diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index f332a0b2..b5338dc4 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -1,4 +1,3 @@ - name: Bug report description: Report something that is broken or incorrect labels: bug diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index f5c7195f..b9915119 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -32,3 +32,6 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}" } profiles: test_full_${{ matrix.platform }},aws_tower + nextflow_config: | + process.errorStrategy = 'retry' + process.maxRetries = 3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index b20a19c2..f775f1ab 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -25,3 +25,6 @@ jobs: "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-test-${{ github.sha }}" } profiles: test,aws_tower + nextflow_config: | + process.errorStrategy = 'retry' + process.maxRetries = 3 diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 1203ec66..d501fff4 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -43,4 +43,3 @@ jobs: Thanks again for your contribution! repo-token: ${{ secrets.GITHUB_TOKEN }} allow-repeats: false - diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3b448773..0c9c5554 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -12,9 +12,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install markdownlint run: npm install -g markdownlint-cli - name: Run Markdownlint @@ -51,9 +49,7 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -65,13 +61,11 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v1 - - uses: actions/setup-node@v1 - with: - node-version: '10' + - uses: actions/setup-node@v2 - name: Install yaml-lint run: npm install -g yaml-lint - name: Run yaml-lint - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") + run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.yamllint.yml # If the above check failed, post a comment on the PR explaining the failure - name: Post PR comment @@ -87,7 +81,7 @@ jobs: * Install `yaml-lint` * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`) * Fix the markdown errors - * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")` + * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml` * Fix any reported errors in your YAML files Once you push these changes the test should pass, and you can hide this comment :+1: @@ -142,4 +136,3 @@ jobs: lint_log.txt lint_results.md PR_number.txt - diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 44d72994..04758f61 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -1,4 +1,3 @@ - name: nf-core linting comment # This workflow is triggered after the linting action is complete # It posts an automated comment to the PR, even if the PR is coming from a fork @@ -27,4 +26,3 @@ jobs: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} number: ${{ steps.pr_number.outputs.pr_number }} path: linting-logs/lint_results.md - diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 00000000..b7d4cee1 --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,14 @@ +image: nfcore/gitpod:latest + +vscode: + extensions: # based on nf-core.nf-core-extensionpack + - codezombiech.gitignore # Language support for .gitignore files + # - cssho.vscode-svgviewer # SVG viewer + - davidanson.vscode-markdownlint # 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 + - oderwat.indent-rainbow # Highlight indentation level + - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.nf-core.yml b/.nf-core.yml index d9341b67..61af60c8 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -4,3 +4,8 @@ lint: - assets/email_template.html - assets/email_template.txt - lib/NfcoreTemplate.groovy + - .github/ISSUE_TEMPLATE/bug_report.yml + - .github/workflows/branch.yml + - .github/workflows/linting_comment.yml + - .github/workflows/linting.yml + - lib/NfcoreSchema.groovy diff --git a/.yamllint.yml b/.yamllint.yml new file mode 100644 index 00000000..6889fa34 --- /dev/null +++ b/.yamllint.yml @@ -0,0 +1,5 @@ +extends: default + +rules: + document-start: disable + line-length: disable diff --git a/CHANGELOG.md b/CHANGELOG.md index bde3bd6a..87f79a1a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,19 @@ 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). +## [[2.3.1](https://github.com/nf-core/viralrecon/releases/tag/2.3.1)] - 2022-02-15 + +### Enhancements & fixes + +* [[#277](https://github.com/nf-core/viralrecon/issues/277)] - Misuse of rstrip in make_variants_long_table.py script + +### Software dependencies + +| Dependency | Old version | New version | +|-------------------------------|-------------|-------------| +| `mosdepth` | 0.3.2 | 0.3.3 | +| `pangolin` | 3.1.19 | 3.1.20 | + ## [[2.3](https://github.com/nf-core/viralrecon/releases/tag/2.3)] - 2022-02-04 ### :warning: Major enhancements @@ -38,9 +51,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | | `--consensus_caller` | | `--callers` | `--variant_caller` | -> **NB:** Parameter has been __updated__ if both old and new parameter information is present. -> **NB:** Parameter has been __added__ if just the new parameter information is present. -> **NB:** Parameter has been __removed__ if new parameter information isn't present. +> **NB:** Parameter has been **updated** if both old and new parameter information is present. +> +> **NB:** Parameter has been **added** if just the new parameter information is present. +> +> **NB:** Parameter has been **removed** if new parameter information isn't present. ### Software dependencies @@ -66,9 +81,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `tabix` | 0.2.6 | 1.11 | | `vcflib` | | 1.0.2 | -> **NB:** Dependency has been __updated__ if both old and new version information is present. -> **NB:** Dependency has been __added__ if just the new version information is present. -> **NB:** Dependency has been __removed__ if new version information isn't present. +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. ## [[2.2](https://github.com/nf-core/viralrecon/releases/tag/2.2)] - 2021-07-29 @@ -89,9 +106,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `pangolin` | 3.0.5 | 3.1.7 | | `samtools` | 1.10 | 1.12 | -> **NB:** Dependency has been __updated__ if both old and new version information is present. -> **NB:** Dependency has been __added__ if just the new version information is present. -> **NB:** Dependency has been __removed__ if new version information isn't present. +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. ## [[2.1](https://github.com/nf-core/viralrecon/releases/tag/2.1)] - 2021-06-15 @@ -117,9 +136,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `--public_data_ids` | | | `--skip_sra_fastq_download` | | -> **NB:** Parameter has been __updated__ if both old and new parameter information is present. -> **NB:** Parameter has been __added__ if just the new parameter information is present. -> **NB:** Parameter has been __removed__ if new parameter information isn't present. +> **NB:** Parameter has been **updated** if both old and new parameter information is present. +> +> **NB:** Parameter has been **added** if just the new parameter information is present. +> +> **NB:** Parameter has been **removed** if new parameter information isn't present. ### Software dependencies @@ -130,9 +151,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `nextclade_js` | 0.14.2 | 0.14.4 | | `pangolin` | 2.4.2 | 3.0.5 | -> **NB:** Dependency has been __updated__ if both old and new version information is present. -> **NB:** Dependency has been __added__ if just the new version information is present. -> **NB:** Dependency has been __removed__ if new version information isn't present. +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. ## [[2.0](https://github.com/nf-core/viralrecon/releases/tag/2.0)] - 2021-05-13 @@ -232,9 +255,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `--unqualified_percent_limit` | | | `--varscan2_strand_filter` | | -> **NB:** Parameter has been __updated__ if both old and new parameter information is present. -> **NB:** Parameter has been __added__ if just the new parameter information is present. -> **NB:** Parameter has been __removed__ if new parameter information isn't present. +> **NB:** Parameter has been **updated** if both old and new parameter information is present. +> +> **NB:** Parameter has been **added** if just the new parameter information is present. +> +> **NB:** Parameter has been **removed** if new parameter information isn't present. ### Software dependencies @@ -283,9 +308,11 @@ Note, since the pipeline is now using Nextflow DSL2, each process will be run wi | `varscan` | 2.4.4 | | | `vg` | 1.24.0 | | -> **NB:** Dependency has been __updated__ if both old and new version information is present. -> **NB:** Dependency has been __added__ if just the new version information is present. -> **NB:** Dependency has been __removed__ if new version information isn't present. +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. ## [[1.1.0](https://github.com/nf-core/viralrecon/releases/tag/1.1.0)] - 2020-06-23 @@ -338,23 +365,23 @@ This pipeline is a re-implementation of the [SARS_Cov2_consensus-nf](https://git ### Pipeline summary -1. Download samples via SRA, ENA or GEO ids ([`ENA FTP`](https://ena-docs.readthedocs.io/en/latest/retrieval/file-download.html), [`parallel-fastq-dump`](https://github.com/rvalieris/parallel-fastq-dump); *if required*) -2. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html); *if required*) +1. Download samples via SRA, ENA or GEO ids ([`ENA FTP`](https://ena-docs.readthedocs.io/en/latest/retrieval/file-download.html), [`parallel-fastq-dump`](https://github.com/rvalieris/parallel-fastq-dump); _if required_) +2. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html); _if required_) 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 4. Adapter trimming ([`fastp`](https://github.com/OpenGene/fastp)) 5. Variant calling 1. Read alignment ([`Bowtie 2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)) 2. Sort and index alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/)) - 3. Primer sequence removal ([`iVar`](https://github.com/andersen-lab/ivar); *amplicon data only*) - 4. