diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe3..b290e090 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -10,15 +10,7 @@ "vscode": { // Set *default* container specific settings.json values on container create. "settings": { - "python.defaultInterpreterPath": "/opt/conda/bin/python", - "python.linting.enabled": true, - "python.linting.pylintEnabled": true, - "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", - "python.formatting.yapfPath": "/opt/conda/bin/yapf", - "python.linting.flake8Path": "/opt/conda/bin/flake8", - "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", - "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.defaultInterpreterPath": "/opt/conda/bin/python" }, // Add the IDs of extensions you want installed when the container is created. diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index bd134c88..0779fb9b 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,9 +9,8 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -:::info -If you need help using or modifying nf-core/smrnaseq then the best place to ask is on the nf-core Slack [#smrnaseq](https://nfcore.slack.com/channels/smrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)). -::: +> [!NOTE] +> If you need help using or modifying nf-core/smrnaseq then the best place to ask is on the nf-core Slack [#smrnaseq](https://nfcore.slack.com/channels/smrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)). ## Contribution workflow @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`. Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. -The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. +The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. ### Naming schemes diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 3cdbf2b7..ef59ff45 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/smrn - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/smrnaseq/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/smrnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 1795a0fb..99c96e77 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters with: @@ -30,7 +30,7 @@ jobs: } profiles: test_full - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 3ed287c5..5386cbc0 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} @@ -25,7 +25,7 @@ jobs: } profiles: test - - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 + - uses: actions/upload-artifact@v4 with: name: Tower debug log file path: | diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 64fcab5e..cdadbf16 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -36,7 +36,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index f823210d..08622fd5 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 748b4311..073e1876 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -35,7 +35,7 @@ jobs: uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1 + uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 with: diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c3674af2..d468aeaa 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT + curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.gitpod.yml b/.gitpod.yml index 363d5b1d..105a1821 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -10,13 +10,11 @@ tasks: vscode: extensions: # based on nf-core.nf-core-extensionpack - - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code + - charliermarsh.ruff # Code linter Ruff diff --git a/CHANGELOG.md b/CHANGELOG.md index 48e2675b..c42d00e3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,22 @@ 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). +## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch + +- [[#328]](https://github.com/nf-core/smrnaseq/pull/328) - Fix [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module +- [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [input channel cardinality](https://github.com/nf-core/smrnaseq/issues/331) in `MIRDEEP2_RUN` module +- [[#334]](https://github.com/nf-core/smrnaseq/pull/334) - Fix [bowtie conda version](https://github.com/nf-core/smrnaseq/issues/333) in `BOWTIE_MAP_SEQ` module +- [[#335]](https://github.com/nf-core/smrnaseq/pull/335) - Final fix for [casting issue](https://github.com/nf-core/smrnaseq/issues/327) in mirtrace module +- [[#337]](https://github.com/nf-core/smrnaseq/pull/337) - Fix [three_prime_adapter issue](https://github.com/nf-core/smrnaseq/issues/326), allow `auto-detect` as value +- [[#342]](https://github.com/nf-core/smrnaseq/pull/342) - Fix [phred offset issue](https://github.com/nf-core/smrnaseq/issues/341), allow specifying phred offset for FASTQ files +- [[#343]](https://github.com/nf-core/smrnaseq/pull/343) - Fix [mirdeep2 output missing](https://github.com/nf-core/smrnaseq/issues/330), fix mirdeep2 outputs missing in outdir + +### Software dependencies + +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `multiqc` | 1.20 | 1.21 | + ## v2.3.0 - 2024-02-23 - Gray Zinc Dalmatian - [[#307]](https://github.com/nf-core/smrnaseq/pull/307) - Clean up config file and improve output folder structure diff --git a/README.md b/README.md index e49ec02b..ccb136f0 100644 --- a/README.md +++ b/README.md @@ -5,15 +5,15 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+CI%22) -[![GitHub Actions Linting Status](https://github.com/nf-core/smrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/smrnaseq/actions?query=workflow%3A%22nf-core+linting%22) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3456879-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3456879) +[![GitHub Actions CI