fastq.gz`: For paired-end data + - `*.umi_extract.log`: The log of the UMI extraction + +
    + +This output directory will only be made when `--extract_umi` has been specified. [UMI-tools](https://github.com/CGATOxford/UMI-tools) is a set of tools for handling Unique Molecular Identifiers in NGS data sets. In this pipeline the `extract` tool has been used to extract UMIs from the FASTQ files. Please refer to the [usage documentation](https://nf-co.re/rnavar/usage#samplesheet-input) for more information. + ## Alignment ### STAR @@ -109,7 +124,7 @@ If multiple libraries/runs have been provided for the same sample in the input s ### MarkDuplicates -[GATK MarkDuplicates](https://gatk.broadinstitute.org/hc/en-us/articles/360042477492-MarkDuplicates-Picard) locates and tags duplicate reads in a `BAM` file. The tool's main output is a new BAM file, in which duplicates have been identified in the SAM flags field for each read. +[Picard MarkDuplicates](https://gatk.broadinstitute.org/hc/en-us/articles/360042477492-MarkDuplicates-Picard) locates and tags duplicate reads in a `BAM` file. The tool's main output is a new BAM file, in which duplicates have been identified in the SAM flags field for each read. ![MultiQC - MarkDuplicate stats](images/read_markduplicates_stats.png) From afa81dd885b04f6901e764674037894147d7c8eb Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 14:44:28 +0100 Subject: [PATCH 260/275] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 10088fce..c6dfb73c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#172](https://github.com/nf-core/rnavar/pull/172) - Added support for TSV, JSON and YAML samplesheets - [#178](https://github.com/nf-core/rnavar/pull/178) - Implement automatic sharding for nf-test tests - [#182](https://github.com/nf-core/rnavar/pull/182) - Bumped all modules to the latest version (as of 03/03/2025) +- [#185](https://github.com/nf-core/rnavar/pull/185) - Updated the documentation ### Fixed From ad4db750da1b4fd284aeb12052dffc8dd8a542d1 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 4 Mar 2025 16:10:06 +0100 Subject: [PATCH 261/275] Update CITATIONS.md Co-authored-by: Maxime U Garcia --- CITATIONS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index 5b825ec2..7014e00d 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -28,7 +28,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [GATK](https://pubmed.ncbi.nlm.nih.gov/20644199/) From e9297af8b4516523f35ee2d1a46a0d475215c863 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Tue, 4 Mar 2025 15:17:01 +0000 Subject: [PATCH 262/275] add nvnieuwk to nextflow.config --- nextflow.config | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/nextflow.config b/nextflow.config index 6d8a6e5f..d955a5c9 100644 --- a/nextflow.config +++ b/nextflow.config @@ -322,6 +322,14 @@ manifest { contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') orcid: '0000-0003-2827-9261' ], + [ + name: 'Nicolas Vannieuwkerke', + affiliation: 'CMGG', + email: 'nicolas.vannieuwkerke@ugent.be', + github: '@nvnieuwk', + contribution: ['maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0009-0003-5619-1555' + ] ] homePage = 'https://github.com/nf-core/rnavar' description = """GATK4 RNA variant calling pipeline""" From db4410b82c3957e1e1ee368e82dfa426b8acbd05 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 16:33:33 +0100 Subject: [PATCH 263/275] add vcf_annotate_all tests --- modules.json | 3 +- modules/nf-core/snpeff/snpeff/main.nf | 3 + .../nf-core/snpeff/snpeff/snpeff-snpeff.diff | 22 ++ subworkflows/local/vcf_annotate_all/main.nf | 9 - .../local/vcf_annotate_all/tests/main.nf.test | 166 +++++++++++++++ .../vcf_annotate_all/tests/main.nf.test.snap | 195 ++++++++++++++++++ .../local/vcf_annotate_bcftools/main.nf | 28 --- tests/nextflow.config | 8 + 8 files changed, 396 insertions(+), 38 deletions(-) create mode 100644 modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff create mode 100644 subworkflows/local/vcf_annotate_all/tests/main.nf.test create mode 100644 subworkflows/local/vcf_annotate_all/tests/main.nf.test.snap delete mode 100644 subworkflows/local/vcf_annotate_bcftools/main.nf diff --git a/modules.json b/modules.json index efc246a5..d6870925 100755 --- a/modules.json +++ b/modules.json @@ -183,7 +183,8 @@ "snpeff/snpeff": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules", "vcf_annotate_snpeff"] + "installed_by": ["modules", "vcf_annotate_snpeff"], + "patch": "modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff" }, "star/align": { "branch": "master", diff --git a/modules/nf-core/snpeff/snpeff/main.nf b/modules/nf-core/snpeff/snpeff/main.nf index 28d13826..a59758b6 100644 --- a/modules/nf-core/snpeff/snpeff/main.nf +++ b/modules/nf-core/snpeff/snpeff/main.nf @@ -52,6 +52,9 @@ process SNPEFF_SNPEFF { def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.ann.vcf + touch ${prefix}.csv + touch ${prefix}.html + touch ${prefix}.genes.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff b/modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff new file mode 100644 index 00000000..3a7f34ec --- /dev/null +++ b/modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff @@ -0,0 +1,22 @@ +Changes in component 'nf-core/snpeff/snpeff' +Changes in 'snpeff/snpeff/main.nf': +--- modules/nf-core/snpeff/snpeff/main.nf ++++ modules/nf-core/snpeff/snpeff/main.nf +@@ -52,6 +52,9 @@ + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.ann.vcf ++ touch ${prefix}.csv ++ touch ${prefix}.html ++ touch ${prefix}.genes.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + +'modules/nf-core/snpeff/snpeff/environment.yml' is unchanged +'modules/nf-core/snpeff/snpeff/meta.yml' is unchanged +'modules/nf-core/snpeff/snpeff/tests/tags.yml' is unchanged +'modules/nf-core/snpeff/snpeff/tests/main.nf.test' is unchanged +'modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap' is unchanged +'modules/nf-core/snpeff/snpeff/tests/nextflow.config' is unchanged +************************************************************ diff --git a/subworkflows/local/vcf_annotate_all/main.nf b/subworkflows/local/vcf_annotate_all/main.nf index 8782a149..d3ff0975 100644 --- a/subworkflows/local/vcf_annotate_all/main.nf +++ b/subworkflows/local/vcf_annotate_all/main.nf @@ -2,7 +2,6 @@ // ANNOTATION // -include { VCF_ANNOTATE_BCFTOOLS } from '../vcf_annotate_bcftools/main' include { VCF_ANNOTATE_ENSEMBLVEP } from '../../nf-core/vcf_annotate_ensemblvep/main' include { VCF_ANNOTATE_ENSEMBLVEP as VCF_ANNOTATE_MERGE } from '../../nf-core/vcf_annotate_ensemblvep/main' include { VCF_ANNOTATE_SNPEFF } from '../../nf-core/vcf_annotate_snpeff/main' @@ -27,14 +26,6 @@ workflow VCF_ANNOTATE_ALL { def json_annotated = Channel.empty() def ch_versions = Channel.empty() - if (tools.split(',').contains('bcfann')) { - VCF_ANNOTATE_BCFTOOLS(vcf) - - vcf_annotated = vcf_annotated.mix(VCF_ANNOTATE_BCFTOOLS.out.vcf_tbi) - ch_versions = ch_versions.mix(VCF_ANNOTATE_BCFTOOLS.out.versions) - } - - if (tools.split(',').contains('merge') || tools.split(',').contains('snpeff')) { VCF_ANNOTATE_SNPEFF(vcf, snpeff_db, snpeff_cache) diff --git a/subworkflows/local/vcf_annotate_all/tests/main.nf.test b/subworkflows/local/vcf_annotate_all/tests/main.nf.test new file mode 100644 