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/); *removal optional*) + 3. Primer sequence removal ([`iVar`](https://github.com/andersen-lab/ivar); _amplicon data only_) + 4. Duplicate read marking ([`picard`](https://broadinstitute.github.io/picard/); _removal optional_) 5. Alignment-level QC ([`picard`](https://broadinstitute.github.io/picard/), [`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/)) - 6. Choice of multiple variant calling and consensus sequence generation routes ([`VarScan 2`](http://dkoboldt.github.io/varscan/), [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/) *||* [`iVar variants and consensus`](https://github.com/andersen-lab/ivar) *||* [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/)) + 6. Choice of multiple variant calling and consensus sequence generation routes ([`VarScan 2`](http://dkoboldt.github.io/varscan/), [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/) _||_ [`iVar variants and consensus`](https://github.com/andersen-lab/ivar) _||_ [`BCFTools`](http://samtools.github.io/bcftools/bcftools.html), [`BEDTools`](https://github.com/arq5x/bedtools2/)) * Variant annotation ([`SnpEff`](http://snpeff.sourceforge.net/SnpEff.html), [`SnpSift`](http://snpeff.sourceforge.net/SnpSift.html)) * Consensus assessment report ([`QUAST`](http://quast.sourceforge.net/quast)) 6. _De novo_ assembly - 1. Primer trimming ([`Cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html); *amplicon data only*) + 1. Primer trimming ([`Cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html); _amplicon data only_) 2. Removal of host reads ([`Kraken 2`](http://ccb.jhu.edu/software/kraken2/)) - 3. Choice of multiple assembly tools ([`SPAdes`](http://cab.spbu.ru/software/spades/) *||* [`metaSPAdes`](http://cab.spbu.ru/software/meta-spades/) *||* [`Unicycler`](https://github.com/rrwick/Unicycler) *||* [`minia`](https://github.com/GATB/minia)) + 3. Choice of multiple assembly tools ([`SPAdes`](http://cab.spbu.ru/software/spades/) _||_ [`metaSPAdes`](http://cab.spbu.ru/software/meta-spades/) _||_ [`Unicycler`](https://github.com/rrwick/Unicycler) _||_ [`minia`](https://github.com/GATB/minia)) * Blast to reference genome ([`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch)) * Contiguate assembly ([`ABACAS`](https://www.sanger.ac.uk/science/tools/pagit)) * Assembly report ([`PlasmidID`](https://github.com/BU-ISCIII/plasmidID)) diff --git a/README.md b/README.md index f915e315..0021583e 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ A number of improvements were made to the pipeline recently, mainly with regard * Lineage analysis ([`Pangolin`](https://github.com/cov-lineages/pangolin)) * Clade assignment, mutation calling and sequence quality checks ([`Nextclade`](https://github.com/nextstrain/nextclade)) 9. Create variants long format table collating per-sample information for individual variants ([`BCFTools`](http://samtools.github.io/bcftools/bcftools.html)), functional effect prediction ([`SnpSift`](http://snpeff.sourceforge.net/SnpSift.html)) and lineage analysis ([`Pangolin`](https://github.com/cov-lineages/pangolin)) -6. _De novo_ assembly +6. *De novo* assembly 1. Primer trimming ([`Cutadapt`](https://cutadapt.readthedocs.io/en/stable/guide.html); *amplicon data only*) 2. Choice of multiple assembly tools ([`SPAdes`](http://cab.spbu.ru/software/spades/) *||* [`Unicycler`](https://github.com/rrwick/Unicycler) *||* [`minia`](https://github.com/GATB/minia)) * Blast to reference genome ([`blastn`](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch)) @@ -82,7 +82,7 @@ A number of improvements were made to the pipeline recently, mainly with regard 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`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 _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`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 *(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))* 3. Download the pipeline and test it on a minimal dataset with a single command: @@ -94,7 +94,7 @@ A number of improvements were made to the pipeline recently, mainly with regard > * 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` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can 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 `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! @@ -214,4 +214,4 @@ You can cite the `nf-core` publication as follows: > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > -> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). +> *Nat Biotechnol.* 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). diff --git a/bin/make_variants_long_table.py b/bin/make_variants_long_table.py index 750ffe16..a19c495f 100755 --- a/bin/make_variants_long_table.py +++ b/bin/make_variants_long_table.py @@ -44,7 +44,7 @@ def make_dir(path): def get_file_dict(file_dir, file_suffix): files = glob.glob(os.path.join(file_dir, f'*{file_suffix}')) - samples = [os.path.basename(x).rstrip(f'{file_suffix}') for x in files] + samples = [os.path.basename(x).removesuffix(f'{file_suffix}') for x in files] return dict(zip(samples, files)) diff --git a/conf/base.config b/conf/base.config index 780d527c..5ecbe848 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/viralrecon Nextflow base config file -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. diff --git a/conf/modules.config b/conf/modules.config index 64efa4c1..18a15697 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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). diff --git a/conf/test.config b/conf/test.config index c3109b6a..d8655763 100644 --- a/conf/test.config +++ b/conf/test.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running minimal tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: diff --git a/conf/test_full.config b/conf/test_full.config index e8a6d2cc..cdd011f3 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running full-size tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a full size pipeline test. Use as follows: diff --git a/docs/usage.md b/docs/usage.md index f131a364..895c9716 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -285,7 +285,13 @@ Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` ``` -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`. 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. +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`. +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 { @@ -295,7 +301,8 @@ process { } ``` -> **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow. +> **NB:** We specify just the process name i.e. `STAR_ALIGN` in the config file and not the full task name string that is printed to screen in the error message or on the terminal whilst the pipeline is running i.e. `RNASEQ:ALIGN_STAR:STAR_ALIGN`. +> You may get a warning suggesting that the process selector isn't recognised but you can ignore that if the process name has been specified correctly. This is something that needs to be fixed upstream in core Nextflow. ### Updating containers diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 40ab65f2..b3d092f8 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -27,7 +27,7 @@ class NfcoreSchema { /* 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') @@ -135,7 +135,7 @@ class NfcoreSchema { } } - //=====================================================================// + //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// // 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)) diff --git a/lib/Utils.groovy b/lib/Utils.groovy index 1b88aec0..28567bd7 100755 --- a/lib/Utils.groovy +++ b/lib/Utils.groovy @@ -29,12 +29,12 @@ class Utils { conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults')) if (conda_check_failed) { - log.warn "=============================================================================\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/user/install.html#set-up-channels\n" + " NB: The order of the channels matters!\n" + - "===================================================================================" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" } } } diff --git a/main.nf b/main.nf index b0337a10..4d662339 100644 --- a/main.nf +++ b/main.nf @@ -1,8 +1,8 @@ #!/usr/bin/env nextflow /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/viralrecon -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/viralrecon Website: https://nf-co.re/viralrecon Slack : https://nfcore.slack.com/channels/viralrecon @@ -12,9 +12,9 @@ nextflow.enable.dsl = 2 /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GENOME PARAMETER VALUES -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ def primer_set = '' @@ -39,17 +39,17 @@ params.nextclade_dataset_reference = WorkflowMain.getGenomeAttribute(params, 'ne params.nextclade_dataset_tag = WorkflowMain.getGenomeAttribute(params, 'nextclade_dataset_tag' , log, primer_set, primer_set_version) /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ VALIDATE & PRINT PARAMETER SUMMARY -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ WorkflowMain.initialise(workflow, params, log) /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOW FOR PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ if (params.platform == 'illumina') { @@ -75,9 +75,9 @@ workflow NFCORE_VIRALRECON { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN ALL WORKFLOWS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -90,7 +90,7 @@ workflow { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ THE END -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ diff --git a/modules.json b/modules.json index 9295f28c..f97222d9 100644 --- a/modules.json +++ b/modules.json @@ -4,157 +4,157 @@ "repos": { "nf-core/modules": { "abacas": { - 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"git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "untar": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" }, "vcflib/vcfuniq": { - "git_sha": "280712419d6ef5e3fecdc6e9eb98f8746fcbe0b7" + "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" } } } diff --git a/modules/local/asciigenome.nf b/modules/local/asciigenome.nf index 30ad698a..09ca6bb6 100644 --- a/modules/local/asciigenome.nf +++ b/modules/local/asciigenome.nf @@ -20,6 +20,9 @@ process ASCIIGENOME { tuple val(meta), path("*pdf"), emit: pdf path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = task.ext.prefix ?: "${meta.id}" def gff_track = gff ? "$gff" : '' diff --git a/modules/local/collapse_primers.nf b/modules/local/collapse_primers.nf index 78e371bd..316d1e2a 100644 --- a/modules/local/collapse_primers.nf +++ b/modules/local/collapse_primers.nf @@ -16,6 +16,9 @@ process COLLAPSE_PRIMERS { path '*.bed' , emit: bed path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/viralrecon/bin/ """ collapse_primer_bed.py \\ diff --git a/modules/local/cutadapt.nf b/modules/local/cutadapt.nf index 76a824e7..a96ea8bb 100644 --- a/modules/local/cutadapt.nf +++ b/modules/local/cutadapt.nf @@ -16,6 +16,9 @@ process CUTADAPT { tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/filter_blastn.nf b/modules/local/filter_blastn.nf index 6acf352f..4173cdb6 100644 --- a/modules/local/filter_blastn.nf +++ b/modules/local/filter_blastn.nf @@ -15,6 +15,9 @@ process FILTER_BLASTN { tuple val(meta), path('*.txt'), emit: txt path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/local/ivar_variants_to_vcf.nf b/modules/local/ivar_variants_to_vcf.nf index a27b6dda..825d87ff 100644 --- a/modules/local/ivar_variants_to_vcf.nf +++ b/modules/local/ivar_variants_to_vcf.nf @@ -16,6 +16,9 @@ process IVAR_VARIANTS_TO_VCF { tuple val(meta), path("*.tsv"), emit: tsv path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/viralrecon/bin/ def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/kraken2_build.nf b/modules/local/kraken2_build.nf index 22c9c2de..c5632aad 100644 --- a/modules/local/kraken2_build.nf +++ b/modules/local/kraken2_build.nf @@ -14,6 +14,9 @@ process KRAKEN2_BUILD { path 'kraken2_db' , emit: db path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/local/make_bed_mask.nf b/modules/local/make_bed_mask.nf index 81546c4b..246a8ec5 100644 --- a/modules/local/make_bed_mask.nf +++ b/modules/local/make_bed_mask.nf @@ -16,6 +16,9 @@ process MAKE_BED_MASK { tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/viralrecon/bin/ def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: 10 diff --git a/modules/local/make_variants_long_table.nf b/modules/local/make_variants_long_table.nf index c4f9996a..d802ecc9 100644 --- a/modules/local/make_variants_long_table.nf +++ b/modules/local/make_variants_long_table.nf @@ -14,6 +14,9 @@ process MAKE_VARIANTS_LONG_TABLE { 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/viralrecon/bin/ def args = task.ext.args ?: '' """ diff --git a/modules/local/multiqc_illumina.nf b/modules/local/multiqc_illumina.nf index eb3a12b9..6591d294 100644 --- a/modules/local/multiqc_illumina.nf +++ b/modules/local/multiqc_illumina.nf @@ -41,6 +41,9 @@ process MULTIQC { 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 custom_config = multiqc_custom_config ? "--config $multiqc_custom_config" : '' diff --git a/modules/local/multiqc_nanopore.nf b/modules/local/multiqc_nanopore.nf index f1cb728d..cbd2b19d 100644 --- a/modules/local/multiqc_nanopore.nf +++ b/modules/local/multiqc_nanopore.nf @@ -33,6 +33,9 @@ process MULTIQC { 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 custom_config = multiqc_custom_config ? "--config $multiqc_custom_config" : '' diff --git a/modules/local/multiqc_tsv_from_list.nf b/modules/local/multiqc_tsv_from_list.nf index 7f7b7c0a..a53c8f73 100644 --- a/modules/local/multiqc_tsv_from_list.nf +++ b/modules/local/multiqc_tsv_from_list.nf @@ -11,6 +11,9 @@ process MULTIQC_TSV_FROM_LIST { output: path "*.tsv" + when: + task.ext.when == null || task.ext.when + exec: // Generate file contents def contents = "" diff --git a/modules/local/plot_base_density.nf b/modules/local/plot_base_density.nf index ec499aba..97e7e93e 100644 --- a/modules/local/plot_base_density.nf +++ b/modules/local/plot_base_density.nf @@ -15,6 +15,9 @@ process PLOT_BASE_DENSITY { tuple val(meta), path('*.tsv'), emit: tsv path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/viralrecon/bin/ def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/local/plot_mosdepth_regions.nf b/modules/local/plot_mosdepth_regions.nf index 38f9f21c..31cbeeb3 100644 --- a/modules/local/plot_mosdepth_regions.nf +++ b/modules/local/plot_mosdepth_regions.nf @@ -16,6 +16,9 @@ process PLOT_MOSDEPTH_REGIONS { path '*heatmap.tsv' , optional:true, emit: heatmap_tsv path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/viralrecon/bin/ def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "mosdepth" diff --git a/modules/local/rename_fasta_header.nf b/modules/local/rename_fasta_header.nf index 64c45a73..7d9c9901 100644 --- a/modules/local/rename_fasta_header.nf +++ b/modules/local/rename_fasta_header.nf @@ -13,6 +13,9 @@ process RENAME_FASTA_HEADER { tuple val(meta), path("*.fa"), emit: fasta path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 60c9c512..ffed8149 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -14,6 +14,9 @@ process SAMPLESHEET_CHECK { path '*.csv' , emit: csv path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: // This script is bundled with the pipeline, in nf-core/viralrecon/bin/ """ check_samplesheet.py \\ diff --git a/modules/local/snpeff_ann.nf b/modules/local/snpeff_ann.nf index 04823334..4ccf4db4 100644 --- a/modules/local/snpeff_ann.nf +++ b/modules/local/snpeff_ann.nf @@ -20,6 +20,9 @@ process SNPEFF_ANN { tuple val(meta), path("*.html") , emit: html path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/snpeff_build.nf b/modules/local/snpeff_build.nf index abdd9b3c..faaeba19 100644 --- a/modules/local/snpeff_build.nf +++ b/modules/local/snpeff_build.nf @@ -16,6 +16,9 @@ process SNPEFF_BUILD { path '*.config' , emit: config path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: def basename = fasta.baseName diff --git a/modules/local/snpsift_extractfields.nf b/modules/local/snpsift_extractfields.nf index 88dfb9f7..573063e0 100644 --- a/modules/local/snpsift_extractfields.nf +++ b/modules/local/snpsift_extractfields.nf @@ -14,6 +14,9 @@ process SNPSIFT_EXTRACTFIELDS { tuple val(meta), path("*.snpsift.txt"), emit: txt path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/abacas/main.nf b/modules/nf-core/modules/abacas/main.nf index 49040214..00c9169f 100644 --- a/modules/nf-core/modules/abacas/main.nf +++ b/modules/nf-core/modules/abacas/main.nf @@ -15,6 +15,9 @@ process ABACAS { tuple val(meta), path('*.abacas*'), emit: results path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/abacas/meta.yml b/modules/nf-core/modules/abacas/meta.yml index 039fb0be..c685e650 100644 --- a/modules/nf-core/modules/abacas/meta.yml +++ b/modules/nf-core/modules/abacas/meta.yml @@ -14,7 +14,7 @@ tools: documentation: http://abacas.sourceforge.net/documentation.html tool_dev_url: None doi: "10.1093/bioinformatics/btp347" - licence: ['GPL v2-or-later'] + licence: ["GPL v2-or-later"] input: - meta: diff --git a/modules/nf-core/modules/artic/guppyplex/main.nf b/modules/nf-core/modules/artic/guppyplex/main.nf index 780f5111..8e6b2879 100644 --- a/modules/nf-core/modules/artic/guppyplex/main.nf +++ b/modules/nf-core/modules/artic/guppyplex/main.nf @@ -14,6 +14,9 @@ process ARTIC_GUPPYPLEX { tuple val(meta), path("*.fastq.gz"), emit: fastq path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/artic/guppyplex/meta.yml b/modules/nf-core/modules/artic/guppyplex/meta.yml index 5056f908..fe288289 100644 --- a/modules/nf-core/modules/artic/guppyplex/meta.yml +++ b/modules/nf-core/modules/artic/guppyplex/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/nf-core/modules/artic/minion/main.nf b/modules/nf-core/modules/artic/minion/main.nf index c25ec0db..af74b132 100644 --- a/modules/nf-core/modules/artic/minion/main.nf +++ b/modules/nf-core/modules/artic/minion/main.nf @@ -31,6 +31,9 @@ process ARTIC_MINION { tuple val(meta), path("*.json"), optional:true , emit: json path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/artic/minion/meta.yml b/modules/nf-core/modules/artic/minion/meta.yml index 464e1dc7..5ef55673 100644 --- a/modules/nf-core/modules/artic/minion/meta.yml +++ b/modules/nf-core/modules/artic/minion/meta.yml @@ -1,6 +1,6 @@ name: artic_minion description: | - Run the alignment/variant-call/consensus logic of the artic pipeline + Run the alignment/variant-call/consensus logic of the artic pipeline keywords: - artic - aggregate @@ -12,7 +12,7 @@ tools: documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map @@ -21,11 +21,11 @@ input: e.g. [ id:'test', single_end:false ] - fastq: type: file - description: FastQ file containing reads + description: FastQ file containing reads pattern: "*.{fastq.gz}" - fast5_dir: type: directory - description: Directory containing MinION FAST5 files + description: Directory containing MinION FAST5 files pattern: "*" - sequencing_summary: type: file diff --git a/modules/nf-core/modules/bandage/image/main.nf b/modules/nf-core/modules/bandage/image/main.nf index bc2a9495..ee504a12 100644 --- a/modules/nf-core/modules/bandage/image/main.nf +++ b/modules/nf-core/modules/bandage/image/main.nf @@ -15,6 +15,9 @@ process BANDAGE_IMAGE { tuple val(meta), path('*.svg'), emit: svg 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}" diff --git a/modules/nf-core/modules/bandage/image/meta.yml b/modules/nf-core/modules/bandage/image/meta.yml index 1c2b9840..1e824c4f 100644 --- a/modules/nf-core/modules/bandage/image/meta.yml +++ b/modules/nf-core/modules/bandage/image/meta.yml @@ -1,44 +1,44 @@ name: bandage_image description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats keywords: - - gfa - - graph - - assembly - - visualisation + - gfa + - graph + - assembly + - visualisation tools: - - bandage: - description: | - Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily - homepage: https://github.com/rrwick/Bandage - documentation: https://github.com/rrwick/Bandage - licence: ['GPL-3.0-or-later'] + - bandage: + description: | + Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily + homepage: https://github.com/rrwick/Bandage + documentation: https://github.com/rrwick/Bandage + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly graph in GFA 1.0 format - pattern: "*.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly graph in GFA 1.0 format + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - png: - type: file - description: Bandage image in PNG format - pattern: "*.png" - - svg: - type: file - description: Bandage image in SVG format - pattern: "*.svg" - - 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 ] + - png: + type: file + description: Bandage image in PNG format + pattern: "*.png" + - svg: + type: file + description: Bandage image in SVG format + pattern: "*.svg" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/nf-core/modules/bcftools/consensus/main.nf b/modules/nf-core/modules/bcftools/consensus/main.nf index 040e6534..a0c436e2 100644 --- a/modules/nf-core/modules/bcftools/consensus/main.nf +++ b/modules/nf-core/modules/bcftools/consensus/main.nf @@ -14,6 +14,9 @@ process BCFTOOLS_CONSENSUS { tuple val(meta), path('*.fa'), emit: fasta 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}" diff --git a/modules/nf-core/modules/bcftools/consensus/meta.yml b/modules/nf-core/modules/bcftools/consensus/meta.yml index 761115a6..05a93a56 100644 --- a/modules/nf-core/modules/bcftools/consensus/meta.yml +++ b/modules/nf-core/modules/bcftools/consensus/meta.yml @@ -1,49 +1,49 @@ name: bcftools_consensus description: Compresses VCF files keywords: - - variant calling - - consensus - - VCF + - variant calling + - consensus + - VCF tools: - - consensus: - description: | - Create consensus sequence by applying VCF variants to a reference fasta file. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - consensus: + description: | + Create consensus sequence by applying VCF variants to a reference fasta file. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf}" - - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA reference consensus file - pattern: "*.{fasta,fa}" - - 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 ] + - fasta: + type: file + description: FASTA reference consensus file + pattern: "*.{fasta,fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bcftools/filter/main.nf b/modules/nf-core/modules/bcftools/filter/main.nf index 98b422b1..82961e32 100644 --- a/modules/nf-core/modules/bcftools/filter/main.nf +++ b/modules/nf-core/modules/bcftools/filter/main.nf @@ -14,6 +14,9 @@ process BCFTOOLS_FILTER { tuple val(meta), path("*.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}" diff --git a/modules/nf-core/modules/bcftools/filter/meta.yml b/modules/nf-core/modules/bcftools/filter/meta.yml index 72d28bf0..05a6d828 100644 --- a/modules/nf-core/modules/bcftools/filter/meta.yml +++ b/modules/nf-core/modules/bcftools/filter/meta.yml @@ -1,41 +1,41 @@ name: bcftools_filter description: Filters VCF files keywords: - - variant calling - - filtering - - VCF + - variant calling + - filtering + - VCF tools: - - filter: - description: | - Apply fixed-threshold filters to VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - filter: + description: | + Apply fixed-threshold filters to VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf}" - - 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 ] + - vcf: + type: file + description: VCF filtered output file + pattern: "*.{vcf}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bcftools/mpileup/main.nf b/modules/nf-core/modules/bcftools/mpileup/main.nf index cdd38eec..676eae7a 100644 --- a/modules/nf-core/modules/bcftools/mpileup/main.nf +++ b/modules/nf-core/modules/bcftools/mpileup/main.nf @@ -19,6 +19,9 @@ process BCFTOOLS_MPILEUP { tuple val(meta), path("*.mpileup") , emit: mpileup, optional: true path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/nf-core/modules/bcftools/mpileup/meta.yml b/modules/nf-core/modules/bcftools/mpileup/meta.yml index 483d0e71..d10dac14 100644 --- a/modules/nf-core/modules/bcftools/mpileup/meta.yml +++ b/modules/nf-core/modules/bcftools/mpileup/meta.yml @@ -1,57 +1,57 @@ name: bcftools_mpileup description: Compresses VCF files keywords: - - variant calling - - mpileup - - VCF + - variant calling + - mpileup + - VCF tools: - - mpileup: - description: | - Generates genotype likelihoods at each genomic position with coverage. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - mpileup: + description: | + Generates genotype likelihoods at each genomic position with coverage. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + 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 file - pattern: "*.