From cfe82532f6f5251ad821c48de717cdd4c958d08e Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Wed, 26 Jun 2024 16:34:08 +0000 Subject: [PATCH 01/70] Replaced local unicycler module with nf-core module. --- conf/test.config | 2 +- modules.json | 5 + modules/nf-core/unicycler/environment.yml | 7 ++ modules/nf-core/unicycler/main.nf | 61 ++++++++++ modules/nf-core/unicycler/meta.yml | 64 +++++++++++ modules/nf-core/unicycler/tests/main.nf.test | 61 ++++++++++ .../nf-core/unicycler/tests/main.nf.test.snap | 104 ++++++++++++++++++ modules/nf-core/unicycler/tests/tags.yml | 2 + workflows/bacass.nf | 2 +- 9 files changed, 306 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/unicycler/environment.yml create mode 100644 modules/nf-core/unicycler/main.nf create mode 100644 modules/nf-core/unicycler/meta.yml create mode 100644 modules/nf-core/unicycler/tests/main.nf.test create mode 100644 modules/nf-core/unicycler/tests/main.nf.test.snap create mode 100644 modules/nf-core/unicycler/tests/tags.yml diff --git a/conf/test.config b/conf/test.config index 0b422f0..ad3ac83 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,7 +23,7 @@ params { input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv' // some extra args to speed tests up - unicycler_args = "--no_correct --no_pilon" + unicycler_args = "" prokka_args = " --fast" assembly_type = 'short' skip_pycoqc = true diff --git a/modules.json b/modules.json index 6dc814a..90f8413 100644 --- a/modules.json +++ b/modules.json @@ -92,6 +92,11 @@ "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26", "installed_by": ["modules"] }, + "unicycler": { + "branch": "master", + "git_sha": "5f65b5398f3fe4b8d51d77ed90b0a8cd8c89bba7", + "installed_by": ["modules"] + }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", diff --git a/modules/nf-core/unicycler/environment.yml b/modules/nf-core/unicycler/environment.yml new file mode 100644 index 0000000..ffe491b --- /dev/null +++ b/modules/nf-core/unicycler/environment.yml @@ -0,0 +1,7 @@ +name: unicycler +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::unicycler=0.5.0 diff --git a/modules/nf-core/unicycler/main.nf b/modules/nf-core/unicycler/main.nf new file mode 100644 index 0000000..f897180 --- /dev/null +++ b/modules/nf-core/unicycler/main.nf @@ -0,0 +1,61 @@ +process UNICYCLER { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/unicycler:0.5.0--py312hc60241a_5' : + 'biocontainers/unicycler:0.5.0--py312hc60241a_5' }" + + input: + tuple val(meta), path(shortreads), path(longreads) + + output: + tuple val(meta), path('*.scaffolds.fa.gz'), emit: scaffolds + tuple val(meta), path('*.assembly.gfa.gz'), emit: gfa + tuple val(meta), path('*.log') , emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def short_reads = shortreads ? ( meta.single_end ? "-s $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" ) : "" + def long_reads = longreads ? "-l $longreads" : "" + """ + unicycler \\ + --threads $task.cpus \\ + $args \\ + $short_reads \\ + $long_reads \\ + --out ./ + + mv assembly.fasta ${prefix}.scaffolds.fa + gzip -n ${prefix}.scaffolds.fa + mv assembly.gfa ${prefix}.assembly.gfa + gzip -n ${prefix}.assembly.gfa + mv unicycler.log ${prefix}.unicycler.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + + cat "" | gzip > ${prefix}.scaffolds.fa.gz + cat "" | gzip > ${prefix}.assembly.gfa.gz + touch ${prefix}.unicycler.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//') + END_VERSIONS + """ + +} diff --git a/modules/nf-core/unicycler/meta.yml b/modules/nf-core/unicycler/meta.yml new file mode 100644 index 0000000..406b147 --- /dev/null +++ b/modules/nf-core/unicycler/meta.yml @@ -0,0 +1,64 @@ +name: unicycler +description: Assembles bacterial genomes +keywords: + - genome + - assembly + - genome assembler + - small genome +tools: + - unicycler: + description: Hybrid assembly pipeline for bacterial genomes + homepage: https://github.com/rrwick/Unicycler + documentation: https://github.com/rrwick/Unicycler + tool_dev_url: https://github.com/rrwick/Unicycler + doi: 10.1371/journal.pcbi.1005595 + licence: ["GPL v3"] +input: + - meta: + type: map + description: | + 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. + - longreads: + type: file + description: | + List of input FastQ files of size 1, PacBio or Nanopore long reads. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - scaffolds: + type: file + description: Fasta file containing scaffolds + pattern: "*.{scaffolds.fa.gz}" + - gfa: + type: file + description: gfa file containing assembly + pattern: "*.{assembly.gfa.gz}" + - log: + type: file + description: unicycler log file + pattern: "*.