index 00000000..72c6204e --- /dev/null +++ b/subworkflows/local/vcf_annotate_all/tests/main.nf.test @@ -0,0 +1,166 @@ +nextflow_workflow { + + name "Test Subworkflow VCF_ANNOTATE_ALL" + script "../main.nf" + workflow "VCF_ANNOTATE_ALL" + + tag "subworkflows" + tag "subworkflows_local" + tag "subworkflows/vcf_annotate_all" + tag "ensemblvep/vep" + tag "snpeff/snpeff" + tag "subworkflows/vcf_annotate_ensemblvep" + tag "subworkflows/vcf_annotate_snpeff" + + options "-stub" + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../../../modules/nf-core/ensemblvep/download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"cache"], + params.vep_genome, + params.vep_species, + params.vep_cache_version + ]) + """ + } + } + + run("SNPEFF_DOWNLOAD") { + script "../../../../modules/nf-core/snpeff/download/main.nf" + + process { + """ + input[0] = Channel.of([ + [id:"cache"], + params.snpeff_db + ]) + """ + } + } + } + + test("vep") { + when { + params { + annotate_tools = "vep" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" + vep_cache_version = "110" + snpeff_db = "WBcel235.105" + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = params.annotate_tools + input[3] = params.snpeff_db // snpeff_db + input[4] = [] // snpeff_cache + input[5] = params.vep_genome // vep_genome + input[6] = params.vep_species // vep_species + input[7] = params.vep_cache_version // vep_cache_version + input[8] = ENSEMBLVEP_DOWNLOAD.out.cache.map { meta, cache -> cache } // vep_cache + input[9] = Channel.value([]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("snpeff") { + when { + params { + annotate_tools = "snpeff" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" + vep_cache_version = "110" + snpeff_db = "WBcel235.105" + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = params.annotate_tools + input[3] = params.snpeff_db // snpeff_db + input[4] = SNPEFF_DOWNLOAD.out.cache // snpeff_cache + input[5] = params.vep_genome // vep_genome + input[6] = params.vep_species // vep_species + input[7] = params.vep_cache_version // vep_cache_version + input[8] = [] // vep_cache + input[9] = Channel.value([]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("merge") { + when { + params { + annotate_tools = "merge" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" + vep_cache_version = "110" + snpeff_db = "WBcel235.105" + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = params.annotate_tools + input[3] = params.snpeff_db // snpeff_db + input[4] = SNPEFF_DOWNLOAD.out.cache // snpeff_cache + input[5] = params.vep_genome // vep_genome + input[6] = params.vep_species // vep_species + input[7] = params.vep_cache_version // vep_cache_version + input[8] = ENSEMBLVEP_DOWNLOAD.out.cache.map { meta, cache -> cache } // vep_cache + input[9] = Channel.value([]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match() } + ) + } + } +} diff --git a/subworkflows/local/vcf_annotate_all/tests/main.nf.test.snap b/subworkflows/local/vcf_annotate_all/tests/main.nf.test.snap new file mode 100644 index 00000000..b7abc1d1 --- /dev/null +++ b/subworkflows/local/vcf_annotate_all/tests/main.nf.test.snap @@ -0,0 +1,195 @@ +{ + "vep": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_VEP.ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_VEP.ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "test_VEP.ann_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "4": [ + "versions.yml:md5,6b4e45ba6bc1085f28e972f10c018f77", + "versions.yml:md5,6c3f1b0776837530cda145392ab8f18b" + ], + "json_ann": [ + + ], + "reports": [ + "test_VEP.ann_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "tab_ann": [ + + ], + "vcf_ann": [ + [ + { + "id": "test" + }, + "test_VEP.ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_VEP.ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6b4e45ba6bc1085f28e972f10c018f77", + "versions.yml:md5,6c3f1b0776837530cda145392ab8f18b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-04T16:19:31.736660565" + }, + "merge": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_VEP.ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_VEP.ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "test_snpEff.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "test_VEP.ann_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "4": [ + "versions.yml:md5,4a322b8b0f7017858530180a68232e96", + "versions.yml:md5,6fb558faa1c4c79e757970991dfbf118", + "versions.yml:md5,abf2b743072f2ba8b250b3925061622f", + "versions.yml:md5,d5804f2a2b5907e982d54dca0ba2db44" + ], + "json_ann": [ + + ], + "reports": [ + [ + "test_snpEff.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "test_VEP.ann_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "tab_ann": [ + + ], + "vcf_ann": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + { + "id": "test" + }, + "test_VEP.ann.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_VEP.ann.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4a322b8b0f7017858530180a68232e96", + "versions.yml:md5,6fb558faa1c4c79e757970991dfbf118", + "versions.yml:md5,abf2b743072f2ba8b250b3925061622f", + "versions.yml:md5,d5804f2a2b5907e982d54dca0ba2db44" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-04T16:32:38.738793297" + }, + "snpeff": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + "test_snpEff.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,4a322b8b0f7017858530180a68232e96", + "versions.yml:md5,d5804f2a2b5907e982d54dca0ba2db44" + ], + "json_ann": [ + + ], + "reports": [ + [ + "test_snpEff.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tab_ann": [ + + ], + "vcf_ann": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4a322b8b0f7017858530180a68232e96", + "versions.yml:md5,d5804f2a2b5907e982d54dca0ba2db44" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-04T16:32:26.089637442" + } +} \ No newline at end of file diff --git a/subworkflows/local/vcf_annotate_bcftools/main.nf b/subworkflows/local/vcf_annotate_bcftools/main.nf deleted file mode 100644 index d0327166..00000000 --- a/subworkflows/local/vcf_annotate_bcftools/main.nf +++ /dev/null @@ -1,28 +0,0 @@ - -// -// Run BCFtools to annotate VCF files -// - -include { BCFTOOLS_ANNOTATE } from '../../../modules/nf-core/bcftools/annotate/main' -include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' - -workflow VCF_ANNOTATE_BCFTOOLS { - take: - vcf // channel: [ val(meta), vcf ] - - main: - def ch_versions = Channel.empty() - - BCFTOOLS_ANNOTATE(vcf.map { meta, vcf_ -> [ meta, vcf_, [], [], [], []]}) - TABIX_TABIX(BCFTOOLS_ANNOTATE.out.vcf) - - vcf_tbi = BCFTOOLS_ANNOTATE.out.vcf.join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true) - - // Gather versions of all tools used - ch_versions = ch_versions.mix(BCFTOOLS_ANNOTATE.out.versions) - ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) - - emit: - vcf_tbi = vcf_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - versions = ch_versions // path: versions.yml -} diff --git a/tests/nextflow.config b/tests/nextflow.config index 8c817b3a..e7fef4b3 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -10,3 +10,11 @@ params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' } + +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} From 006610fe648493efee76ca0033d58b7e5bf20f93 