{bam}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - save_mpileup: - type: boolean - description: Save mpileup file generated by bcftools mpileup - patter: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - save_mpileup: + type: boolean + description: Save mpileup file generated by bcftools mpileup + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF gzipped output file - pattern: "*.{vcf.gz}" - - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" - - stats: - type: file - description: Text output file containing stats - pattern: "*{stats.txt}" - - 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 ] + - vcf: + type: file + description: VCF gzipped output file + pattern: "*.{vcf.gz}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - stats: + type: file + description: Text output file containing stats + pattern: "*{stats.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bcftools/norm/main.nf b/modules/nf-core/modules/bcftools/norm/main.nf index e8bf6324..cd681f21 100644 --- a/modules/nf-core/modules/bcftools/norm/main.nf +++ b/modules/nf-core/modules/bcftools/norm/main.nf @@ -15,6 +15,9 @@ process BCFTOOLS_NORM { tuple val(meta), path("*.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}" diff --git a/modules/nf-core/modules/bcftools/norm/meta.yml b/modules/nf-core/modules/bcftools/norm/meta.yml index 27978a53..ce4aee85 100644 --- a/modules/nf-core/modules/bcftools/norm/meta.yml +++ b/modules/nf-core/modules/bcftools/norm/meta.yml @@ -6,41 +6,41 @@ keywords: - variant calling - VCF tools: - - norm: - description: | - Normalize VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - norm: + description: | + Normalize VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be normalized - e.g. 'file1.vcf' - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf' + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf.gz}" - - 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 ] + - vcf: + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" + - "@abhi18av" diff --git a/modules/nf-core/modules/bcftools/query/main.nf b/modules/nf-core/modules/bcftools/query/main.nf index a165b103..8921abdd 100644 --- a/modules/nf-core/modules/bcftools/query/main.nf +++ b/modules/nf-core/modules/bcftools/query/main.nf @@ -17,6 +17,9 @@ process BCFTOOLS_QUERY { tuple val(meta), path("*.txt"), emit: txt 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}" diff --git a/modules/nf-core/modules/bcftools/query/meta.yml b/modules/nf-core/modules/bcftools/query/meta.yml index e49f13c8..fd4fd473 100644 --- a/modules/nf-core/modules/bcftools/query/meta.yml +++ b/modules/nf-core/modules/bcftools/query/meta.yml @@ -6,56 +6,56 @@ keywords: - bcftools - VCF tools: - - query: - description: | - Extracts fields from VCF or BCF files and outputs them in user-defined format. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - query: + description: | + Extracts fields from VCF or BCF files and outputs them in user-defined format. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be qeuried. - pattern: "*.{vcf.gz, vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be qeuried. + pattern: "*.{vcf.gz, vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. + pattern: "*.tbi" + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - txt: - type: file - description: BCFTools query output file - pattern: "*.txt" - - 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 ] + - txt: + type: file + description: BCFTools query output file + pattern: "*.txt" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@drpatelh" diff --git a/modules/nf-core/modules/bcftools/stats/main.nf b/modules/nf-core/modules/bcftools/stats/main.nf index 54a28bce..7e150d1f 100644 --- a/modules/nf-core/modules/bcftools/stats/main.nf +++ b/modules/nf-core/modules/bcftools/stats/main.nf @@ -14,6 +14,9 @@ process BCFTOOLS_STATS { tuple val(meta), path("*stats.txt"), emit: stats 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}" diff --git a/modules/nf-core/modules/bcftools/stats/meta.yml b/modules/nf-core/modules/bcftools/stats/meta.yml index 505bf729..304b88ec 100644 --- a/modules/nf-core/modules/bcftools/stats/meta.yml +++ b/modules/nf-core/modules/bcftools/stats/meta.yml @@ -1,42 +1,42 @@ name: bcftools_stats description: Generates stats from VCF files keywords: - - variant calling - - stats - - VCF + - variant calling + - stats + - VCF tools: - - stats: - description: | - Parses VCF or BCF and produces text file stats which is suitable for - machine processing and can be plotted using plot-vcfstats. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - stats: + description: | + Parses VCF or BCF and produces text file stats which is suitable for + machine processing and can be plotted using plot-vcfstats. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: Text output file containing stats - pattern: "*_{stats.txt}" - - 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 ] + - stats: + type: file + description: Text output file containing stats + pattern: "*_{stats.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bedtools/getfasta/main.nf b/modules/nf-core/modules/bedtools/getfasta/main.nf index 5a283e94..4ce8c01e 100644 --- a/modules/nf-core/modules/bedtools/getfasta/main.nf +++ b/modules/nf-core/modules/bedtools/getfasta/main.nf @@ -15,6 +15,9 @@ process BEDTOOLS_GETFASTA { path "*.fa" , emit: fasta path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${bed.baseName}" diff --git a/modules/nf-core/modules/bedtools/getfasta/meta.yml b/modules/nf-core/modules/bedtools/getfasta/meta.yml index 38715c3d..11335100 100644 --- a/modules/nf-core/modules/bedtools/getfasta/meta.yml +++ b/modules/nf-core/modules/bedtools/getfasta/meta.yml @@ -1,34 +1,34 @@ name: bedtools_getfasta description: extract sequences in a FASTA file based on intervals defined in a feature file. keywords: - - bed - - fasta - - getfasta + - bed + - fasta + - getfasta 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/intersect.html - licence: ['MIT'] + - 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/intersect.html + licence: ["MIT"] input: - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - fasta: - type: file - description: Output fasta file with extracted sequences - pattern: "*.{fa}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - fasta: + type: file + description: Output fasta file with extracted sequences + pattern: "*.{fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bedtools/maskfasta/main.nf b/modules/nf-core/modules/bedtools/maskfasta/main.nf index 7eeb4c7d..04ba116b 100644 --- a/modules/nf-core/modules/bedtools/maskfasta/main.nf +++ b/modules/nf-core/modules/bedtools/maskfasta/main.nf @@ -15,6 +15,9 @@ process BEDTOOLS_MASKFASTA { tuple val(meta), path("*.fa"), emit: fasta 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}" diff --git a/modules/nf-core/modules/bedtools/maskfasta/meta.yml b/modules/nf-core/modules/bedtools/maskfasta/meta.yml index 0b7aa3ed..cc33df3e 100644 --- a/modules/nf-core/modules/bedtools/maskfasta/meta.yml +++ b/modules/nf-core/modules/bedtools/maskfasta/meta.yml @@ -1,44 +1,44 @@ name: bedtools_maskfasta description: masks sequences in a FASTA file based on intervals defined in a feature file. keywords: - - bed - - fasta - - maskfasta + - bed + - fasta + - maskfasta 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/intersect.html - licence: ['MIT'] + - 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/intersect.html + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Output masked fasta file - pattern: "*.{fa}" - - 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 ] + - fasta: + type: file + description: Output masked fasta file + pattern: "*.{fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bedtools/merge/main.nf b/modules/nf-core/modules/bedtools/merge/main.nf index 5f1da95b..6d1daa03 100644 --- a/modules/nf-core/modules/bedtools/merge/main.nf +++ b/modules/nf-core/modules/bedtools/merge/main.nf @@ -14,6 +14,9 @@ process BEDTOOLS_MERGE { 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}" diff --git a/modules/nf-core/modules/bedtools/merge/meta.yml b/modules/nf-core/modules/bedtools/merge/meta.yml index 40a42b7b..76743679 100644 --- a/modules/nf-core/modules/bedtools/merge/meta.yml +++ b/modules/nf-core/modules/bedtools/merge/meta.yml @@ -1,39 +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 + - 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'] + - 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}" + - 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" + - 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" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/nf-core/modules/blast/blastn/main.nf b/modules/nf-core/modules/blast/blastn/main.nf index 3a0bafe0..b85f6c8e 100644 --- a/modules/nf-core/modules/blast/blastn/main.nf +++ b/modules/nf-core/modules/blast/blastn/main.nf @@ -15,6 +15,9 @@ process BLAST_BLASTN { tuple val(meta), path('*.blastn.txt'), emit: txt 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}" diff --git a/modules/nf-core/modules/blast/blastn/meta.yml b/modules/nf-core/modules/blast/blastn/meta.yml index 39acb663..2742278d 100644 --- a/modules/nf-core/modules/blast/blastn/meta.yml +++ b/modules/nf-core/modules/blast/blastn/meta.yml @@ -1,41 +1,41 @@ name: blast_blastn description: Queries a BLAST DNA database keywords: - - fasta - - blast - - blastn - - DNA sequence + - fasta + - blast + - blastn + - DNA sequence tools: - - blast: - description: | - BLAST finds regions of similarity between biological sequences. - homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi - documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs - doi: 10.1016/S0022-2836(05)80360-2 - licence: ['US-Government-Work'] + - blast: + description: | + BLAST finds regions of similarity between biological sequences. + homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi + documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs + doi: 10.1016/S0022-2836(05)80360-2 + licence: ["US-Government-Work"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta}" - - db: - type: directory - description: Directory containing blast database - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta}" + - db: + type: directory + description: Directory containing blast database + pattern: "*" output: - - txt: - type: file - description: File containing blastn hits - pattern: "*.{blastn.txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - txt: + type: file + description: File containing blastn hits + pattern: "*.{blastn.