{log}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@JoseEspinosa" + - "@drpatelh" + - "@d4straub" +maintainers: + - "@JoseEspinosa" + - "@drpatelh" + - "@d4straub" diff --git a/modules/nf-core/unicycler/tests/main.nf.test b/modules/nf-core/unicycler/tests/main.nf.test new file mode 100644 index 0000000..416b50b --- /dev/null +++ b/modules/nf-core/unicycler/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process UNICYCLER" + script "../main.nf" + process "UNICYCLER" + + tag "modules" + tag "modules_nfcore" + tag "unicycler" + + test("bacteroides_fragilis - nanopore") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [], + [ file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.scaffolds, + process.out.gfa, + file(process.out.log.get(0).get(1)).name, + process.out.versions).match() + } + ) + } + } + + test("bacteroides_fragilis - nanopore - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [], + [ file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + } + +} diff --git a/modules/nf-core/unicycler/tests/main.nf.test.snap b/modules/nf-core/unicycler/tests/main.nf.test.snap new file mode 100644 index 0000000..4e627b3 --- /dev/null +++ b/modules/nf-core/unicycler/tests/main.nf.test.snap @@ -0,0 +1,104 @@ +{ + "bacteroides_fragilis - nanopore": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.scaffolds.fa.gz:md5,8f2b98020361b047eec9dc4c23792d37" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.assembly.gfa.gz:md5,849cec81b0ebf8b34554cf56ce0939d2" + ] + ], + "test.unicycler.log", + [ + "versions.yml:md5,3a81549d1e874ec0214fd1a08384b8b5" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-18T18:40:42.723547744" + }, + "bacteroides_fragilis - nanopore - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.scaffolds.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.assembly.gfa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.unicycler.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,3a81549d1e874ec0214fd1a08384b8b5" + ], + "gfa": [ + [ + { + "id": "test", + "single_end": true + }, + "test.assembly.gfa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.unicycler.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "scaffolds": [ + [ + { + "id": "test", + "single_end": true + }, + "test.scaffolds.fa.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3a81549d1e874ec0214fd1a08384b8b5" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-18T18:40:59.5110618" + } +} \ No newline at end of file diff --git a/modules/nf-core/unicycler/tests/tags.yml b/modules/nf-core/unicycler/tests/tags.yml new file mode 100644 index 0000000..25b2cf2 --- /dev/null +++ b/modules/nf-core/unicycler/tests/tags.yml @@ -0,0 +1,2 @@ +unicycler: + - "modules/nf-core/unicycler/**" diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 448d0cb..faa9524 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -27,7 +27,7 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true // MODULE: Local to the pipeline // include { PYCOQC } from '../modules/local/pycoqc' -include { UNICYCLER } from '../modules/local/unicycler' +include { UNICYCLER } from '../modules/nf-core/unicycler/main' include { NANOPOLISH } from '../modules/local/nanopolish' include { MEDAKA } from '../modules/local/medaka' include { KRAKEN2_DB_PREPARATION } from '../modules/local/kraken2_db_preparation' From 24f0cbc74ab8782db1e15a29fc49429324c542bc Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Thu, 27 Jun 2024 14:09:09 +0000 Subject: [PATCH 02/70] Removed deprecated unicycler parameters from test_dfast. --- conf/test.config | 1 - conf/test_dfast.config | 1 - 2 files changed, 2 deletions(-) diff --git a/conf/test.config b/conf/test.config index ad3ac83..90115da 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,7 +23,6 @@ params { input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv' // some extra args to speed tests up - unicycler_args = "" prokka_args = " --fast" assembly_type = 'short' skip_pycoqc = true diff --git a/conf/test_dfast.config b/conf/test_dfast.config index 9edc4a7..e2d0afe 100644 --- a/conf/test_dfast.config +++ b/conf/test_dfast.config @@ -23,7 +23,6 @@ params { input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv' // some extra args to speed tests up - unicycler_args = "--no_correct --no_pilon" annotation_tool = 'dfast' assembly_type = 'short' skip_pycoqc = true From 2baeb3b7c53f2642e44d9a99bd56463f952fbb4b Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Thu, 27 Jun 2024 14:18:51 +0000 Subject: [PATCH 03/70] Updated CHANGELOG. --- CHANGELOG.