Status](https://github.com/nf-core/smrnaseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/smrnaseq/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/nf-core/smrnaseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/smrnaseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/smrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10696391?labelColor=000000)](https://doi.org/10.5281/zenodo.10696391) +[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/smrnaseq) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/smrnaseq) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23smrnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/smrnaseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index cb6b62c8..9264f6fa 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/smrnaseq + This report has been generated by the nf-core/smrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-smrnaseq-methods-description": diff --git a/conf/modules.config b/conf/modules.config index f7a50622..e67745fe 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -47,12 +47,12 @@ process { // withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' { ext.args = [ "", - params.trim_fastq ? "" : "--disable_adapter_trimming", - params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1. - params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed. - params.fastp_min_length > 0 ? "-l ${params.fastp_min_length}" : "", - params.fastp_max_length > 0 ? "--max_len1 ${params.fastp_max_length}" : "", - params.three_prime_adapter == null ? '' : "--adapter_sequence ${params.three_prime_adapter}" + params.trim_fastq ? "" : "--disable_adapter_trimming", + params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1. + params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed. + params.fastp_min_length > 0 ? "-l ${params.fastp_min_length}" : "", + params.fastp_max_length > 0 ? "--max_len1 ${params.fastp_max_length}" : "", + params.three_prime_adapter == "auto-detect" ? "" : "--adapter_sequence ${params.three_prime_adapter}" ].join(" ").trim() publishDir = [ [ @@ -329,14 +329,14 @@ process { // // MIRDEEP // - withName: 'MIRDEEP2_MAPPER' { + withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_MAPPER' { publishDir = [ path: { "${params.outdir}/mirdeep2/mapper" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - withName: 'MIRDEEP2_RUN' { + withName: 'NFCORE_SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN' { publishDir = [ path: { "${params.outdir}/mirdeep2/run" }, mode: params.publish_dir_mode, diff --git a/docs/output.md b/docs/output.md index d2358724..10d3e677 100644 --- a/docs/output.md +++ b/docs/output.md @@ -153,7 +153,7 @@ MultiQC reports the number of reads that were removed by each of the contaminant ## miRTrace -[miRTrace](https://github.com/friedlanderlab/mirtrace) is a quality control specifically for small RNA sequencing data (smRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). +[miRTrace](https://github.com/friedlanderlab/mirtrace) is a quality control specifically for small RNA sequencing data (smRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). By default, the pipeline sets the PHRED-offset to the most common +33, so if you need to adjust this, use the `params.phred_offset` option to include this accordingly for your FASTQ files. **Output directory: `results/mirtrace`** diff --git a/docs/usage.md b/docs/usage.md index b5eb01f0..881bb2ff 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -18,7 +18,7 @@ This option indicates the experimental protocol used for the sample preparation. The parameter `--three_prime_adapter` is set to the Illumina TruSeq single index adapter sequence `AGATCGGAAGAGCACACGTCTGAACTCCAGTCA`. This is also to ensure, that the auto-detect functionality of `FASTP` is disabled. Please make sure to adapt this adapter sequence accordingly for your run. -:warning: At least the `custom` protocol has to be specified, otherwise the pipeline won't run. In case you specify the `custom` protocol, ensure that the parameters above are set accordingly or the defaults will be applied. If you want to auto-detect the adapters using `fastp`, please set `--three_prime_adapter` to `""`. +:warning: At least the `custom` protocol has to be specified, otherwise the pipeline won't run. In case you specify the `custom` protocol, ensure that the parameters above are set accordingly or the defaults will be applied. If you want to auto-detect the adapters using `fastp`, please set `--three_prime_adapter` to `auto-detect`. ### `mirtrace_species` or `mirgenedb_species` diff --git a/modules.json b/modules.json index ad13815e..109997b3 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "cat/cat": { "branch": "master", - "git_sha": "81f27e75847087865299cc46605deb3b09b4e0a2", + "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8", "installed_by": ["modules"] }, "cat/fastq": { @@ -17,17 +17,17 @@ }, "fastp": { "branch": "master", - "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56", + "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { "branch": "master", - "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", + "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["fastq_fastqc_umitools_fastp"] }, "multiqc": { "branch": "master", - "git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290", + "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", "installed_by": ["modules"] }, "samtools/flagstat": { @@ -47,7 +47,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": ["bam_sort_stats_samtools", "modules"] }, "samtools/stats": { @@ -57,12 +57,12 @@ }, "umicollapse": { "branch": "master", - "git_sha": "ba3f3df395d2719dcef5c67189042a1dc555c701", + "git_sha": "b97197968ac12dde2463fa54541f6350c46f2035", "installed_by": ["modules"] }, "umitools/extract": { "branch": "master", - "git_sha": "ff7e93715a2acecf3f143ec78c9858deba2984d0", + "git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744", "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "untarfiles": { @@ -76,7 +76,7 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", + "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": ["subworkflows"] }, "bam_stats_samtools": { @@ -86,22 +86,22 @@ }, "fastq_fastqc_umitools_fastp": { "branch": "master", - "git_sha": "003920c7f9a8ae19b69a97171922880220bedf56", + "git_sha": "cabcc0dadf8366aa7a9930066a7b3dd90d9825d5", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "262b17ed2aad591039f914951659177e6c39a8d8", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", - "git_sha": "cd08c91373cd00a73255081340e4914485846ba1", + "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", "installed_by": ["subworkflows"] } } diff --git a/modules/local/bowtie_map_mirna.nf b/modules/local/bowtie_map_mirna.nf index 148b47f5..d6b0ea8f 100644 --- a/modules/local/bowtie_map_mirna.nf +++ b/modules/local/bowtie_map_mirna.nf @@ -2,7 +2,7 @@ process BOWTIE_MAP_SEQ { tag "$meta.id" label 'process_medium' - conda 'bowtie=1.3.0-2 bioconda::samtools=1.13' + conda 'bowtie=1.3.0 bioconda::samtools=1.13' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' : 'biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' }" diff --git a/modules/local/mirdeep2_run.nf b/modules/local/mirdeep2_run.nf index 442f26f3..ba37a4ac 100644 --- a/modules/local/mirdeep2_run.nf +++ b/modules/local/mirdeep2_run.nf @@ -12,8 +12,8 @@ process MIRDEEP2_RUN { input: path(fasta) tuple path(reads), path(arf) - tuple val(meta2), path(hairpin) - tuple val(meta2), path(mature) + path(hairpin) + path(mature) output: path 'result*.{bed,csv,html}', emit: result diff --git a/modules/local/mirtrace.nf b/modules/local/mirtrace.nf index 500de058..87526016 100644 --- a/modules/local/mirtrace.nf +++ b/modules/local/mirtrace.nf @@ -8,6 +8,7 @@ process MIRTRACE_RUN { input: tuple val(adapter), val(ids), path(reads) + path(mirtrace_config) output: path "mirtrace/*" , emit: mirtrace @@ -18,26 +19,20 @@ process MIRTRACE_RUN { script: // mirtrace protocol defaults to 'params.protocol' if not set - def primer = adapter ? "--adapter ${adapter}" : "" def protocol = params.protocol == 'custom' ? '' : "--protocol $params.protocol" def java_mem = '' if(task.memory){ tmem = task.memory.toBytes() java_mem = "-Xms${tmem} -Xmx${tmem}" } - def config_lines = [ids,reads] - .transpose() - .collect({ id, path -> "echo '${path},${id}' >> mirtrace_config" }) + """ export mirtracejar=\$(dirname \$(which mirtrace)) - ${config_lines.join("\n ")} - java $java_mem -jar \$mirtracejar/mirtrace.jar --mirtrace-wrapper-name mirtrace qc \\ --species $params.mirtrace_species \\ - $primer \\ $protocol \\ - --config mirtrace_config \\ + --config $mirtrace_config \\ --write-fasta \\ --output-dir mirtrace \\ --force diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test index aaae04f9..fcee2d19 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -19,8 +19,8 @@ nextflow_process { [ [ id:'genome', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -45,8 +45,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -72,8 +72,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] ] """ @@ -83,7 +83,8 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} ) } } @@ -101,8 +102,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true) ] ] """ @@ -130,8 +131,8 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) ] ] """ @@ -141,7 +142,8 @@ nextflow_process { def lines = path(process.out.file_out.get(0).get(1)).linesGzip assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} ) } } @@ -158,7 +160,7 @@ nextflow_process { [ [ id:'test', single_end:true ], [ - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] ] """ @@ -174,4 +176,3 @@ nextflow_process { } } } - diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap index 0c9bfe8d..423571ba 100644 --- a/modules/nf-core/cat/cat/tests/main.nf.test.snap +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -1,4 +1,10 @@ { + "test_cat_unzipped_zipped_size": { + "content": [ + 375 + ], + "timestamp": "2023-10-16T14:33:08.049445686" + }, "test_cat_unzipped_unzipped": { "content": [ { @@ -61,36 +67,31 @@ ], "timestamp": "2023-10-16T14:32:49.642741302" }, - "test_cat_zipped_zipped": { + "test_cat_zipped_zipped_lines": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.gff3.gz:md5,c439d3b60e7bc03e8802a451a0d9a5d9" - ] - ], - "1": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ], - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "test.gff3.gz:md5,c439d3b60e7bc03e8802a451a0d9a5d9" - ] - ], - "versions": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ] - } + [ + "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", + "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", + "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", + "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ] + ], + "timestamp": "2023-10-16T14:32:33.629048645" + }, + "test_cat_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] ], - "timestamp": "2024-01-12T14:02:02.999254641" + "timestamp": "2023-10-16T14:33:08.038830506" }, "test_cat_one_file_unzipped_zipped_lines": { "content": [ @@ -105,41 +106,16 @@ ], "timestamp": "2023-10-16T14:33:21.39642399" }, - "test_cat_unzipped_zipped": { + "test_cat_zipped_zipped_size": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2" - ] - ], - "1": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ], - "file_out": [ - [ - { - "id": "test", - "single_end": true - }, - "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2" - ] - ], - "versions": [ - "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" - ] - } + 78 ], - "timestamp": "2024-01-12T14:08:26.948048418" + "timestamp": "2023-10-16T14:32:33.641869244" }, "test_cat_one_file_unzipped_zipped_size": { "content": [ 374 ], - "timestamp": "2024-01-12T14:10:22.445700266" + "timestamp": "2023-10-16T14:33:21.4094373" } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 2a3b679e..4fc19b74 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -29,7 +29,7 @@ process FASTP { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def adapter_list = adapter_fasta ? "--adapter_fasta ${adapter_fasta}" : "" - def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' + def fail_fastq = save_trimmed_fail && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : save_trimmed_fail && !meta.single_end ? "--failed_out ${prefix}.paired.fail.fastq.gz --unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' // Added soft-links to original fastqs for consistent naming in MultiQC // Use single ended for interleaved. Add --interleaved_in in config. if ( task.ext.args?.contains('--interleaved_in') ) { diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test index 9b3f9a38..6f1f4897 100644 --- a/modules/nf-core/fastp/tests/main.nf.test +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -251,7 +251,8 @@ nextflow_process { } test("fastp test_fastp_interleaved") { - config './nextflow.config' + + config './nextflow.interleaved.config' when { params { outdir = "$outputDir" @@ -277,7 +278,7 @@ nextflow_process { def html_text = [ "Q20 bases:25.719000 K (93.033098%)", "paired end (151 cycles + 151 cycles)"] def log_text = [ "Q20 bases: 12922(92.9841%)", - "reads passed filter: 198"] + "reads passed filter: 162"] def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE - { assert path(process.out.reads_fail.get(0).get(1).get(1)).linesGzip.contains(failed_read2_line) } + { assert path(process.out.reads_fail.get(0).get(1).get(2)).linesGzip.contains(failed_read2_line) } } }, { html_text.each { html_part -> diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap index b4c0e1dd..3e876288 100644 --- a/modules/nf-core/fastp/tests/main.nf.test.snap +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -7,7 +7,7 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,168f516f7bd4b7b6c32da7cba87299a4" + "test.fastp.json:md5,b24e0624df5cc0b11cd5ba21b726fb22" ] ] ], @@ -15,7 +15,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-17T18:08:06.123035" + "timestamp": "2024-03-18T16:19:15.063001" }, "test_fastp_paired_end_merged-for_stub_match": { "content": [ @@ -65,7 +65,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-17T18:06:00.223817" + "timestamp": "2024-03-18T16:18:43.526412" }, "versions_paired_end": { "content": [ @@ -112,7 +112,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T12:03:37.827323085" + "timestamp": "2024-03-18T16:19:15.111894" }, "test_fastp_paired_end_merged_match": { "content": [ @@ -283,7 +283,7 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-01T11:57:30.791982648" + "timestamp": "2024-03-18T16:18:43.580336" }, "versions_paired_end_merged_adapterlist": { "content": [ diff --git a/modules/nf-core/fastp/tests/nextflow.interleaved.config b/modules/nf-core/fastp/tests/nextflow.interleaved.config new file mode 100644 index 00000000..4be8dbd2 --- /dev/null +++ b/modules/nf-core/fastp/tests/nextflow.interleaved.config @@ -0,0 +1,5 @@ +process { + withName: FASTP { + ext.args = "--interleaved_in -e 30" + } +} diff --git a/modules/nf-core/fastp/tests/nextflow.config b/modules/nf-core/fastp/tests/nextflow.save_failed.config similarity index 50% rename from modules/nf-core/fastp/tests/nextflow.config rename to modules/nf-core/fastp/tests/nextflow.save_failed.config index 0f7849ad..53b61b0c 100644 --- a/modules/nf-core/fastp/tests/nextflow.config +++ b/modules/nf-core/fastp/tests/nextflow.save_failed.config @@ -1,6 +1,5 @@ process { - withName: FASTP { - ext.args = "--interleaved_in" + ext.args = "-e 30" } } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9e19a74c..d79f1c86 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -25,6 +25,11 @@ process FASTQC { def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // FastQC memory value allowed range (100 - 10000) + def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -33,6 +38,7 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ + --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 2212096a..ca39fb67 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.20 + - bioconda::multiqc=1.21 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 354f4430..47ac352f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : - 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index c204b488..bfebd802 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:28:51.744211298" + "timestamp": "2024-02-29T08:48:55.657331" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:28.847433492" + "timestamp": "2024-02-29T08:49:49.071937" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,d320d4c37e349c5588e07e7a31cd4186" + "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-02-14T09:29:13.223621555" + "timestamp": "2024-02-29T08:49:25.457567" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index cdd8305d..fc374f98 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -8,11 +8,14 @@ process SAMTOOLS_SORT { 'biocontainers/samtools:1.19.2--h50ea8bc_0' }" input: - tuple val(meta), path(bam) + tuple val(meta) , path(bam) + tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam - tuple val(meta), path("*.csi"), emit: csi, optional: true + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true path "versions.yml" , emit: versions when: @@ -21,14 +24,24 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt cram") ? "cram" : + "bam" + def reference = fasta ? "--reference ${fasta}" : "" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + samtools cat \\ + --threads $task.cpus \\ + ${bam} \\ + | \\ samtools sort \\ $args \\ - -@ $task.cpus \\ - -o ${prefix}.bam \\ - -T $prefix \\ - $bam + -T ${prefix} \\ + --threads $task.cpus \\ + ${reference} \\ + -o ${prefix}.${extension} \\ + - cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -40,6 +53,7 @@ process SAMTOOLS_SORT { def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bam + touch ${prefix}.bam.