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/blast/makeblastdb/main.nf b/modules/nf-core/modules/blast/makeblastdb/main.nf index b4c426a4..12208ea8 100644 --- a/modules/nf-core/modules/blast/makeblastdb/main.nf +++ b/modules/nf-core/modules/blast/makeblastdb/main.nf @@ -14,6 +14,9 @@ process BLAST_MAKEBLASTDB { path 'blast_db' , emit: db path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/blast/makeblastdb/meta.yml b/modules/nf-core/modules/blast/makeblastdb/meta.yml index c9d18cba..83c4b292 100644 --- a/modules/nf-core/modules/blast/makeblastdb/meta.yml +++ b/modules/nf-core/modules/blast/makeblastdb/meta.yml @@ -1,31 +1,31 @@ name: blast_makeblastdb description: Builds a BLAST database keywords: - - fasta - - blast - - database + - fasta + - blast + - database tools: - - blast: - description: | - BLAST finds regions of similarity between biological sequences. - homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi - documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs - doi: 10.1016/S0022-2836(05)80360-2 - licence: ['US-Government-Work'] + - blast: + description: | + BLAST finds regions of similarity between biological sequences. + homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi + documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs + doi: 10.1016/S0022-2836(05)80360-2 + licence: ["US-Government-Work"] input: - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - db: - type: directory - description: Output directory containing blast database files - pattern: "*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - db: + type: directory + description: Output directory containing blast database files + pattern: "*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bowtie2/align/main.nf b/modules/nf-core/modules/bowtie2/align/main.nf index 20b08f72..7e8a9659 100644 --- a/modules/nf-core/modules/bowtie2/align/main.nf +++ b/modules/nf-core/modules/bowtie2/align/main.nf @@ -18,6 +18,9 @@ process BOWTIE2_ALIGN { tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/nf-core/modules/bowtie2/align/meta.yml b/modules/nf-core/modules/bowtie2/align/meta.yml index 77c9e397..f80421ec 100644 --- a/modules/nf-core/modules/bowtie2/align/meta.yml +++ b/modules/nf-core/modules/bowtie2/align/meta.yml @@ -1,51 +1,51 @@ name: bowtie2_align description: Align reads to a reference genome using bowtie2 keywords: - - align - - fasta - - genome - - reference + - align + - fasta + - genome + - reference tools: - - bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ['GPL-3.0-or-later'] + - bowtie2: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 + licence: ["GPL-3.0-or-later"] 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. - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.ebwt" + - 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. + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.ebwt" output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - - log: - type: file - description: Aligment log - pattern: "*.log" + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - log: + type: file + description: Aligment log + pattern: "*.log" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/bowtie2/build/main.nf b/modules/nf-core/modules/bowtie2/build/main.nf index da2e9ed5..a4da62d0 100644 --- a/modules/nf-core/modules/bowtie2/build/main.nf +++ b/modules/nf-core/modules/bowtie2/build/main.nf @@ -14,6 +14,9 @@ process BOWTIE2_BUILD { path 'bowtie2' , emit: index path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/bowtie2/build/meta.yml b/modules/nf-core/modules/bowtie2/build/meta.yml index ecc54e9b..2da9a217 100644 --- a/modules/nf-core/modules/bowtie2/build/meta.yml +++ b/modules/nf-core/modules/bowtie2/build/meta.yml @@ -1,33 +1,33 @@ name: bowtie2_build description: Builds bowtie index for reference genome keywords: - - build - - index - - fasta - - genome - - reference + - build + - index + - fasta + - genome + - reference tools: - - bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ['GPL-3.0-or-later'] + - bowtie2: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 + licence: ["GPL-3.0-or-later"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.bt2" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.bt2" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf index d02598e1..bf0877c3 100644 --- a/modules/nf-core/modules/cat/fastq/main.nf +++ b/modules/nf-core/modules/cat/fastq/main.nf @@ -14,6 +14,9 @@ process CAT_FASTQ { tuple val(meta), path("*.merged.fastq.gz"), emit: reads 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}" diff --git a/modules/nf-core/modules/cat/fastq/meta.yml b/modules/nf-core/modules/cat/fastq/meta.yml index 1992fa34..c836598e 100644 --- a/modules/nf-core/modules/cat/fastq/meta.yml +++ b/modules/nf-core/modules/cat/fastq/meta.yml @@ -1,39 +1,39 @@ name: cat_fastq description: Concatenates fastq files keywords: - - fastq - - concatenate + - fastq + - concatenate tools: - - cat: - description: | - 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'] + - cat: + description: | + 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"] 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 to be concatenated. + - 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 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}" - - 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 ] + - reads: + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf index 934bb467..327d5100 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf @@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { 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/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml index 5b5b8a60..60b546a0 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml @@ -8,7 +8,7 @@ tools: 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'] + licence: ["MIT"] input: - versions: type: file diff --git a/modules/nf-core/modules/custom/getchromsizes/main.nf b/modules/nf-core/modules/custom/getchromsizes/main.nf index 270b3f48..39da7d34 100644 --- a/modules/nf-core/modules/custom/getchromsizes/main.nf +++ b/modules/nf-core/modules/custom/getchromsizes/main.nf @@ -15,6 +15,9 @@ process CUSTOM_GETCHROMSIZES { path '*.fai' , emit: fai path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/custom/getchromsizes/meta.yml b/modules/nf-core/modules/custom/getchromsizes/meta.yml index eb1db4bb..ee6c2571 100644 --- a/modules/nf-core/modules/custom/getchromsizes/meta.yml +++ b/modules/nf-core/modules/custom/getchromsizes/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://www.htslib.org/doc/samtools.html tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + licence: ["MIT"] input: - fasta: @@ -33,7 +33,6 @@ output: description: File containing software version pattern: "versions.yml" - authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/modules/fastp/main.nf b/modules/nf-core/modules/fastp/main.nf index a406036a..d8218350 100644 --- a/modules/nf-core/modules/fastp/main.nf +++ b/modules/nf-core/modules/fastp/main.nf @@ -21,6 +21,9 @@ process FASTP { tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' // Added soft-links to original fastqs for consistent naming in MultiQC diff --git a/modules/nf-core/modules/fastp/meta.yml b/modules/nf-core/modules/fastp/meta.yml index a1875faf..f53bb09f 100644 --- a/modules/nf-core/modules/fastp/meta.yml +++ b/modules/nf-core/modules/fastp/meta.yml @@ -10,7 +10,7 @@ tools: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. documentation: https://github.com/OpenGene/fastp doi: https://doi.org/10.1093/bioinformatics/bty560 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf index d250eca0..ed6b8c50 100644 --- a/modules/nf-core/modules/fastqc/main.nf +++ b/modules/nf-core/modules/fastqc/main.nf @@ -15,6 +15,9 @@ process FASTQC { tuple val(meta), path("*.zip") , emit: zip path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' // Add soft-links to original FastQs for consistent naming in pipeline diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml index b09553a3..4da5bb5a 100644 --- a/modules/nf-core/modules/fastqc/meta.yml +++ b/modules/nf-core/modules/fastqc/meta.yml @@ -1,52 +1,52 @@ name: fastqc description: Run FastQC on sequenced reads keywords: - - quality control - - qc - - adapters - - fastq + - quality control + - qc + - adapters + - fastq tools: - - fastqc: - description: | - 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/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ['GPL-2.0-only'] + - fastqc: + description: | + 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/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] 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}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - 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 ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf index 77a4e546..9d4b0666 100644 --- a/modules/nf-core/modules/gunzip/main.nf +++ b/modules/nf-core/modules/gunzip/main.nf @@ -14,6 +14,9 @@ process GUNZIP { 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' diff --git a/modules/nf-core/modules/gunzip/meta.yml b/modules/nf-core/modules/gunzip/meta.yml index ea1f1546..4d2ebc84 100644 --- a/modules/nf-core/modules/gunzip/meta.yml +++ b/modules/nf-core/modules/gunzip/meta.yml @@ -1,34 +1,34 @@ name: gunzip description: Compresses and decompresses files. keywords: - - gunzip - - compression + - gunzip + - compression 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'] + - 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"] 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: "*.*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@jfy133" + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/modules/ivar/consensus/main.nf b/modules/nf-core/modules/ivar/consensus/main.nf index 96d00ce2..db6301e9 100644 --- a/modules/nf-core/modules/ivar/consensus/main.nf +++ b/modules/nf-core/modules/ivar/consensus/main.nf @@ -18,6 +18,9 @@ process IVAR_CONSENSUS { tuple val(meta), path("*.mpileup") , optional:true, emit: mpileup path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/nf-core/modules/ivar/consensus/meta.yml b/modules/nf-core/modules/ivar/consensus/meta.yml index aa08ad98..fb562603 100644 --- a/modules/nf-core/modules/ivar/consensus/meta.yml +++ b/modules/nf-core/modules/ivar/consensus/meta.yml @@ -1,56 +1,56 @@ name: ivar_consensus description: Generate a consensus sequence from a BAM file using iVar keywords: - - amplicon sequencing - - consensus - - fasta + - amplicon sequencing + - consensus + - fasta tools: - - ivar: - description: | - iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. - homepage: https://github.com/andersen-lab/ivar - documentation: https://andersen-lab.github.io/ivar/html/manualpage.html - licence: ['GPL-3.0-or-later'] + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar consensus - patter: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file + pattern: "*.bam" + - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM file + pattern: "*.fa" + - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar consensus + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: iVar generated consensus sequence - pattern: "*.fa" - - qual: - type: file - description: iVar generated quality file - pattern: "*.qual.txt" - - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" - - 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 ] + - fasta: + type: file + description: iVar generated consensus sequence + pattern: "*.fa" + - qual: + type: file + description: iVar generated quality file + pattern: "*.qual.txt" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@andersgs" - - "@drpatelh" + - "@andersgs" + - "@drpatelh" diff --git a/modules/nf-core/modules/ivar/trim/main.nf b/modules/nf-core/modules/ivar/trim/main.nf index 4d0c70a2..819aa5dd 100644 --- a/modules/nf-core/modules/ivar/trim/main.nf +++ b/modules/nf-core/modules/ivar/trim/main.nf @@ -16,6 +16,9 @@ process IVAR_TRIM { 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}" diff --git a/modules/nf-core/modules/ivar/trim/meta.yml b/modules/nf-core/modules/ivar/trim/meta.yml index 44bc742e..d01dd1a2 100644 --- a/modules/nf-core/modules/ivar/trim/meta.yml +++ b/modules/nf-core/modules/ivar/trim/meta.yml @@ -1,52 +1,52 @@ name: ivar_trim description: Trim primer sequences rom a BAM file with iVar keywords: - - amplicon sequencing - - trimming - - fasta + - amplicon sequencing + - trimming + - fasta tools: - - ivar: - description: | - iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. - homepage: https://github.com/andersen-lab/ivar - documentation: https://andersen-lab.github.io/ivar/html/manualpage.html - licence: ['GPL-3.0-or-later'] + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Co-ordinate sorted BAM file - pattern: "*.bam" - - bai: - type: file - description: Index file for co-ordinate sorted BAM file - pattern: "*.bai" - - bed: - type: file - description: BED file with primer labels and positions - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Co-ordinate sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index file for co-ordinate sorted BAM file + pattern: "*.bai" + - bed: + type: file + description: BED file with primer labels and positions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: iVar generated trimmed bam file (unsorted) - pattern: "*.bam" - - log: - type: file - description: Log file generated by iVar for use with MultiQC - pattern: "*.log" - - 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 ] + - bam: + type: file + description: iVar generated trimmed bam file (unsorted) + pattern: "*.bam" + - log: + type: file + description: Log file generated by iVar for use with MultiQC + pattern: "*.