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Tue, 4 Mar 2025 15:34:34 +0000 Subject: [PATCH 264/275] remove comments --- nextflow.config | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index d955a5c9..7a2b2dbc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -305,13 +305,12 @@ manifest { name = 'nf-core/rnavar' author = """Praveen Raj, Maxime U Garcia""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ name: 'Praveen Raj', affiliation: '', email: '', github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + contribution: [], orcid: '' ], [ @@ -319,7 +318,7 @@ manifest { affiliation: 'Seqera', email: 'maxime.garcia@seqera.io', github: '@maxulysse', - contribution: ['author'], // List of contribution types ('author', 'maintainer' or 'contributor') + contribution: ['author'], orcid: '0000-0003-2827-9261' ], [ @@ -327,7 +326,7 @@ manifest { affiliation: 'CMGG', email: 'nicolas.vannieuwkerke@ugent.be', github: '@nvnieuwk', - contribution: ['maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + contribution: ['maintainer'], orcid: '0009-0003-5619-1555' ] ] From bbd2eca80442aff532657a50f9f4927ef70dbb6b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Tue, 4 Mar 2025 17:19:16 +0100 Subject: [PATCH 265/275] add splitncigar tests --- .../local/splitncigar/tests/main.nf.test | 130 ++++++++++++++++++ .../local/splitncigar/tests/main.nf.test.snap | 82 +++++++++++ 2 files changed, 212 insertions(+) create mode 100644 subworkflows/local/splitncigar/tests/main.nf.test create mode 100644 subworkflows/local/splitncigar/tests/main.nf.test.snap diff --git a/subworkflows/local/splitncigar/tests/main.nf.test b/subworkflows/local/splitncigar/tests/main.nf.test new file mode 100644 index 00000000..e2496bb0 --- /dev/null +++ b/subworkflows/local/splitncigar/tests/main.nf.test @@ -0,0 +1,130 @@ +nextflow_workflow { + + name "Test Subworkflow SPLITNCIGAR" + script "../main.nf" + workflow "SPLITNCIGAR" + + tag "subworkflows" + tag "subworkflows_local" + tag "subworkflows/splitncigar" + tag "samtools/merge" + tag "samtools/index" + tag "gatk4/splitncigarreads" + + test("bam") { + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.value([ + [id:"fai"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + input[3] = Channel.value([ + [id:"dict"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + input[4] = Channel.of([[ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.filtered_intervals.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) + ]]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam_bai.collect { [it[0], bam(it[1]).readsMD5, file(it[2].toString()).name] }, + workflow.out.versions + ).match() } + ) + } + } + + test("cram") { + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.value([ + [id:"fai"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + input[3] = Channel.value([ + [id:"dict"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + input[4] = Channel.of([[ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.filtered_intervals.interval_list', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.interval_list', checkIfExists: true) + ]]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam_bai.collect { [it[0], bam(it[1]).readsMD5, file(it[2].toString()).name] }, + workflow.out.versions + ).match() } + ) + } + } + + test("no_intervals") { + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.value([ + [id:"fai"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + input[3] = Channel.value([ + [id:"dict"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + input[4] = Channel.of([[]]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam_bai.collect { [it[0], bam(it[1]).readsMD5, file(it[2].toString()).name] }, + workflow.out.versions + ).match() } + ) + } + } +} diff --git a/subworkflows/local/splitncigar/tests/main.nf.test.snap b/subworkflows/local/splitncigar/tests/main.nf.test.snap new file mode 100644 index 00000000..b87a39c9 --- /dev/null +++ b/subworkflows/local/splitncigar/tests/main.nf.test.snap @@ -0,0 +1,82 @@ +{ + "cram": { + "content": [ + [ + [ + { + "groupSize": 2, + "groupTarget": { + "id": "test" + } + }, + "67daadcc078bb45be360e1f2af46a8e5", + "test.bam.bai" + ] + ], + [ + "versions.yml:md5,2ee606c033a70f44ba961106bb4727dd", + "versions.yml:md5,7809d5e62a9a71923012f7d06dc7a0fb", + "versions.yml:md5,7809d5e62a9a71923012f7d06dc7a0fb", + "versions.yml:md5,f2707dd02aa42f4f8154476966707508" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-04T17:15:55.786758395" + }, + "no_intervals": { + "content": [ + [ + [ + { + "groupSize": 0, + "groupTarget": { + "id": "test" + } + }, + "7ebc60b3ccddb8489781f46522bc5da1", + "test.bam.bai" + ] + ], + [ + "versions.yml:md5,2ee606c033a70f44ba961106bb4727dd", + "versions.yml:md5,7809d5e62a9a71923012f7d06dc7a0fb", + "versions.yml:md5,f2707dd02aa42f4f8154476966707508" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-04T17:16:38.597763964" + }, + "bam": { + "content": [ + [ + [ + { + "groupSize": 2, + "groupTarget": { + "id": "test" + } + }, + "67daadcc078bb45be360e1f2af46a8e5", + "test.bam.bai" + ] + ], + [ + "versions.yml:md5,2ee606c033a70f44ba961106bb4727dd", + "versions.yml:md5,7809d5e62a9a71923012f7d06dc7a0fb", + "versions.yml:md5,7809d5e62a9a71923012f7d06dc7a0fb", + "versions.yml:md5,f2707dd02aa42f4f8154476966707508" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-04T17:15:10.999131603" + } +} \ No newline at end of file From 99ef03ab46fbd0a5a2ea3420dddc4c526a1964e7 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 11:13:06 +0100 Subject: [PATCH 266/275] test recalibrate --- .../local/recalibrate/tests/main.nf.test | 156 ++++++++++++++++++ .../local/recalibrate/tests/main.nf.test.snap | 62 +++++++ 2 files changed, 218 insertions(+) create mode 100644 subworkflows/local/recalibrate/tests/main.nf.test create mode 100644 subworkflows/local/recalibrate/tests/main.nf.test.snap diff --git a/subworkflows/local/recalibrate/tests/main.nf.test b/subworkflows/local/recalibrate/tests/main.nf.test new file mode 100644 index 00000000..8594feb1 --- /dev/null +++ b/subworkflows/local/recalibrate/tests/main.nf.test @@ -0,0 +1,156 @@ +nextflow_workflow { + + name "Test Subworkflow RECALIBRATE" + script "../main.nf" + workflow "RECALIBRATE" + + tag "subworkflows" + tag "subworkflows_local" + tag "subworkflows/recalibrate" + tag "samtools/stats" + tag "samtools/index" + tag "gatk4/applybqsr" + + setup { + run("GATK4_BASERECALIBRATOR") { + script "../../../../modules/nf-core/gatk4/baserecalibrator/main.nf" + + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.filtered_intervals.interval_list', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:"fasta"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.value([ + [id:"fai"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + input[3] = Channel.value([ + [id:"dict"], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + input[4] = Channel.value([ + [id:"known_sites"], + [ + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf.gz', checkIfExists: true) + ] + ]) + input[5] = Channel.value([ + [id:"known_sites"], + [ + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf.gz.tbi', checkIfExists: true) + ] + ]) + """ + } + } + } + + test("bam - stats") { + when { + workflow { + """ + input[0] = false + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + .join(GATK4_BASERECALIBRATOR.out.table) + .map { meta, bam, bai, table -> + [ + meta, + bam, + bai, + table, + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.filtered_intervals.interval_list', checkIfExists: true) + ] + } + input[2] = Channel.value( + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ) + input[3] = Channel.value( + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ) + input[4] = Channel.value( + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } + if(key == "bam") { + return [key, val.collect { [it[0], bam(it[1]).readsMD5, file(it[2].toString()).name]}] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } + + test("bam - no stats") { + when { + workflow { + """ + input[0] = true + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + .join(GATK4_BASERECALIBRATOR.out.table) + .map { meta, bam, bai, table -> + [ + meta, + bam, + bai, + table, + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.filtered_intervals.interval_list', checkIfExists: true) + ] + } + input[2] = Channel.value( + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ) + input[3] = Channel.value( + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ) + input[4] = Channel.value( + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } + if(key == "bam") { + return [key, val.collect { [it[0], bam(it[1]).readsMD5, file(it[2].toString()).name]}] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/recalibrate/tests/main.nf.test.snap b/subworkflows/local/recalibrate/tests/main.nf.test.snap new file mode 100644 index 00000000..b037a774 --- /dev/null +++ b/subworkflows/local/recalibrate/tests/main.nf.test.snap @@ -0,0 +1,62 @@ +{ + "bam - no stats": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "22e22cd4b7da6967236f1c83277ea7e3", + "test.bam.bai" + ] + ], + "qc": [ + + ], + "versions": [ + "versions.yml:md5,5ac2b80142e8e414d486250387f61a89", + "versions.yml:md5,f1363028c76dcca37889e58983308a06" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T11:08:10.892788095" + }, + "bam - stats": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "22e22cd4b7da6967236f1c83277ea7e3", + "test.bam.bai" + ] + ], + "qc": [ + [ + { + "id": "test" + }, + "test.stats:md5,2a87573703c093ff146c3489f1aded78" + ] + ], + "versions": [ + "versions.yml:md5,40d9d05926d5b2862a346cf91e38655e", + "versions.yml:md5,5ac2b80142e8e414d486250387f61a89", + "versions.yml:md5,f1363028c76dcca37889e58983308a06" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T11:07:08.566902029" + } +} \ No newline at end of file From 47c0f42d9932ce86802d28109b5dd8ef186dd39c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 13:23:51 +0100 Subject: [PATCH 267/275] test prepare_genome --- .../{main.nf.test => tests/functions.nf.test} | 2 +- .../local/prepare_genome/tests/main.nf.test | 156 +++++++++++++ .../prepare_genome/tests/main.nf.test.snap | 221 ++++++++++++++++++ 3 files changed, 378 insertions(+), 1 deletion(-) rename subworkflows/local/prepare_genome/{main.nf.test => tests/functions.nf.test} (98%) create mode 100644 subworkflows/local/prepare_genome/tests/main.nf.test create mode 100644 subworkflows/local/prepare_genome/tests/main.nf.test.snap diff --git a/subworkflows/local/prepare_genome/main.nf.test b/subworkflows/local/prepare_genome/tests/functions.nf.test similarity index 98% rename from subworkflows/local/prepare_genome/main.nf.test rename to subworkflows/local/prepare_genome/tests/functions.nf.test index e93b854f..87f39689 100644 --- a/subworkflows/local/prepare_genome/main.nf.test +++ b/subworkflows/local/prepare_genome/tests/functions.nf.test @@ -2,7 +2,7 @@ nextflow_function { name "Test Functions" - script "subworkflows/local/prepare_genome/main.nf" + script "../main.nf" function "isCompatibleStarIndex" test("Test Function isCompatibleStarIndex - matching numbers") { diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test new file mode 100644 index 00000000..b528762c --- /dev/null +++ b/subworkflows/local/prepare_genome/tests/main.nf.test @@ -0,0 +1,156 @@ +nextflow_workflow { + + name "Test Subworkflow PREPARE_GENOME" + script "../main.nf" + workflow "PREPARE_GENOME" + + tag "subworkflows" + tag "subworkflows_local" + tag "subworkflows/prepare_genome" + tag "bedtools/merge" + tag "bedtools/stats" + tag "gatk4/createsequencedictionary" + tag "gffread" + tag "gtf2bed" + tag "samtools/faidx" + tag "star/genomegenerate" + tag "gunzip" + tag "tabix/tabix" + tag "tabix/bgziptabix" + tag "untar" + tag "star/indexversion" + tag "remove_unknown_regions" + + test("only essentials") { + when { + params { + params.fasta = "genome.fasta" + params.dict = null + params.fai = null + params.star_index = null + params.gff = null + params.gtf = "genome.gtf" + params.exon_bed = null + params.dbsnp = null + params.dbsnp_tbi = null + params.known_indels = null + params.known_indels_tbi = null + params.feature_type = "exon" + } + + workflow { + """ + input[0] = Channel.value([ + [id:'fasta'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.empty() + input[2] = Channel.empty() + input[3] = Channel.value([[], []]) + input[4] = Channel.empty() + input[5] = Channel.value([ + [id:'gtf'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + ]) + input[6] = Channel.empty() + input[7] = Channel.empty() + input[8] = Channel.empty() + input[9] = Channel.empty() + input[10] = params.feature_type + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } else if(key == "star_index") { + return [key, val.collect { [it[0], path(it[1]).list().collect { file(it.toString()).name }] }] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } + + test("all") { + when { + params { + params.fasta = "genome.fasta" + params.dict = "genome.dict" + params.fai = "genome.fasta.fai" + params.star_index = "star/" + params.gff = null + params.gtf = "genome.gtf" + params.exon_bed = "exon.bed" + params.dbsnp = "dbsnp.vcf" + params.dbsnp_tbi = null + params.known_indels = "indels.vcf.gz" + params.known_indels_tbi = "indels.vcf.gz.tbi" + params.feature_type = "exon" + } + + workflow { + """ + input[0] = Channel.value([ + [id:'fasta'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:'dict'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + input[2] = Channel.value([ + [id:'fai'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ]) + input[3] = Channel.value([ + [id:'star'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/index/star/star.tar.gz', checkIfExists: true) + ]) + input[4] = Channel.empty() + input[5] = Channel.value([ + [id:'gtf'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + ]) + input[6] = Channel.value([ + [id:'exon_bed'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ]) + input[7] = Channel.value([ + [id:'dbsnp'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true) + ]) + input[8] = Channel.value( + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf.gz', checkIfExists: true) + ) + input[9] = Channel.value( + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf.gz.tbi', checkIfExists: true) + ) + input[10] = params.feature_type + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } else if(key == "star_index") { + return [key, val.collect { [it[0], path(it[1]).list().collect { file(it.toString()).name }] }] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap new file mode 100644 index 00000000..f7cdeef9 --- /dev/null +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -0,0 +1,221 @@ +{ + "all": { + "content": [ + { + "dbsnp": [ + [ + { + "id": "dbsnp" + }, + "dbsnp.vcf.gz:md5,1bb8724dcbe6fa3101a814c0be51d1ea" + ] + ], + "dbsnp_tbi": [ + [ + { + "id": "dbsnp" + }, + "dbsnp.vcf.gz.tbi:md5,747c6529930c04120f367110a9ea5e63" + ] + ], + "dict": [ + [ + { + "id": "dict" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict" + ] + ], + "exon_bed": [ + [ + { + "id": "exon_bed" + }, + "exon_bed.exon.