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 2200de72..341a7d0e 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -23,8 +23,18 @@ input: e.g. [ id:'test', single_end:false ] - bam: type: file - description: BAM/CRAM/SAM file + description: BAM/CRAM/SAM file(s) pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - meta: type: map @@ -33,19 +43,29 @@ output: e.g. [ id:'test', single_end:false ] - bam: type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - versions: + description: Sorted BAM file + pattern: "*.{bam}" + - cram: type: file - description: File containing software versions - pattern: "versions.yml" + description: Sorted CRAM file + pattern: "*.{cram}" + - crai: + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: type: file description: BAM index file (optional) pattern: "*.csi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" + - "@matthdsm" maintainers: - "@drpatelh" - "@ewels" + - "@matthdsm" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index 31e24b88..8360e2b1 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -13,15 +13,43 @@ nextflow_process { config "./nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("cram") { + + config "./nextflow.config" + + when { process { """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -37,7 +65,7 @@ nextflow_process { test("bam_stub") { config "./nextflow.config" - options "-stub-run" + options "-stub" when { params { @@ -49,6 +77,10 @@ nextflow_process { [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index a7cf0210..38477656 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -1,4 +1,69 @@ { + "cram": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "4": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "versions": [ + "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-04T15:08:00.830294" + }, "bam_stub_bam": { "content": [ "test.sorted.bam" @@ -30,13 +95,25 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,c6ea1346ec4aae007eb40b708935088c" + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" ] ], "1": [ ], "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] + ], + "4": [ "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" ], "bam": [ @@ -45,11 +122,23 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,c6ea1346ec4aae007eb40b708935088c" + "test.sorted.bam:md5,bc0b7c25da26384a006ed84cc9e4da23" ] ], - "csi": [ + "crai": [ + + ], + "cram": [ + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,8d4e836c2fed6c0bf874d5e8cdba5831" + ] ], "versions": [ "versions.yml:md5,e6d43fefc9a8bff91c2ce6e3a1716eca" @@ -58,8 +147,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-13T16:14:52.736359271" + "timestamp": "2024-03-04T15:07:48.773803" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config index d0f35086..f642771f 100644 --- a/modules/nf-core/samtools/sort/tests/nextflow.config +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -1,7 +1,8 @@ process { withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } + ext.prefix = { "${meta.id}.sorted" } + ext.args = "--write-index" } } diff --git a/modules/nf-core/umicollapse/tests/main.nf.test b/modules/nf-core/umicollapse/tests/main.nf.test index 36cd748b..2dec45b2 100644 --- a/modules/nf-core/umicollapse/tests/main.nf.test +++ b/modules/nf-core/umicollapse/tests/main.nf.test @@ -34,10 +34,7 @@ nextflow_process { script "../../bwa/index/main.nf" process{ """ - input[0] = [ - [ id:'sarscov2'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] + input[0] = [[ id:'sarscov2'],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] """ } } @@ -47,7 +44,8 @@ nextflow_process { """ input[0] = UMITOOLS_EXTRACT.out.reads input[1] = BWA_INDEX.out.index - input[2] = true + input[2] = [[ id:'sarscov2'],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = true """ } } @@ -117,7 +115,8 @@ nextflow_process { """ input[0] = UMITOOLS_EXTRACT.out.reads input[1] = BWA_INDEX.out.index - input[2] = true + input[2] = [[ id:'sarscov2'],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = true """ } } @@ -214,7 +213,8 @@ nextflow_process { """ input[0] = UMITOOLS_EXTRACT.out.reads input[1] = BWA_INDEX.out.index - input[2] = true + input[2] = [[ id:'sarscov2'],file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] + input[3] = true """ } } diff --git a/modules/nf-core/umicollapse/tests/main.nf.test.snap b/modules/nf-core/umicollapse/tests/main.nf.test.snap index 23916f0b..861e9ca6 100644 --- a/modules/nf-core/umicollapse/tests/main.nf.test.snap +++ b/modules/nf-core/umicollapse/tests/main.nf.test.snap @@ -16,9 +16,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-19T11:24:31.850566925" + "timestamp": "2024-03-14T13:41:23.869211282" }, "umicollapse fastq tests": { "content": [ @@ -117,8 +117,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nextflow": "23.10.1" }, - "timestamp": "2024-02-19T11:24:44.166029769" + "timestamp": "2024-03-14T13:41:54.486079388" } } \ No newline at end of file diff --git a/modules/nf-core/umitools/extract/tests/main.nf.test b/modules/nf-core/umitools/extract/tests/main.nf.test index 83a77a1b..2a8eba15 100644 --- a/modules/nf-core/umitools/extract/tests/main.nf.test +++ b/modules/nf-core/umitools/extract/tests/main.nf.test @@ -12,9 +12,6 @@ nextflow_process { test("Should run without failures") { when { - params { - outdir = "$outputDir" - } process { """ input[0] = [ [ id:'test', single_end:true ], // meta map @@ -26,10 +23,9 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.versions).match("versions") } + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") } ) } - } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 272b7372..147461f1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -68,6 +68,9 @@ params { pirna = null other_contamination = null + //FASTQ handling defaults, for mirtrace + phred_offset = 33 + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' @@ -305,7 +308,7 @@ manifest { description = """Small RNA-Seq Best Practice Analysis Pipeline.