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@andersgs" - - "@drpatelh" + - "@andersgs" + - "@drpatelh" diff --git a/modules/nf-core/modules/ivar/variants/main.nf b/modules/nf-core/modules/ivar/variants/main.nf index bb6e402b..85c4cacd 100644 --- a/modules/nf-core/modules/ivar/variants/main.nf +++ b/modules/nf-core/modules/ivar/variants/main.nf @@ -18,6 +18,9 @@ process IVAR_VARIANTS { tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/nf-core/modules/ivar/variants/meta.yml b/modules/nf-core/modules/ivar/variants/meta.yml index 29cbd958..6677ffb2 100644 --- a/modules/nf-core/modules/ivar/variants/meta.yml +++ b/modules/nf-core/modules/ivar/variants/meta.yml @@ -1,56 +1,56 @@ name: ivar_variants description: Call variants from a BAM file using iVar keywords: - - amplicon sequencing - - variants - - fasta + - amplicon sequencing + - variants + - fasta tools: - - ivar: - description: | - iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. - homepage: https://github.com/andersen-lab/ivar - documentation: https://andersen-lab.github.io/ivar/html/manualpage.html - licence: ['GPL-3.0-or-later'] + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - gff: - type: file - description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. - patter: "*.gff" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar variants - patter: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file + pattern: "*.bam" + - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM file + pattern: "*.fa" + - gff: + type: file + description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. + patter: "*.gff" + - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar variants + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tsv: - type: file - description: iVar generated TSV file with the variants - pattern: "*.tsv" - - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" - - 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 ] + - tsv: + type: file + description: iVar generated TSV file with the variants + pattern: "*.tsv" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@andersgs" - - "@drpatelh" + - "@andersgs" + - "@drpatelh" diff --git a/modules/nf-core/modules/kraken2/kraken2/main.nf b/modules/nf-core/modules/kraken2/kraken2/main.nf index eaabb229..3ec5df52 100644 --- a/modules/nf-core/modules/kraken2/kraken2/main.nf +++ b/modules/nf-core/modules/kraken2/kraken2/main.nf @@ -17,6 +17,9 @@ process KRAKEN2_KRAKEN2 { tuple val(meta), path('*report.txt') , emit: txt 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}" diff --git a/modules/nf-core/modules/kraken2/kraken2/meta.yml b/modules/nf-core/modules/kraken2/kraken2/meta.yml index 4b894705..9d6a3855 100644 --- a/modules/nf-core/modules/kraken2/kraken2/meta.yml +++ b/modules/nf-core/modules/kraken2/kraken2/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/modules/minia/main.nf b/modules/nf-core/modules/minia/main.nf index 968cafa5..87dd74f9 100644 --- a/modules/nf-core/modules/minia/main.nf +++ b/modules/nf-core/modules/minia/main.nf @@ -16,6 +16,9 @@ process MINIA { tuple val(meta), path('*.h5') , emit: h5 path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/minia/meta.yml b/modules/nf-core/modules/minia/meta.yml index 397a1d49..ae86f75c 100644 --- a/modules/nf-core/modules/minia/meta.yml +++ b/modules/nf-core/modules/minia/meta.yml @@ -9,7 +9,7 @@ tools: a human genome on a desktop computer in a day. The output of Minia is a set of contigs. homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia - licence: ['AGPL-3.0-or-later'] + licence: ["AGPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/nf-core/modules/mosdepth/main.nf b/modules/nf-core/modules/mosdepth/main.nf index d2669b7e..ff91e06f 100644 --- a/modules/nf-core/modules/mosdepth/main.nf +++ b/modules/nf-core/modules/mosdepth/main.nf @@ -2,10 +2,10 @@ process MOSDEPTH { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null) + conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0' : - 'quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0' }" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : + 'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}" input: tuple val(meta), path(bam), path(bai) @@ -14,18 +14,28 @@ process MOSDEPTH { output: tuple val(meta), path('*.global.dist.txt') , emit: global_txt - tuple val(meta), path('*.region.dist.txt') , emit: regions_txt + tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed - tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi - tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed - tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi + tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true + tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true + tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true + tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true + tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi , optional:true path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def interval = window_size ? "--by ${window_size}" : "--by ${bed}" + if (window_size) { + interval = "--by ${window_size}" + } else if ( bed ) { + interval = "--by ${bed}" + } else { + interval = "" + } """ mosdepth \\ $interval \\ @@ -37,4 +47,22 @@ process MOSDEPTH { mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${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 ${prefix}.regions.bed.gz.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/modules/mosdepth/meta.yml b/modules/nf-core/modules/mosdepth/meta.yml index be568aa6..636e966b 100644 --- a/modules/nf-core/modules/mosdepth/meta.yml +++ b/modules/nf-core/modules/mosdepth/meta.yml @@ -11,7 +11,7 @@ tools: Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map @@ -73,5 +73,6 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" + - "@ramprasadn" diff --git a/modules/nf-core/modules/nanoplot/main.nf b/modules/nf-core/modules/nanoplot/main.nf index c3fb8a37..083e2374 100644 --- a/modules/nf-core/modules/nanoplot/main.nf +++ b/modules/nf-core/modules/nanoplot/main.nf @@ -17,6 +17,9 @@ process NANOPLOT { 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 input_file = ("$ontfile".endsWith(".fastq.gz")) ? "--fastq ${ontfile}" : diff --git a/modules/nf-core/modules/nanoplot/meta.yml b/modules/nf-core/modules/nanoplot/meta.yml index 52ebb622..28c8c2d3 100644 --- a/modules/nf-core/modules/nanoplot/meta.yml +++ b/modules/nf-core/modules/nanoplot/meta.yml @@ -1,59 +1,59 @@ name: nanoplot description: Run NanoPlot on nanopore-sequenced reads keywords: - - quality control - - qc - - fastq - - sequencing summary - - nanopore + - quality control + - qc + - fastq + - sequencing summary + - nanopore tools: - - nanoplot: - description: | - NanoPlot is a tool for ploting long-read sequencing data and - alignment. - homepage: http://nanoplot.bioinf.be - documentation: https://github.com/wdecoster/NanoPlot - licence: ['GPL-3.0-or-later'] + - nanoplot: + description: | + NanoPlot is a tool for ploting long-read sequencing data and + alignment. + homepage: http://nanoplot.bioinf.be + documentation: https://github.com/wdecoster/NanoPlot + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input basecalled-FastQ files. - - summary_txt: - type: file - description: | - List of sequencing_summary.txt files from running basecalling. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + List of input basecalled-FastQ files. + - summary_txt: + type: file + description: | + List of sequencing_summary.txt files from running basecalling. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: NanoPlot report - pattern: "*{.html}" - - png: - type: file - description: Plots generated by NanoPlot - pattern: "*{.png}" - - txt: - type: file - description: Stats from NanoPlot - pattern: "*{.txt}" - - log: - type: file - description: log file of NanoPlot run - pattern: "*{.log}" - - 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 ] + - html: + type: file + description: NanoPlot report + pattern: "*{.html}" + - png: + type: file + description: Plots generated by NanoPlot + pattern: "*{.png}" + - txt: + type: file + description: Stats from NanoPlot + pattern: "*{.txt}" + - log: + type: file + description: log file of NanoPlot run + pattern: "*{.log}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@yuukiiwa" + - "@drpatelh" + - "@yuukiiwa" diff --git a/modules/nf-core/modules/nextclade/datasetget/main.nf b/modules/nf-core/modules/nextclade/datasetget/main.nf index 75bb88f3..4dd82ee3 100644 --- a/modules/nf-core/modules/nextclade/datasetget/main.nf +++ b/modules/nf-core/modules/nextclade/datasetget/main.nf @@ -16,6 +16,9 @@ process NEXTCLADE_DATASETGET { path "$prefix" , emit: dataset path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${dataset}" diff --git a/modules/nf-core/modules/nextclade/datasetget/meta.yml b/modules/nf-core/modules/nextclade/datasetget/meta.yml index 1246d918..d5f65cda 100644 --- a/modules/nf-core/modules/nextclade/datasetget/meta.yml +++ b/modules/nf-core/modules/nextclade/datasetget/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - dataset: diff --git a/modules/nf-core/modules/nextclade/run/main.nf b/modules/nf-core/modules/nextclade/run/main.nf index b3d101ce..4d4bdb88 100644 --- a/modules/nf-core/modules/nextclade/run/main.nf +++ b/modules/nf-core/modules/nextclade/run/main.nf @@ -18,6 +18,9 @@ process NEXTCLADE_RUN { tuple val(meta), path("${prefix}.tree.json"), emit: json_tree path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/nextclade/run/meta.yml b/modules/nf-core/modules/nextclade/run/meta.yml index 40a863e6..d8f1eb37 100644 --- a/modules/nf-core/modules/nextclade/run/meta.yml +++ b/modules/nf-core/modules/nextclade/run/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/nf-core/modules/pangolin/main.nf b/modules/nf-core/modules/pangolin/main.nf index 6c8682e3..5af557ac 100644 --- a/modules/nf-core/modules/pangolin/main.nf +++ b/modules/nf-core/modules/pangolin/main.nf @@ -2,10 +2,10 @@ process PANGOLIN { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::pangolin=3.1.19' : null) + conda (params.enable_conda ? 