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "fasta": [ + [ + { + "id": "fasta" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" + ] + ], + "fasta_fai": [ + [ + { + "id": "fasta" + }, + "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685" + ] + ], + "gtf": [ + [ + { + "id": "gtf" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" + ] + ], + "known_indels": [ + [ + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf.gz" + ] + ], + "known_indels_tbi": [ + [ + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf.gz.tbi" + ] + ], + "star_index": [ + [ + { + "id": "star" + }, + [ + "Genome", + "Log.out", + "SA", + "SAindex", + "chrLength.txt", + "chrName.txt", + "chrNameLength.txt", + "chrStart.txt", + "exonGeTrInfo.tab", + "exonInfo.tab", + "geneInfo.tab", + "genomeParameters.txt", + "sjdbInfo.txt", + "sjdbList.fromGTF.out.tab", + "sjdbList.out.tab", + "transcriptInfo.tab" + ] + ] + ], + "versions": [ + "versions.yml:md5,2f8adf49812faab29b90f617e24e7ddc", + "versions.yml:md5,3c6fc57c4c3bf7b143933b0b89ab0386", + "versions.yml:md5,7263c03ca9c7d18bc40fc8d27a5936fa", + "versions.yml:md5,7303f194674b485c6914e28422822a12", + "versions.yml:md5,f104f9bec6db3d55c728ffd041131110" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:22:39.746029169" + }, + "only essentials": { + "content": [ + { + "dbsnp": [ + [ + [ + + ], + [ + + ] + ] + ], + "dbsnp_tbi": [ + [ + [ + + ], + [ + + ] + ] + ], + "dict": [ + [ + { + "id": "fasta" + }, + "genome.dict:md5,2433fe2ba31257337bf4c4bd4cb8da15" + ] + ], + "exon_bed": [ + [ + { + "id": "gtf" + }, + "gtf.exon.bed:md5,17192418c24c524881e7d970f94a4a26" + ] + ], + "fasta": [ + [ + { + "id": "fasta" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" + ] + ], + "fasta_fai": [ + [ + { + "id": "fasta" + }, + "genome.fasta.fai:md5,3520cd30e1b100e55f578db9c855f685" + ] + ], + "gtf": [ + [ + { + "id": "gtf" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" + ] + ], + "known_indels": [ + + ], + "known_indels_tbi": [ + + ], + "star_index": [ + [ + { + "id": "fasta" + }, + [ + "Genome", + "Log.out", + "SA", + "SAindex", + "chrLength.txt", + "chrName.txt", + "chrNameLength.txt", + "chrStart.txt", + "exonGeTrInfo.tab", + "exonInfo.tab", + "geneInfo.tab", + "genomeParameters.txt", + "sjdbInfo.txt", + "sjdbList.fromGTF.out.tab", + "sjdbList.out.tab", + "transcriptInfo.tab" + ] + ] + ], + "versions": [ + "versions.yml:md5,265795dcfabc74e982198a30abb773d5", + "versions.yml:md5,2f8adf49812faab29b90f617e24e7ddc", + "versions.yml:md5,3c6fc57c4c3bf7b143933b0b89ab0386", + "versions.yml:md5,7303f194674b485c6914e28422822a12", + "versions.yml:md5,d2d7ee90a0fefed6042fe0e063c1cbac", + "versions.yml:md5,fd6b20eb9694865490d59c0ca57e04fb" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:18:52.117370876" + } +} \ No newline at end of file From 6ea6d5fe8b163ffe2b491db496bb7cd0de8bd56a Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 13:37:35 +0100 Subject: [PATCH 268/275] test prepare_alignment --- .../prepare_alignment/tests/main.nf.test | 112 ++++++++++++++++++ .../prepare_alignment/tests/main.nf.test.snap | 78 ++++++++++++ 2 files changed, 190 insertions(+) create mode 100644 subworkflows/local/prepare_alignment/tests/main.nf.test create mode 100644 subworkflows/local/prepare_alignment/tests/main.nf.test.snap diff --git a/subworkflows/local/prepare_alignment/tests/main.nf.test b/subworkflows/local/prepare_alignment/tests/main.nf.test new file mode 100644 index 00000000..8a9f370a --- /dev/null +++ b/subworkflows/local/prepare_alignment/tests/main.nf.test @@ -0,0 +1,112 @@ +nextflow_workflow { + + name "Test Subworkflow PREPARE_ALIGNMENT" + script "../main.nf" + workflow "PREPARE_ALIGNMENT" + + tag "subworkflows" + tag "subworkflows_local" + tag "subworkflows/prepare_alignment" + tag "samtools/convert" + tag "samtools/index" + + test("only bam") { + when { + + workflow { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.empty() + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } else if(key == "bam") { + return [key, val.collect { [it[0], it[1], file(it[2]).name]}] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } + + test("only cram - no index") { + when { + + workflow { + """ + input[0] = Channel.empty() + input[1] = Channel.of([ + [id:'test'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram', checkIfExists: true), + [] + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } else if(key == "bam") { + return [key, val.collect { [it[0], it[1], file(it[2]).name]}] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } + + test("bam, cram - no index, index") { + when { + + workflow { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + [] + ]) + input[1] = Channel.of([ + [id:'test'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } else if(key == "bam") { + return [key, val.collect { [it[0], it[1], file(it[2]).name]}] + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/prepare_alignment/tests/main.nf.test.snap b/subworkflows/local/prepare_alignment/tests/main.nf.test.snap new file mode 100644 index 00000000..6f6ff2b9 --- /dev/null +++ b/subworkflows/local/prepare_alignment/tests/main.nf.test.snap @@ -0,0 +1,78 @@ +{ + "only cram - no index": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram", + "test.rna.paired_end.sorted.cram.crai" + ] + ], + "versions": [ + "versions.yml:md5,b9253c084ace536ae84f4df30fe71912" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:36:56.176207564" + }, + "bam, cram - no index, index": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", + "test.rna.paired_end.sorted.bam.bai" + ], + [ + { + "id": "test" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram", + "test.rna.paired_end.sorted.cram.crai" + ] + ], + "versions": [ + "versions.yml:md5,b9253c084ace536ae84f4df30fe71912" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:37:07.592019675" + }, + "only bam": { + "content": [ + { + "bam": [ + [ + { + "id": "test" + }, + "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", + "test.rna.paired_end.sorted.bam.bai" + ] + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:32:21.806173639" + } +} \ No newline at end of file From 62f742cebf2731c96b88e524cb7112e5dbf21c09 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 13:47:02 +0100 Subject: [PATCH 269/275] test cram_qc_mosdepth_samtools --- .../tests/main.nf.test | 49 +++++++++++++++++++ .../tests/main.nf.test.snap | 37 ++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test create mode 100644 subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test.snap diff --git a/subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test