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.0' + version = '2.3.1' doi = '10.5281/zenodo.3456879' } diff --git a/nextflow_schema.json b/nextflow_schema.json index cf2d0382..42680715 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -272,6 +272,11 @@ "type": "boolean", "description": "Save merged reads.", "default": true + }, + "phred_offset": { + "type": "integer", + "default": 33, + "description": "The PHRED quality offset to be used for any input fastq files. Default is 33, standard Illumina 1.8+ format." } } }, diff --git a/subworkflows/local/mirtrace.nf b/subworkflows/local/mirtrace.nf index 317c4444..528e4233 100644 --- a/subworkflows/local/mirtrace.nf +++ b/subworkflows/local/mirtrace.nf @@ -9,7 +9,19 @@ workflow MIRTRACE { reads // channel: [ val(adapterseq), [ val(ids) ], [ path(reads) ] ] main: - reads | MIRTRACE_RUN + + //Staging the files as path() but then getting the filenames for the config file that mirtrace needs + //Directly using val(reads) as in previous versions is not reliable as staging between work directories is not 100% reliable if not explicitly defined via nextflow itself + //mirtrace is a bit peculiar in parsing these config files, so looked it up in the source how its done. this way should work + ch_mirtrace_config = + reads.map { adapter, ids, reads -> [adapter, ids,reads]} + .transpose() + .collectFile { adapter, id, path -> "./${path.getFileName().toString()},${id},${adapter},${params.phred_offset}\n" } // operations need a channel, so, should be outside the module + + MIRTRACE_RUN ( + reads, + ch_mirtrace_config + ) emit: results = MIRTRACE_RUN.out.mirtrace diff --git a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf index af31a5ea..9d728769 100644 --- a/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the nf-core/pipeline pipeline +// Subworkflow with functionality specific to the nf-core/smrnaseq pipeline // /* @@ -153,8 +153,8 @@ workflow PIPELINE_COMPLETION { // def validateInputParameters() { genomeExistsError() +} -}// // Validate channels from input samplesheet // def validateInputSamplesheet(input) { @@ -192,7 +192,9 @@ def genomeExistsError() { "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" error(error_string) } -}// +} + +// // Generate methods description for MultiQC // def toolCitationText() { diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf index fc1c652b..b716375b 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf +++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf @@ -15,7 +15,7 @@ workflow BAM_SORT_STATS_SAMTOOLS { ch_versions = Channel.empty() - SAMTOOLS_SORT ( ch_bam ) + SAMTOOLS_SORT ( ch_bam, ch_fasta ) ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first()) SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam ) diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test index 8f1d82d3..961b5b4f 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test @@ -3,6 +3,8 @@ nextflow_workflow { name "Test Workflow FASTQ_FASTQC_UMITOOLS_FASTP" script "../main.nf" workflow "FASTQ_FASTQC_UMITOOLS_FASTP" + config './nextflow.config' + tag "subworkflows" tag "subworkflows_nfcore" tag "subworkflows/fastq_fastqc_umitools_fastp" @@ -29,8 +31,10 @@ nextflow_workflow { input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] ]) input[1] = skip_fastqc input[2] = with_umi @@ -48,14 +52,503 @@ nextflow_workflow { then { assertAll( { assert workflow.success }, - { assert snapshot(workflow.out.reads).match("reads") }, - { assert snapshot(workflow.out.umi_log).match("umi_log") }, - { assert snapshot(workflow.out.trim_json).match("trim_json") }, - { assert snapshot(workflow.out.trim_reads_fail).match("trim_reads_fail") }, - { assert snapshot(workflow.out.trim_reads_merged).match("trim_reads_merged") }, - { assert snapshot(workflow.out.adapter_seq).match("adapter_seq") }, - { assert snapshot(workflow.out.trim_read_count).match("trim_read_count") }, - { assert snapshot(workflow.out.versions).match("versions") }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert workflow.out.fastqc_trim_html }, + { assert workflow.out.fastqc_trim_zip } + ) + } + } + + test("skip_fastqc") { + + when { + workflow { + """ + skip_fastqc = true + with_umi = false + skip_umi_extract = false + umi_discard_read = 1 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end: false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert !workflow.out.fastqc_raw_html }, + { assert !workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert !workflow.out.fastqc_trim_html }, + { assert !workflow.out.fastqc_trim_zip } + ) + } + } + + test("with_umi") { + + when { + workflow { + """ + skip_fastqc = false + with_umi = true + skip_umi_extract = false + umi_discard_read = 1 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert workflow.out.fastqc_trim_html }, + { assert workflow.out.fastqc_trim_zip } + ) + } + } + + + test("skip_umi_extract") { + + when { + workflow { + """ + skip_fastqc = false + with_umi = true + skip_umi_extract = true + umi_discard_read = 1 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert workflow.out.fastqc_trim_html }, + { assert workflow.out.fastqc_trim_zip } + ) + } + } + + test("umi_discard_read = 2") { + + when { + workflow { + """ + skip_fastqc = false + with_umi = true + skip_umi_extract = true + umi_discard_read = 2 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert workflow.out.fastqc_trim_html }, + { assert workflow.out.fastqc_trim_zip } + ) + } + } + + test("skip_trimming") { + + when { + workflow { + """ + skip_fastqc = false + with_umi = false + skip_umi_extract = false + umi_discard_read = 1 + skip_trimming = true + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads.get(0).get(0), // Reads meta map + // Because the input