'bioconda::pangolin=3.1.20' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pangolin:3.1.19--pyhdfd78af_0' : - 'quay.io/biocontainers/pangolin:3.1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/pangolin:3.1.20--pyhdfd78af_0' : + 'quay.io/biocontainers/pangolin:3.1.20--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) @@ -14,6 +14,9 @@ process PANGOLIN { tuple val(meta), path('*.csv'), emit: report path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/pangolin/meta.yml b/modules/nf-core/modules/pangolin/meta.yml index a2c0979a..93c25a75 100644 --- a/modules/nf-core/modules/pangolin/meta.yml +++ b/modules/nf-core/modules/pangolin/meta.yml @@ -1,34 +1,34 @@ name: pangolin description: Phylogenetic Assignment of Named Global Outbreak LINeages keywords: - - covid - - pangolin - - lineage + - covid + - pangolin + - lineage tools: - - star: - description: | - Phylogenetic Assignment of Named Global Outbreak LINeages - homepage: https://github.com/cov-lineages/pangolin#pangolearn-description - manual: https://github.com/cov-lineages/pangolin#pangolearn-description - licence: ['GPL-3.0-or-later'] + - star: + description: | + Phylogenetic Assignment of Named Global Outbreak LINeages + homepage: https://github.com/cov-lineages/pangolin#pangolearn-description + manual: https://github.com/cov-lineages/pangolin#pangolearn-description + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - - fasta: - type: file - description: | - The genome assembly to be evaluated + - meta: + type: map + description: | + Groovy Map containing sample information + - fasta: + type: file + description: | + The genome assembly to be evaluated output: - - report: - type: file - description: Pangolin lineage report - pattern: "*.{csv}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - report: + type: file + description: Pangolin lineage report + pattern: "*.{csv}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@kevinmenden" - - "@drpatelh" + - "@kevinmenden" + - "@drpatelh" diff --git a/modules/nf-core/modules/picard/collectmultiplemetrics/main.nf b/modules/nf-core/modules/picard/collectmultiplemetrics/main.nf index 9511f7a4..e023ea3c 100644 --- a/modules/nf-core/modules/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/modules/picard/collectmultiplemetrics/main.nf @@ -16,6 +16,9 @@ process PICARD_COLLECTMULTIPLEMETRICS { tuple val(meta), path("*.pdf") , emit: pdf 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}" diff --git a/modules/nf-core/modules/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/modules/picard/collectmultiplemetrics/meta.yml index 613afc62..68b5c65e 100644 --- a/modules/nf-core/modules/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/modules/picard/collectmultiplemetrics/meta.yml @@ -1,50 +1,50 @@ name: picard_collectmultiplemetrics description: Collect multiple metrics from a BAM file keywords: - - alignment - - metrics - - statistics - - insert - - quality - - bam + - alignment + - metrics + - statistics + - insert + - quality + - bam 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'] + - 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 ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Genome fasta file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: Genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - - pdf: - type: file - description: PDF plots of metrics - pattern: "*.{pdf}" - - 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 ] + - metrics: + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" + - pdf: + type: file + description: PDF plots of metrics + pattern: "*.{pdf}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/nf-core/modules/picard/markduplicates/main.nf b/modules/nf-core/modules/picard/markduplicates/main.nf index 7990d7e6..5196b6ed 100644 --- a/modules/nf-core/modules/picard/markduplicates/main.nf +++ b/modules/nf-core/modules/picard/markduplicates/main.nf @@ -16,6 +16,9 @@ process PICARD_MARKDUPLICATES { 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}" diff --git a/modules/nf-core/modules/picard/markduplicates/meta.yml b/modules/nf-core/modules/picard/markduplicates/meta.yml index c9a08b36..842817bc 100644 --- a/modules/nf-core/modules/picard/markduplicates/meta.yml +++ b/modules/nf-core/modules/picard/markduplicates/meta.yml @@ -14,7 +14,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/modules/plasmidid/main.nf b/modules/nf-core/modules/plasmidid/main.nf index 7404a678..7911d806 100644 --- a/modules/nf-core/modules/plasmidid/main.nf +++ b/modules/nf-core/modules/plasmidid/main.nf @@ -22,6 +22,9 @@ process PLASMIDID { tuple val(meta), path("${prefix}/kmer/") , emit: kmer path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/plasmidid/meta.yml b/modules/nf-core/modules/plasmidid/meta.yml index 8cde23c5..4887cb9a 100644 --- a/modules/nf-core/modules/plasmidid/meta.yml +++ b/modules/nf-core/modules/plasmidid/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/BU-ISCIII/plasmidID#readme tool_dev_url: https://github.com/BU-ISCIII/plasmidID doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/nf-core/modules/pycoqc/main.nf b/modules/nf-core/modules/pycoqc/main.nf index e966b31c..a5e6fcb2 100644 --- a/modules/nf-core/modules/pycoqc/main.nf +++ b/modules/nf-core/modules/pycoqc/main.nf @@ -15,6 +15,9 @@ process PYCOQC { path "*.json" , emit: json path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/pycoqc/meta.yml b/modules/nf-core/modules/pycoqc/meta.yml index 33bd6b07..83748855 100644 --- a/modules/nf-core/modules/pycoqc/meta.yml +++ b/modules/nf-core/modules/pycoqc/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://tleonardi.github.io/pycoQC/ tool_dev_url: https://github.com/tleonardi/pycoQC doi: "10.21105/joss.01236" - licence: ['GNU General Public v3 (GPL v3)'] + licence: ["GNU General Public v3 (GPL v3)"] input: - meta: diff --git a/modules/nf-core/modules/quast/main.nf b/modules/nf-core/modules/quast/main.nf index e88051b5..beb797d4 100644 --- a/modules/nf-core/modules/quast/main.nf +++ b/modules/nf-core/modules/quast/main.nf @@ -18,6 +18,9 @@ process QUAST { path '*.tsv' , emit: tsv path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: 'quast' diff --git a/modules/nf-core/modules/quast/meta.yml b/modules/nf-core/modules/quast/meta.yml index 05faa8b8..f4bc38fc 100644 --- a/modules/nf-core/modules/quast/meta.yml +++ b/modules/nf-core/modules/quast/meta.yml @@ -10,7 +10,7 @@ tools: QUAST calculates quality metrics for genome assemblies homepage: http://bioinf.spbau.ru/quast doi: https://doi.org/10.1093/bioinformatics/btt086 - licence: ['GPL-2.0-only'] + licence: ["GPL-2.0-only"] input: - consensus: type: file diff --git a/modules/nf-core/modules/samtools/flagstat/main.nf b/modules/nf-core/modules/samtools/flagstat/main.nf index 119adf77..c267922b 100644 --- a/modules/nf-core/modules/samtools/flagstat/main.nf +++ b/modules/nf-core/modules/samtools/flagstat/main.nf @@ -14,6 +14,9 @@ process SAMTOOLS_FLAGSTAT { tuple val(meta), path("*.flagstat"), emit: flagstat path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/samtools/flagstat/meta.yml b/modules/nf-core/modules/samtools/flagstat/meta.yml index 9bd9ff89..95269063 100644 --- a/modules/nf-core/modules/samtools/flagstat/meta.yml +++ b/modules/nf-core/modules/samtools/flagstat/meta.yml @@ -1,49 +1,49 @@ name: samtools_flagstat description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type keywords: - - stats - - mapping - - counts - - bam - - sam - - cram + - stats + - mapping + - counts + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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}" - - 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 ] + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/nf-core/modules/samtools/idxstats/main.nf b/modules/nf-core/modules/samtools/idxstats/main.nf index fc54e676..8a057413 100644 --- a/modules/nf-core/modules/samtools/idxstats/main.nf +++ b/modules/nf-core/modules/samtools/idxstats/main.nf @@ -14,6 +14,9 @@ process SAMTOOLS_IDXSTATS { tuple val(meta), path("*.idxstats"), emit: idxstats path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/samtools/idxstats/meta.yml b/modules/nf-core/modules/samtools/idxstats/meta.yml index ec542f34..3710ab88 100644 --- a/modules/nf-core/modules/samtools/idxstats/meta.yml +++ b/modules/nf-core/modules/samtools/idxstats/meta.yml @@ -1,50 +1,50 @@ name: samtools_idxstats description: Reports alignment summary statistics for a BAM/CRAM/SAM file keywords: - - stats - - mapping - - counts - - chromosome - - bam - - sam - - cram + - stats + - mapping + - counts + - chromosome + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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}" - - 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 ] + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/nf-core/modules/samtools/index/main.nf b/modules/nf-core/modules/samtools/index/main.nf index c4fa2c63..dfe0234f 100644 --- a/modules/nf-core/modules/samtools/index/main.nf +++ b/modules/nf-core/modules/samtools/index/main.nf @@ -16,6 +16,9 @@ process SAMTOOLS_INDEX { tuple val(meta), path("*.crai"), optional:true, emit: crai path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/samtools/index/meta.yml b/modules/nf-core/modules/samtools/index/meta.yml index 0905b3cd..e5cadbc2 100644 --- a/modules/nf-core/modules/samtools/index/meta.yml +++ b/modules/nf-core/modules/samtools/index/meta.yml @@ -1,53 +1,53 @@ name: samtools_index description: Index SAM/BAM/CRAM file keywords: - - index - - bam - - sam - - cram + - index + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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 ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" 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}" - - csi: - type: file - description: CSI index file - pattern: "*.{csi}" - - 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 ] + - 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}" + - csi: + type: file + description: CSI index file + pattern: "*.{csi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@ewels" - - "@maxulysse" + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/nf-core/modules/samtools/mpileup/main.nf b/modules/nf-core/modules/samtools/mpileup/main.nf index c40f46d1..77afae60 100644 --- a/modules/nf-core/modules/samtools/mpileup/main.nf +++ b/modules/nf-core/modules/samtools/mpileup/main.nf @@ -15,6 +15,9 @@ process SAMTOOLS_MPILEUP { tuple val(meta), path("*.mpileup"), emit: mpileup 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}" diff --git a/modules/nf-core/modules/samtools/mpileup/meta.yml b/modules/nf-core/modules/samtools/mpileup/meta.yml index fac7a5bc..c384f5c6 100644 --- a/modules/nf-core/modules/samtools/mpileup/meta.yml +++ b/modules/nf-core/modules/samtools/mpileup/meta.yml @@ -1,48 +1,48 @@ name: samtools_mpileup -description: BAM +description: BAM keywords: - - mpileup - - bam - - sam - - cram + - mpileup + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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: FASTA reference file - pattern: "*.{fasta,fa}" + - 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: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mpileup: - type: file - description: mpileup file - pattern: "*.{mpileup}" - - 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 ] + - mpileup: + type: file + description: mpileup file + pattern: "*.