b/subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test new file mode 100644 index 00000000..2da7df84 --- /dev/null +++ b/subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test @@ -0,0 +1,49 @@ +nextflow_workflow { + + name "Test Subworkflow CRAM_QC_MOSDEPTH_SAMTOOLS" + script "../main.nf" + workflow "CRAM_QC_MOSDEPTH_SAMTOOLS" + + tag "subworkflows" + tag "subworkflows_local" + tag "subworkflows/cram_qc_mosdepth_samtools" + tag "samtools/stats" + tag "mosdepth" + + test("default") { + when { + + workflow { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true), + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam.bai', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:'fasta'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.value([ + [id:'intervals'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.collectEntries { key, val -> + if(key.matches("\\d+")) { + return null + } + return [key,val] + }.findAll { it != null } + ).match() } + ) + } + } +} diff --git a/subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test.snap b/subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test.snap new file mode 100644 index 00000000..a1d861be --- /dev/null +++ b/subworkflows/local/cram_qc_mosdepth_samtools/tests/main.nf.test.snap @@ -0,0 +1,37 @@ +{ + "default": { + "content": [ + { + "reports": [ + [ + { + "id": "test" + }, + "test.mosdepth.global.dist.txt:md5,da4f2a9da24de7763247444ed9fc6d53" + ], + [ + { + "id": "test" + }, + "test.mosdepth.region.dist.txt:md5,da4f2a9da24de7763247444ed9fc6d53" + ], + [ + { + "id": "test" + }, + "test.stats:md5,1d1697d8b45e9f1c3280020155ee23d5" + ] + ], + "versions": [ + "versions.yml:md5,1ba7e2d7c7c5d0f310ceb2f8e8846a4a", + "versions.yml:md5,ebf112f4081a4bc0e13520fe22ac26bd" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:46:12.688489101" + } +} \ No newline at end of file From c0778fc88e9403fdea8b60de3a9803454640db89 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 13:55:27 +0100 Subject: [PATCH 270/275] test gtf2bed --- modules/local/gtf2bed/tests/main.nf.test | 51 ++++++++++++++ modules/local/gtf2bed/tests/main.nf.test.snap | 68 +++++++++++++++++++ 2 files changed, 119 insertions(+) create mode 100644 modules/local/gtf2bed/tests/main.nf.test create mode 100644 modules/local/gtf2bed/tests/main.nf.test.snap diff --git a/modules/local/gtf2bed/tests/main.nf.test b/modules/local/gtf2bed/tests/main.nf.test new file mode 100644 index 00000000..2634ba5d --- /dev/null +++ b/modules/local/gtf2bed/tests/main.nf.test @@ -0,0 +1,51 @@ +nextflow_process { + + name "Test Process GTF2BED" + script "../main.nf" + process "GTF2BED" + + test("Should run without failures") { + + when { + process { + """ + input[0] = Channel.value([ + [id:'gtf'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + ]) + input[1] = "exon" + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + + test("Should run without failures - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.value([ + [id:'gtf'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) + ]) + input[1] = "exon" + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + +} diff --git a/modules/local/gtf2bed/tests/main.nf.test.snap b/modules/local/gtf2bed/tests/main.nf.test.snap new file mode 100644 index 00000000..6d36cae0 --- /dev/null +++ b/modules/local/gtf2bed/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + { + "id": "gtf" + }, + "exome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d84bb02fbdc62a11a4c2e284aef3c0f1" + ], + "bed": [ + [ + { + "id": "gtf" + }, + "exome.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d84bb02fbdc62a11a4c2e284aef3c0f1" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:54:35.299310495" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "gtf" + }, + "exome.bed:md5,17192418c24c524881e7d970f94a4a26" + ] + ], + "1": [ + "versions.yml:md5,d84bb02fbdc62a11a4c2e284aef3c0f1" + ], + "bed": [ + [ + { + "id": "gtf" + }, + "exome.bed:md5,17192418c24c524881e7d970f94a4a26" + ] + ], + "versions": [ + "versions.yml:md5,d84bb02fbdc62a11a4c2e284aef3c0f1" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:54:22.027715852" + } +} \ No newline at end of file From a34755edfe99b955c883ff552f5b18cdeef7f1e0 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 13:58:17 +0100 Subject: [PATCH 271/275] test remove_unknown_regions --- .../remove_unkown_regions/tests/main.nf.test | 57 ++++++++++++++++ .../tests/main.nf.test.snap | 68 +++++++++++++++++++ 2 files changed, 125 insertions(+) create mode 100644 modules/local/remove_unkown_regions/tests/main.nf.test create mode 100644 modules/local/remove_unkown_regions/tests/main.nf.test.snap diff --git a/modules/local/remove_unkown_regions/tests/main.nf.test b/modules/local/remove_unkown_regions/tests/main.nf.test new file mode 100644 index 00000000..86b541ac --- /dev/null +++ b/modules/local/remove_unkown_regions/tests/main.nf.test @@ -0,0 +1,57 @@ +nextflow_process { + + name "Test Process REMOVE_UNKNOWN_REGIONS" + script "../main.nf" + process "REMOVE_UNKNOWN_REGIONS" + + test("Should run without failures") { + + when { + process { + """ + input[0] = Channel.value([ + [id:'exon_bed'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:'dict'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + + test("Should run without failures - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.value([ + [id:'exon_bed'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ]) + input[1] = Channel.value([ + [id:'dict'], + file(params.pipelines_testdata_base_path + '/genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ]) + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + +} diff --git a/modules/local/remove_unkown_regions/tests/main.nf.test.snap b/modules/local/remove_unkown_regions/tests/main.nf.test.snap new file mode 100644 index 00000000..b89a5b8c --- /dev/null +++ b/modules/local/remove_unkown_regions/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + { + "id": "exon_bed" + }, + "exon_bed.exon.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4e809973b78e4e60b7134a81a1eb592b" + ], + "bed": [ + [ + { + "id": "exon_bed" + }, + "exon_bed.exon.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4e809973b78e4e60b7134a81a1eb592b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:57:48.655747686" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + { + "id": "exon_bed" + }, + "exon_bed.exon.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "1": [ + "versions.yml:md5,4e809973b78e4e60b7134a81a1eb592b" + ], + "bed": [ + [ + { + "id": "exon_bed" + }, + "exon_bed.exon.