file is passed to the output file, we have to do check the filename only + file(workflow.out.reads.get(0).get(1).get(0)).name, + file(workflow.out.reads.get(0).get(1).get(1)).name, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert !workflow.out.trim_html }, + { assert !workflow.out.trim_log }, + { assert !workflow.out.fastqc_trim_html }, + { assert !workflow.out.fastqc_trim_zip } + ) + } + } + + test("save_trimmed_fail") { + + config './nextflow.save_trimmed.config' + + when { + workflow { + """ + skip_fastqc = false + with_umi = false + skip_umi_extract = false + umi_discard_read = 1 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert workflow.out.fastqc_trim_html }, + { assert workflow.out.fastqc_trim_zip } + ) + } + } + + test("save_merged") { + + when { + workflow { + """ + skip_fastqc = false + with_umi = false + skip_umi_extract = false + umi_discard_read = 1 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true + min_trimmed_reads = 1 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, + + { assert workflow.out.fastqc_raw_html }, + { assert workflow.out.fastqc_raw_zip }, + { assert workflow.out.trim_html }, + { assert workflow.out.trim_log }, + { assert workflow.out.fastqc_trim_html }, + { assert workflow.out.fastqc_trim_zip } + ) + } + } + + test("min_trimmed_reads = 26") { + // Subworkflow should stop after FASTP which trims down to 25 reads + + when { + workflow { + """ + skip_fastqc = false + with_umi = false + skip_umi_extract = false + umi_discard_read = 1 + skip_trimming = false + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true + min_trimmed_reads = 26 + + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = skip_fastqc + input[2] = with_umi + input[3] = skip_umi_extract + input[4] = umi_discard_read + input[5] = skip_trimming + input[6] = adapter_fasta + input[7] = save_trimmed_fail + input[8] = save_merged + input[9] = min_trimmed_reads + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.reads, + workflow.out.umi_log, + workflow.out.trim_json, + workflow.out.trim_reads_fail, + workflow.out.trim_reads_merged, + workflow.out.adapter_seq, + workflow.out.trim_read_count, + workflow.out.versions + ).match() + }, { assert workflow.out.fastqc_raw_html }, { assert workflow.out.fastqc_raw_zip }, diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap index 89ba8da1..3e11d9ec 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/main.nf.test.snap @@ -1,30 +1,186 @@ { - "trim_reads_merged": { + "skip_fastqc": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", + "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" + ] + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + ] + ], [ + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "unspecified" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 198 + ] + ], + [ + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.041635573" + "timestamp": "2024-03-18T16:53:49.315194" }, - "trim_reads_fail": { + "save_trimmed_fail": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastp.fastq.gz:md5,6ff32a64c5188b9a9192be1398c262c7", + "test_2.fastp.fastq.gz:md5,db0cb7c9977e94ac2b4b446ebd017a8a" + ] + ] + ], [ + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.paired.fail.fastq.gz:md5,409b687c734cedd7a1fec14d316e1366", + "test_1.fail.fastq.gz:md5,4f273cf3159c13f79e8ffae12f5661f6", + "test_2.fail.fastq.gz:md5,f97b9edefb5649aab661fbc9e71fc995" + ] + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "unspecified" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 162 + ] + ], + [ + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.033284693" + "timestamp": "2024-03-18T16:51:45.34934" }, - "versions": { + "skip_umi_extract": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", + "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" + ] + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + ] + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "unspecified" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 198 + ] + ], [ "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", @@ -35,10 +191,25 @@ "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.121510557" + "timestamp": "2024-03-18T12:07:40.34249" }, - "trim_json": { + "umi_discard_read = 2": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", + "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" + ] + ] + ], + [ + + ], [ [ { @@ -47,16 +218,81 @@ }, "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" ] + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "unspecified" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 198 + ] + ], + [ + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.024410724" + "timestamp": "2024-03-18T12:08:24.141938" }, - "adapter_seq": { + "save_merged": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672", + "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba" + ] + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5" + ] + ], [ [ { @@ -65,15 +301,65 @@ }, "unspecified" ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 75 + ] + ], + [ + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.08674429" + "timestamp": "2024-03-18T12:10:18.546963" }, - "reads": { + "skip_trimming": { + "content": [ + { + "id": "test", + "single_end": false + }, + "test_1.fastq.gz", + "test_2.fastq.gz", + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-03-19T15:49:26.574759" + }, + "sarscov2 paired-end [fastq]": { "content": [ [ [ @@ -86,42 +372,178 @@ "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" ] ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" + ] + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "unspecified" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 198 + ] + ], + [ + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:49.994419936" + "timestamp": "2024-03-18T16:53:39.139038" }, - "umi_log": { + "min_trimmed_reads = 26": { "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastp.fastq.gz:md5,54b726a55e992a869fd3fa778afe1672", + "test_2.fastp.fastq.gz:md5,29d3b33b869f7b63417b8ff07bb128ba" + ] + ] + ], [ + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastp.json:md5,b712fd68ed0322f4bec49ff2a5237fcc" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "unspecified" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + 75 + ] + ], + [ + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.017720214" + "timestamp": "2024-03-18T11:52:23.849945" }, - "trim_read_count": { + "with_umi": { "content": [ [ [ { "id": "test", - "single_end": false + "single_end": true }, - 198 + "test.fastp.fastq.gz:md5,ba8c6c3a7ce718d9a2c5857e2edf53bc" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,d39c5c6d9a2e35fb60d26ced46569af6" ] + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + 99 + ] + ], + [ + "versions.yml:md5,01f264f78de3c6d893c449cc6d3cd721", + "versions.yml:md5,85bd0117e5778fff18e3920972a296ad", + "versions.yml:md5,c50aa59475ab901bc6f9a2cf7b1a14e0", + "versions.yml:md5,f3dcaae948e8eed92b4a5557b4c6668e" ] ], "meta": { "nf-test": "0.8.4", "nextflow": "23.10.1" }, - "timestamp": "2024-01-12T08:38:50.102326089" + "timestamp": "2024-03-18T17:31:09.193212" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config new file mode 100644 index 00000000..12f7b257 --- /dev/null +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + + withName: UMITOOLS_EXTRACT { + ext.args = '--bc-pattern="NNNN" --bc-pattern2="NNNN"' + } + + withName: UMICOLLAPSE { + ext.prefix = { "${meta.id}.dedup" } + } + +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config new file mode 100644 index 00000000..2430e9d5 --- /dev/null +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/tests/nextflow.save_trimmed.config @@ -0,0 +1,6 @@ +process { + // Make filtering more aggressive to make more reads fail + withName: FASTP { + ext.args = "-e 30" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test index 8ed4310c..68718e4f 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test @@ -51,4 +51,4 @@ nextflow_function { ) } } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap index db2030f8..e3f0baf4 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap @@ -3,10 +3,18 @@ "content": [ "v9.9.9" ], - "timestamp": "2024-01-19T11:32:36.031083" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:05.308243" }, "Test Function checkCondaChannels": { "content": null, - "timestamp": "2024-01-19T11:32:50.456" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:12.425833" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index f7c54bc6..ca964ce8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -11,9 +11,6 @@ nextflow_workflow { test("Should run no inputs") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = false @@ -39,9 +36,6 @@ nextflow_workflow { test("Should print version") { when { - params { - outdir = "tests/results" - } workflow { """ print_version = true @@ -68,19 +62,16 @@ nextflow_workflow { test("Should dump params") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = 'results' check_conda_channels = false input[0] = false input[1] = true - input[2] = params.outdir + input[2] = outdir input[3] = false """ } @@ -96,19 +87,16 @@ nextflow_workflow { test("Should not create params JSON if no output directory") { when { - params { - outdir = "$outputDir" - } workflow { """ print_version = false dump_parameters = true - outdir = params.outdir + outdir = null check_conda_channels = false input[0] = false input[1] = true - input[2] = null + input[2] = outdir input[3] = false """ } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index 53574ffe..d0a926bf 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -6,4 +6,4 @@ manifest { nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 10f948e6..1037232c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -1,25 +1,41 @@ { "Test Function checkProfileProvided": { "content": null, - "timestamp": "2024-02-09T15:43:55.145717" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:03.360873" }, "Test Function checkConfigProvided": { "content": [ true ], - "timestamp": "2024-01-19T11:34:13.548431224" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:02:59.729647" }, "Test Function nfCoreLogo": { "content": [ "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" ], - "timestamp": "2024-01-19T11:34:38.840454873" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:10.562934" }, "Test Function workflowCitation": { "content": [ "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" ], - "timestamp": "2024-01-19T11:34:22.24352016" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:07.019761" }, "Test Function without logColours": { "content": [ @@ -73,13 +89,21 @@ "biwhite": "" } ], - "timestamp": "2024-01-19T11:35:04.418416984" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:17.969323" }, "Test Function dashedLine": { "content": [ "-\u001b[2m----------------------------------------------------\u001b[0m-" ], - "timestamp": "2024-01-19T11:34:55.420000755" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:14.366181" }, "Test Function with logColours": { "content": [ @@ -133,6 +157,10 @@ "biwhite": "\u001b[1;97m" } ], - "timestamp": "2024-01-19T11:35:13.436366565" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:21.714424" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap index d07ce54c..859d1030 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap @@ -10,6 +10,10 @@ ] } ], - "timestamp": "2024-01-19T11:35:22.538940073" + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-02-28T12:03:25.726491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 517ee54e..5784a33f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -197,4 +197,4 @@ nextflow_workflow { ) } } -} \ No newline at end of file +}