{mpileup}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@joseespinosa" + - "@drpatelh" + - "@joseespinosa" diff --git a/modules/nf-core/modules/samtools/sort/main.nf b/modules/nf-core/modules/samtools/sort/main.nf index 42c7bbf4..0f2237cc 100644 --- a/modules/nf-core/modules/samtools/sort/main.nf +++ b/modules/nf-core/modules/samtools/sort/main.nf @@ -14,6 +14,9 @@ process SAMTOOLS_SORT { tuple val(meta), path("*.bam"), emit: bam 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}" diff --git a/modules/nf-core/modules/samtools/sort/meta.yml b/modules/nf-core/modules/samtools/sort/meta.yml index 3402a068..a820c55a 100644 --- a/modules/nf-core/modules/samtools/sort/meta.yml +++ b/modules/nf-core/modules/samtools/sort/meta.yml @@ -1,44 +1,44 @@ name: samtools_sort description: Sort SAM/BAM/CRAM file keywords: - - sort - - bam - - sam - - cram + - sort + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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 ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" 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}" - - 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 ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@ewels" + - "@drpatelh" + - "@ewels" diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/modules/samtools/stats/main.nf index 7209070d..f6fe3bfe 100644 --- a/modules/nf-core/modules/samtools/stats/main.nf +++ b/modules/nf-core/modules/samtools/stats/main.nf @@ -15,6 +15,9 @@ process SAMTOOLS_STATS { tuple val(meta), path("*.stats"), emit: stats path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def reference = fasta ? "--reference ${fasta}" : "" diff --git a/modules/nf-core/modules/samtools/stats/meta.yml b/modules/nf-core/modules/samtools/stats/meta.yml index 869e62e3..cac50b1c 100644 --- a/modules/nf-core/modules/samtools/stats/meta.yml +++ b/modules/nf-core/modules/samtools/stats/meta.yml @@ -1,53 +1,53 @@ name: samtools_stats description: Produces comprehensive statistics from SAM/BAM/CRAM file keywords: - - statistics - - counts - - bam - - sam - - cram + - statistics + - counts + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + 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: + - 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}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats: type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: + description: File containing samtools stats output + pattern: "*.{stats}" + - versions: type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - 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}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@FriederikeHanssen" + - "@drpatelh" + - "@FriederikeHanssen" diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf index cb205d0b..aee21a4e 100644 --- a/modules/nf-core/modules/samtools/view/main.nf +++ b/modules/nf-core/modules/samtools/view/main.nf @@ -16,6 +16,9 @@ process SAMTOOLS_VIEW { tuple val(meta), path("*.cram"), emit: cram, optional: true path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/nf-core/modules/samtools/view/meta.yml b/modules/nf-core/modules/samtools/view/meta.yml index 8abf34af..5604bfa7 100644 --- a/modules/nf-core/modules/samtools/view/meta.yml +++ b/modules/nf-core/modules/samtools/view/meta.yml @@ -1,53 +1,53 @@ name: samtools_view description: filter/convert SAM/BAM/CRAM file keywords: - - view - - bam - - sam - - cram + - view + - bam + - sam + - 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: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - 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: hhttp://www.htslib.org/doc/samtools.html + 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: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - 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/SAM file + pattern: "*.{bam,cram,sam}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: filtered/converted BAM/SAM file - pattern: "*.{bam,sam}" - - cram: - type: file - description: filtered/converted 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 ] + - bam: + type: file + description: filtered/converted BAM/SAM file + pattern: "*.{bam,sam}" + - cram: + type: file + description: filtered/converted CRAM file + pattern: "*.cram" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@joseespinosa" - - "@FriederikeHanssen" + - "@drpatelh" + - "@joseespinosa" + - "@FriederikeHanssen" diff --git a/modules/nf-core/modules/spades/main.nf b/modules/nf-core/modules/spades/main.nf index ba690d35..b7ece6f6 100644 --- a/modules/nf-core/modules/spades/main.nf +++ b/modules/nf-core/modules/spades/main.nf @@ -20,6 +20,9 @@ process SPADES { 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}" diff --git a/modules/nf-core/modules/spades/meta.yml b/modules/nf-core/modules/spades/meta.yml index b6878d3d..e49cd139 100644 --- a/modules/nf-core/modules/spades/meta.yml +++ b/modules/nf-core/modules/spades/meta.yml @@ -13,7 +13,7 @@ tools: documentation: http://cab.spbu.ru/files/release3.15.0/manual.html tool_dev_url: https://github.com/ablab/spades doi: 10.1089/cmb.2012.0021 - licence: ['GPL v2'] + licence: ["GPL v2"] input: - meta: type: map @@ -36,8 +36,7 @@ input: List of input FastQ files of size 1, originating from Oxford Nanopore technology. - hmm: type: file - description: - File or directory with amino acid HMMs for Spades HMM-guided mode. + description: File or directory with amino acid HMMs for Spades HMM-guided mode. output: - meta: type: map diff --git a/modules/nf-core/modules/tabix/bgzip/main.nf b/modules/nf-core/modules/tabix/bgzip/main.nf index ed9362b2..90940a5d 100644 --- a/modules/nf-core/modules/tabix/bgzip/main.nf +++ b/modules/nf-core/modules/tabix/bgzip/main.nf @@ -14,6 +14,9 @@ process TABIX_BGZIP { tuple val(meta), path("*.gz"), emit: gz 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}" diff --git a/modules/nf-core/modules/tabix/bgzip/meta.yml b/modules/nf-core/modules/tabix/bgzip/meta.yml index f8318c7c..207427e4 100644 --- a/modules/nf-core/modules/tabix/bgzip/meta.yml +++ b/modules/nf-core/modules/tabix/bgzip/meta.yml @@ -1,41 +1,41 @@ name: tabix_bgzip description: Compresses files keywords: - - compress - - bgzip - - tabix + - compress + - bgzip + - tabix tools: - - bgzip: - description: | - Bgzip compresses files in a similar manner to, and compatible with, gzip. - homepage: https://www.htslib.org/doc/tabix.html - documentation: http://www.htslib.org/doc/bgzip.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - bgzip: + description: | + Bgzip compresses files in a similar manner to, and compatible with, gzip. + homepage: https://www.htslib.org/doc/tabix.html + documentation: http://www.htslib.org/doc/bgzip.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: text file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: text file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: Output compressed file - pattern: "*.{gz}" - - 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 ] + - file: + type: file + description: Output compressed file + pattern: "*.{gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@maxulysse" + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/modules/tabix/tabix/main.nf b/modules/nf-core/modules/tabix/tabix/main.nf index c721a554..5f516261 100644 --- a/modules/nf-core/modules/tabix/tabix/main.nf +++ b/modules/nf-core/modules/tabix/tabix/main.nf @@ -14,6 +14,9 @@ process TABIX_TABIX { tuple val(meta), path("*.tbi"), emit: tbi path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' """ diff --git a/modules/nf-core/modules/tabix/tabix/meta.yml b/modules/nf-core/modules/tabix/tabix/meta.yml index 2e37c4ff..89478abe 100644 --- a/modules/nf-core/modules/tabix/tabix/meta.yml +++ b/modules/nf-core/modules/tabix/tabix/meta.yml @@ -1,41 +1,41 @@ name: tabix_tabix description: create tabix index from a sorted bgzip tab-delimited genome file keywords: - - index - - tabix - - vcf + - index + - tabix + - vcf tools: - - tabix: - description: Generic indexer for TAB-delimited genome position files. - homepage: https://www.htslib.org/doc/tabix.html - documentation: https://www.htslib.org/doc/tabix.1.html - doi: 10.1093/bioinformatics/btq671 - licence: ['MIT'] + - tabix: + description: Generic indexer for TAB-delimited genome position files. + homepage: https://www.htslib.org/doc/tabix.html + documentation: https://www.htslib.org/doc/tabix.1.html + doi: 10.1093/bioinformatics/btq671 + licence: ["MIT"] 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}" - - 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 ] + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@maxulysse" + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/nf-core/modules/unicycler/main.nf b/modules/nf-core/modules/unicycler/main.nf index 1ccc72a9..4d3721b0 100644 --- a/modules/nf-core/modules/unicycler/main.nf +++ b/modules/nf-core/modules/unicycler/main.nf @@ -16,6 +16,9 @@ process UNICYCLER { 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}" diff --git a/modules/nf-core/modules/unicycler/meta.yml b/modules/nf-core/modules/unicycler/meta.yml index b04ac882..918faaf8 100644 --- a/modules/nf-core/modules/unicycler/meta.yml +++ b/modules/nf-core/modules/unicycler/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/rrwick/Unicycler tool_dev_url: https://github.com/rrwick/Unicycler doi: 10.1371/journal.pcbi.1005595 - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: type: map @@ -20,14 +20,14 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - shortreads: - type: file - description: | - List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + type: file + description: | + List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. - longreads: - type: file - description: | - List of input FastQ files of size 1, PacBio or Nanopore long reads. + type: file + description: | + List of input FastQ files of size 1, PacBio or Nanopore long reads. output: - meta: type: map diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf index 6d1996e7..01205e60 100644 --- a/modules/nf-core/modules/untar/main.nf +++ b/modules/nf-core/modules/untar/main.nf @@ -14,6 +14,9 @@ process UNTAR { path "$untar" , emit: untar path "versions.yml", emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' diff --git a/modules/nf-core/modules/untar/meta.yml b/modules/nf-core/modules/untar/meta.yml index 51f94995..e877a97c 100644 --- a/modules/nf-core/modules/untar/meta.yml +++ b/modules/nf-core/modules/untar/meta.yml @@ -1,28 +1,28 @@ name: untar description: Extract files. keywords: - - untar - - uncompress + - untar + - uncompress tools: - - untar: - description: | - Extract tar.gz files. - documentation: https://www.gnu.org/software/tar/manual/ - licence: ['GPL-3.0-or-later'] + - untar: + description: | + Extract tar.gz files. + documentation: https://www.gnu.org/software/tar/manual/ + licence: ["GPL-3.0-or-later"] input: - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - untar: - type: file - description: - pattern: "*.*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - untar: + type: file + description: + pattern: "*.*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/modules/vcflib/vcfuniq/main.nf b/modules/nf-core/modules/vcflib/vcfuniq/main.nf index 37fc51bc..a01e8485 100644 --- a/modules/nf-core/modules/vcflib/vcfuniq/main.nf +++ b/modules/nf-core/modules/vcflib/vcfuniq/main.nf @@ -16,6 +16,9 @@ process VCFLIB_VCFUNIQ { tuple val(meta), path("*.gz"), emit: vcf path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/nf-core/modules/vcflib/vcfuniq/meta.yml b/modules/nf-core/modules/vcflib/vcfuniq/meta.yml index 3bfc679b..50a3617a 100644 --- a/modules/nf-core/modules/vcflib/vcfuniq/meta.yml +++ b/modules/nf-core/modules/vcflib/vcfuniq/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/vcflib/vcflib documentation: https://github.com/vcflib/vcflib#USAGE doi: "https://doi.org/10.1101/2021.05.21.445151" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/nextflow.config b/nextflow.config index 19e1f2a0..dba1ec4f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ nf-core/viralrecon Nextflow config file -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- */ @@ -234,7 +234,7 @@ manifest { description = 'Assembly and intrahost/low-frequency variant calling for viral samples' mainScript = 'main.nf' nextflowVersion = '!>=21.10.3' - version = '2.3' + version = '2.3.1' } // Load modules.config for DSL2 module specific options