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7" + ] + ], + "versions": [ + "versions.yml:md5,4e809973b78e4e60b7134a81a1eb592b" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T13:57:35.622566479" + } +} \ No newline at end of file From e04af454dbb0041d0eef74e37261e9988a5201ac Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 14:01:08 +0100 Subject: [PATCH 272/275] changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 10088fce..ac6df197 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#157](https://github.com/nf-core/rnavar/pull/157) - Added support for `bam` and `cram` input files - [#169](https://github.com/nf-core/rnavar/pull/169) - Added the `--star_max_intron_size` parameter to set the `--alignIntronMax` argument in STAR - [#180](https://github.com/nf-core/rnavar/pull/180) - Added support for UMI extraction. Specify `--extract_umi` to enable this feature +- [#187](https://github.com/nf-core/rnavar/pull/187) - Added unit tests for local subworkflows and processes ### Changed From 69f190f973c2000feff757fde4fd2bddc8303a7c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 14:49:51 +0100 Subject: [PATCH 273/275] correctly run tests --- .../prepare_alignment/tests/main.nf.test.snap | 14 +++++++------- .../local/prepare_genome/tests/main.nf.test.snap | 14 +++++++------- tests/nextflow.config | 1 + 3 files changed, 15 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/prepare_alignment/tests/main.nf.test.snap b/subworkflows/local/prepare_alignment/tests/main.nf.test.snap index 6f6ff2b9..caa34108 100644 --- a/subworkflows/local/prepare_alignment/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_alignment/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram", + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram", "test.rna.paired_end.sorted.cram.crai" ] ], @@ -20,7 +20,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-03-05T13:36:56.176207564" + "timestamp": "2025-03-05T14:42:59.447861122" }, "bam, cram - no index, index": { "content": [ @@ -30,14 +30,14 @@ { "id": "test" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", "test.rna.paired_end.sorted.bam.bai" ], [ { "id": "test" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram", + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/cram/test.rna.paired_end.sorted.cram", "test.rna.paired_end.sorted.cram.crai" ] ], @@ -50,7 +50,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-03-05T13:37:07.592019675" + "timestamp": "2025-03-05T14:43:15.493280437" }, "only bam": { "content": [ @@ -60,7 +60,7 @@ { "id": "test" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam", "test.rna.paired_end.sorted.bam.bai" ] ], @@ -73,6 +73,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-03-05T13:32:21.806173639" + "timestamp": "2025-03-05T14:42:44.032096236" } } \ No newline at end of file diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap index f7cdeef9..0135521e 100644 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ b/subworkflows/local/prepare_genome/tests/main.nf.test.snap @@ -23,7 +23,7 @@ { "id": "dict" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.dict" + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.dict" ] ], "exon_bed": [ @@ -39,7 +39,7 @@ { "id": "fasta" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.fasta" ] ], "fasta_fai": [ @@ -55,7 +55,7 @@ { "id": "gtf" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.gtf" ] ], "known_indels": [ @@ -106,7 +106,7 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-03-05T13:22:39.746029169" + "timestamp": "2025-03-05T14:45:47.366394095" }, "only essentials": { "content": [ @@ -152,7 +152,7 @@ { "id": "fasta" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta" + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.fasta" ] ], "fasta_fai": [ @@ -168,7 +168,7 @@ { "id": "gtf" }, - "/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.gtf" + "/nf-core/test-datasets/raw/refs/heads/rnavar/data/genomics/homo_sapiens/genome/genome.gtf" ] ], "known_indels": [ @@ -216,6 +216,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-03-05T13:18:52.117370876" + "timestamp": "2025-03-05T14:45:25.808187589" } } \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config index e7fef4b3..e78fcc18 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -9,6 +9,7 @@ params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/refs/heads/rnavar/data' } process { From b469d1353f473efbe790f3a42216b997d0d87389 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Wed, 5 Mar 2025 15:33:57 +0100 Subject: [PATCH 274/275] update snpeff/snpeff --- modules.json | 5 +- .../nf-core/snpeff/snpeff/snpeff-snpeff.diff | 22 ----- .../nf-core/snpeff/snpeff/tests/main.nf.test | 36 +++++++++ .../snpeff/snpeff/tests/main.nf.test.snap | 81 +++++++++++++++++++ 4 files changed, 119 insertions(+), 25 deletions(-) delete mode 100644 modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff diff --git a/modules.json b/modules.json index d6870925..8acbdf4c 100755 --- a/modules.json +++ b/modules.json @@ -182,9 +182,8 @@ }, "snpeff/snpeff": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules", "vcf_annotate_snpeff"], - "patch": "modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff" + "git_sha": "22f895866a1ad01556db175f9c0925ca90615d10", + "installed_by": ["modules", "vcf_annotate_snpeff"] }, "star/align": { "branch": "master", diff --git a/modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff b/modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff deleted file mode 100644 index 3a7f34ec..00000000 --- a/modules/nf-core/snpeff/snpeff/snpeff-snpeff.diff +++ /dev/null @@ -1,22 +0,0 @@ -Changes in component 'nf-core/snpeff/snpeff' -Changes in 'snpeff/snpeff/main.nf': ---- modules/nf-core/snpeff/snpeff/main.nf -+++ modules/nf-core/snpeff/snpeff/main.nf -@@ -52,6 +52,9 @@ - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.ann.vcf -+ touch ${prefix}.csv -+ touch ${prefix}.html -+ touch ${prefix}.genes.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - -'modules/nf-core/snpeff/snpeff/environment.yml' is unchanged -'modules/nf-core/snpeff/snpeff/meta.yml' is unchanged -'modules/nf-core/snpeff/snpeff/tests/tags.yml' is unchanged -'modules/nf-core/snpeff/snpeff/tests/main.nf.test' is unchanged -'modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap' is unchanged -'modules/nf-core/snpeff/snpeff/tests/nextflow.config' is unchanged -************************************************************ diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test index 2be0b7d7..661e9672 100644 --- a/modules/nf-core/snpeff/snpeff/tests/main.nf.test +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -48,4 +48,40 @@ nextflow_process { ) } } + + test("test_SNPEFF_SNPEFF - stub") { + + options "-stub" + + setup { + run("SNPEFF_DOWNLOAD") { + script "../../download/main.nf" + process { + """ + input[0] = Channel.of([[id:params.snpeff_db], params.snpeff_db]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ]) + input[1] = params.snpeff_db + input[2] = SNPEFF_DOWNLOAD.out.cache + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } } diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap index 0891b844..9fc0c9f5 100644 --- a/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test.snap @@ -27,5 +27,86 @@ "nextflow": "24.02.0" }, "timestamp": "2024-03-18T17:37:18.874822" + }, + "test_SNPEFF_SNPEFF - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.ann.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,25d44a118d558b331d51ec00be0d997c" + ], + "genes_txt": [ + [ + { + "id": "test" + }, + "test.genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "summary_html": [ + [ + { + "id": "test" + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.ann.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,25d44a118d558b331d51ec00be0d997c" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-03-05T14:55:15.626663647" } } \ No newline at end of file From 56bd9df8310203ba2e335e9a265ad863e3d37124 Mon Sep 17 00:00:00 2001 From: nvnieuwk Date: Thu, 6 Mar 2025 14:13:42 +0000 Subject: [PATCH 275/275] fix issue with star index being queue channel --- subworkflows/local/prepare_genome/main.nf | 1 + tests/csv/1.0/fastq_multiple.csv | 3 + tests/multiple_fastqs.nf.test | 35 ++++++ tests/multiple_fastqs.nf.test.snap | 132 ++++++++++++++++++++++ 4 files changed, 171 insertions(+) create mode 100644 tests/csv/1.0/fastq_multiple.csv create mode 100644 tests/multiple_fastqs.nf.test create mode 100644 tests/multiple_fastqs.nf.test.snap diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf index 67ab101e..adc69f39 100755 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/local/prepare_genome/main.nf @@ -203,6 +203,7 @@ workflow PREPARE_GENOME { def star_index_output = STAR_GENOMEGENERATE.out.index .mix(star_index_check.compatible) + .collect() emit: dict = ch_dict // path: genome.fasta.dict diff --git a/tests/csv/1.0/fastq_multiple.csv b/tests/csv/1.0/fastq_multiple.csv new file mode 100644 index 00000000..c56a17f4 --- /dev/null +++ b/tests/csv/1.0/fastq_multiple.csv @@ -0,0 +1,3 @@ +sample,fastq_1,fastq_2 +GM12878,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz +GM12879,https://github.com/nf-core/test-datasets/raw/modules/data/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz diff --git a/tests/multiple_fastqs.nf.test b/tests/multiple_fastqs.nf.test new file mode 100644 index 00000000..bfd619ea --- /dev/null +++ b/tests/multiple_fastqs.nf.test @@ -0,0 +1,35 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_rnavar" + + test("Test multiple FASTQ files") { + + when { + params { + outdir = "$outputDir" + input = "${projectDir}/tests/csv/1.0/fastq_multiple.csv" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name + ).match() } + ) + } + } +} diff --git a/tests/multiple_fastqs.nf.test.snap b/tests/multiple_fastqs.nf.test.snap new file mode 100644 index 00000000..8a53435b --- /dev/null +++ b/tests/multiple_fastqs.nf.test.snap @@ -0,0 +1,132 @@ +{ + "Test multiple FASTQ files": { + "content": [ + 72, + { + "APPLYBQSR": { + "gatk4": "4.6.1.0" + }, + "CAT_FASTQ": { + "cat": 9.5 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.6.1.0" + }, + "GATK4_BEDTOINTERVALLIST": { + "gatk4": "4.6.1.0" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.6.1.0" + }, + "GATK4_INTERVALLISTTOOLS": { + "gatk4": "4.6.1.0" + }, + "GATK4_MERGEVCFS": { + "gatk4": "4.6.1.0" + }, + "GATK4_SPLITNCIGARREADS": { + "gatk4": "4.6.1.0" + }, + "GATK4_VARIANTFILTRATION": { + "gatk4": "4.6.1.0" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.3.0" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.21 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.21 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.21 + }, + "SAMTOOLS_MERGE": { + "samtools": 1.21 + }, + "SAMTOOLS_SORT": { + "samtools": 1.21 + }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, + "STAR_ALIGN": { + "star": "2.7.11b", + "samtools": 1.21, + "gawk": "5.1.0" + }, + "TABIX": { + "tabix": 1.2 + }, + "Workflow": { + "nf-core/rnavar": "v2.0.0dev" + } + }, + [ + "pipeline_info", + "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", + "preprocessing", + "preprocessing/GM12878", + "preprocessing/GM12878/GM12878.md.bam", + "preprocessing/GM12878/GM12878.md.bam.bai", + "preprocessing/GM12878/GM12878.recal.bam", + "preprocessing/GM12878/GM12878.recal.bam.bai", + "preprocessing/GM12879", + "preprocessing/GM12879/GM12879.md.bam", + "preprocessing/GM12879/GM12879.md.bam.bai", + "preprocessing/GM12879/GM12879.recal.bam", + "preprocessing/GM12879/GM12879.recal.bam.bai", + "reports", + "reports/multiqc_data", + "reports/multiqc_data/multiqc.log", + "reports/multiqc_data/multiqc_citations.txt", + "reports/multiqc_data/multiqc_data.json", + "reports/multiqc_data/multiqc_software_versions.txt", + "reports/multiqc_data/multiqc_sources.txt", + "reports/multiqc_report.html", + "reports/stats", + "reports/stats/GM12878", + "reports/stats/GM12878/GM12878.flagstat", + "reports/stats/GM12878/GM12878.stats", + "reports/stats/GM12878/STAR_log", + "reports/stats/GM12878/STAR_log/GM12878.Log.final.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.out", + "reports/stats/GM12878/STAR_log/GM12878.Log.progress.out", + "reports/stats/GM12878/STAR_log/GM12878.SJ.out.tab", + "reports/stats/GM12879", + "reports/stats/GM12879/GM12879.flagstat", + "reports/stats/GM12879/GM12879.stats", + "reports/stats/GM12879/STAR_log", + "reports/stats/GM12879/STAR_log/GM12879.Log.final.out", + "reports/stats/GM12879/STAR_log/GM12879.Log.out", + "reports/stats/GM12879/STAR_log/GM12879.Log.progress.out", + "reports/stats/GM12879/STAR_log/GM12879.SJ.out.tab", + "samtools", + "samtools/GM12878.bam", + "samtools/GM12878.bam.bai", + "samtools/GM12879.bam", + "samtools/GM12879.bam.bai", + "variant_calling", + "variant_calling/GM12878", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz", + "variant_calling/GM12878/GM12878.haplotypecaller.vcf.gz.tbi", + "variant_calling/GM12879", + "variant_calling/GM12879/GM12879.haplotypecaller.filtered.vcf.gz", + "variant_calling/GM12879/GM12879.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/GM12879/GM12879.haplotypecaller.vcf.gz", + "variant_calling/GM12879/GM12879.haplotypecaller.vcf.gz.tbi" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-06T14:12:44.894977284" + } +} \ No newline at end of file
    Process Name \\", - " \\ Software Version
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    yaml5.4.1
    TOOL1tool10.11.9
    TOOL2tool21.9
    WorkflowNextflow
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(workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { @@ -60,4 +62,16 @@ class WorkflowMain { } return null } + + // + // Exit pipeline if --profile contains spaces + // + private static void checkProfile(profile, args, log) { + if (profile.endsWith(',')) { + Nextflow.error "Profile cannot end with a trailing comma. Please remove the comma from the end of the profile string.\nHint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." + } + if (args[0]) { + log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${args[0]}` has been detected.\n Hint: A common mistake is to provide multiple values to `-profile` separated by spaces. Please use commas to separate profiles instead,e.g., `-profile docker,test`." + } + } } diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar deleted file mode 100644 index 805c8bb5e4fd43a12a5891eea5a68788309629b0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 2291171 zcma%i1CS<7mu}m(-Ea4_?dhK8v~AnAZQHhO+qP}n-E-&Lf8*Yb{bM(7MpZ;s){{|L znGpxiIY(9k6buar3JMCSNkdW|=)W{*ATS^)VMTsgF=-L{?{Od?P#{?eNT`1hApZ%I z{U0Zz{YCuW$x{5%Vj{u{igZ#U4^op8k`lCZbMO+hRMV3)4e|_&%)3YSbmCGpVp4NX zni_mKLGakt&P12{r^KCD0GPa9sIuy`fu+agt?8O-hY9i{WloGe}y@kSsDEY_Fud9 z-?2ab4J)MQXe4E3Xl-U<>PRMQZ)0m@@90KnV5#Te5Tz`pvZ0Lj4F<9%Flh(`Qb;Tn zMV!iFmH{S^fF*j#MCKRUd`7m>9||*;WE32I_6pg4-Q1C#ke$$aVmP-TtfJ+j+N9;Q z>bxN=bCVQkg$Jzty71(+~A9}ZfANuYIVnTdW!??Sj)Ti-Qpk8XgPDab8pk2QD&dwUl=iFhd1c$C2uMVagr zWc@z9s$#g__{3?VGb#)^fSNp^lZh zU>MI!D?+L)nyth{@@L0+B&_M8iR08L)G6#PZQLFmvz-9DlZkwRWigRIyI4xYr7>tRJ-N6MlBB`nJQ!!8D)mI2lB3PP;dC{<{Td>^ 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