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d476ac..21eaa7f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,20 @@ 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). +## v2.4.0 nf-core/bacass + +### `Changed` + +- [#150](https://github.com/nf-core/bacass/pull/150) Replace local unicycler module with nf-core module + bump version + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` + ## v2.3.1 nf-core/bacass: "Navy Iron Oyster" 2024/06/24 ### `Changed` From e9228123f49651f663632799177b39067cfb639c Mon Sep 17 00:00:00 2001 From: Florian Wuennemann Date: Thu, 27 Jun 2024 15:38:47 +0000 Subject: [PATCH 04/70] Removed no longer needed unicycler local files. --- modules/local/unicycler/environment.yml | 7 ---- modules/local/unicycler/main.nf | 50 ------------------------- 2 files changed, 57 deletions(-) delete mode 100644 modules/local/unicycler/environment.yml delete mode 100644 modules/local/unicycler/main.nf diff --git a/modules/local/unicycler/environment.yml b/modules/local/unicycler/environment.yml deleted file mode 100644 index 9e32bbc..0000000 --- a/modules/local/unicycler/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: unicycler -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - unicycler=0.4.8 diff --git a/modules/local/unicycler/main.nf b/modules/local/unicycler/main.nf deleted file mode 100644 index eea7238..0000000 --- a/modules/local/unicycler/main.nf +++ /dev/null @@ -1,50 +0,0 @@ -process UNICYCLER { - tag "$meta.id" - label 'process_high' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/unicycler:0.4.8--py38h8162308_3' : - 'biocontainers/unicycler:0.4.8--py38h8162308_3' }" - - input: - tuple val(meta), path(shortreads), path(longreads) - - output: - tuple val(meta), path('*.scaffolds.fa.gz'), emit: scaffolds - tuple val(meta), path('*.assembly.gfa.gz'), emit: gfa - tuple val(meta), path('*.log') , emit: log - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - if(params.assembly_type == 'long'){ - input_reads = "-l $longreads" - } else if (params.assembly_type == 'short'){ - input_reads = "-1 ${shortreads[0]} -2 ${shortreads[1]}" - } else if (params.assembly_type == 'hybrid'){ - input_reads = "-1 ${shortreads[0]} -2 ${shortreads[1]} -l $longreads" - } - """ - unicycler \\ - --threads $task.cpus \\ - $args \\ - $input_reads \\ - --out ./ - - mv assembly.fasta ${prefix}.scaffolds.fa - gzip -n ${prefix}.scaffolds.fa - mv assembly.gfa ${prefix}.assembly.gfa - gzip -n ${prefix}.assembly.gfa - mv unicycler.log ${prefix}.unicycler.log - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//') - END_VERSIONS - """ -} From a49930e40a6bfdf05f52d86849a43c113fbf9cd0 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 12:15:18 +0200 Subject: [PATCH 05/70] fix missing dev tag in bumped version --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 21eaa7f..02daaed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0 nf-core/bacass +## v2.4.0dev nf-core/bacass ### `Changed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 95b5ae9..e647ad5 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/bacass + This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-bacass-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3935924..ad40756 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.1' + version = '2.4.0dev' doi = '10.5281/zenodo.2669428' } From 04091a32dca2e89cf4387ec3c0a22ebd7574425d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 13:36:51 +0200 Subject: [PATCH 06/70] remove files_unchanged items form linting --- .nf-core.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 216c313..0b077e6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,9 +2,6 @@ repository_type: pipeline lint: files_exist: - conf/igenomes.config - files_unchanged: - - .github/CONTRIBUTING.md - - .github/PULL_REQUEST_TEMPLATE.md nextflow_config: - config_defaults: - params.dfast_config From 1bb32782bc0ec76ade0c950d0ea98c22dd8bc3f8 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 13:39:13 +0200 Subject: [PATCH 07/70] fix files_unchanged to make a proper linting check --- .github/CONTRIBUTING.md | 14 +++++--------- .github/PULL_REQUEST_TEMPLATE.md | 1 + 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index e96ce76..24edde8 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -26,7 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -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. +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. @@ -47,14 +51,6 @@ Each `nf-core` pipeline should be set up with a minimal set of test-data. If there are any failures then the automated tests fail. These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. -You can run pipeline tests with the following command: - -```bash -nextflow run nf-core/bacass \ - -profile , \ - --outdir -``` - ## Patch :warning: Only in the unlikely and regretful event of a release happening with a bug. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 7344110..99d5b0f 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. From b73c536630edbbfbf0226eef9c8fe2d2f76f4789 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 13:47:01 +0200 Subject: [PATCH 08/70] added changelog #153 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 02daaed..6a24efb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#153](https://github.com/nf-core/bacass/pull/153) Update `.nf-core.yml` to fix files_unchanged section for accurate linting checks. + ### `Dependencies` ### `Deprecated` From e8442e2d8b3470e5da74a16524cbb4e811c01c4c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 11:12:56 +0200 Subject: [PATCH 09/70] fix kmerfinder script to download reference --- bin/download_reference.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/download_reference.py b/bin/download_reference.py index 88e8936..2c09cb8 100755 --- a/bin/download_reference.py +++ b/bin/download_reference.py @@ -122,7 +122,7 @@ def download_references(file, reference, out_dir): ref_query = f"{assembly_accession}_{asm_name}" # Check if ref_query matches the search value - if ref_query == top_reference: + if top_reference in ref_query: # make url # Append the 20th element of the row to the URL list: assembly_url = row[19] + "/" + ref_query dir_url.append(assembly_url) From 3bfab1518f823f1af78dc1976d4c32d01cc6bf39 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 11:13:27 +0200 Subject: [PATCH 10/70] add more resources to kmerfinder module to avoid memory related issues --- modules/local/kmerfinder.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/kmerfinder.nf b/modules/local/kmerfinder.nf index cca5f35..66a48f1 100644 --- a/modules/local/kmerfinder.nf +++ b/modules/local/kmerfinder.nf @@ -1,6 +1,6 @@ process KMERFINDER { tag "$meta.id" - label 'process_medium' + label 'process_high' conda "bioconda::kmerfinder=3.0.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? From 3e9cf3f521c6f4cae8cfbe4250887d8be770664f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 10 Jul 2024 15:19:28 +0200 Subject: [PATCH 11/70] added changelog #154 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a24efb..583e1d8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues. - [#153](https://github.com/nf-core/bacass/pull/153) Update `.nf-core.yml` to fix files_unchanged section for accurate linting checks. ### `Dependencies` From 084fec4984fa0d71032931ea15f55fc924a6ea36 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 10:09:03 +0200 Subject: [PATCH 12/70] fixed current zenodo url to kmerfinderdb --- conf/test_full.config | 2 +- modules/local/kmerfinder.nf | 11 +++++++---- nextflow_schema.json | 4 ++-- subworkflows/local/kmerfinder_subworkflow.nf | 3 ++- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index f51aa6d..f3dc621 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -17,6 +17,6 @@ params { // Input data for full size test input = params.pipelines_testdata_base_path + 'bacass/bacass_full.tsv' kraken2db = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz' - kmerfinderdb = 'https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz' + kmerfinderdb = 'https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz' ncbi_assembly_metadata = 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt' } diff --git a/modules/local/kmerfinder.nf b/modules/local/kmerfinder.nf index 66a48f1..38532de 100644 --- a/modules/local/kmerfinder.nf +++ b/modules/local/kmerfinder.nf @@ -8,7 +8,8 @@ process KMERFINDER { 'biocontainers/kmerfinder:3.0.2--hdfd78af_0' }" input: - tuple val(meta), path(reads), path(kmerfinder_db) + tuple val(meta), path(reads), path(kmerfinderdb_path) + val tax_group output: tuple val(meta), path("*_results.txt") , emit: report @@ -18,14 +19,15 @@ process KMERFINDER { script: def prefix = task.ext.prefix ?: "${meta.id}" def in_reads = reads[0] && reads[1] ? "${reads[0]} ${reads[1]}" : "${reads}" - // WARNING: Ensure to update software version in this line if you modify the container/environment. + // WARNING: Ensure to update software or database version in this line if you modify the container/environment. def kmerfinder_version = "3.0.2" + def kmerfinderdb_version = "20190108" """ kmerfinder.py \\ --infile $in_reads \\ --output_folder . \\ - --db_path ${kmerfinder_db}/bacteria.ATG \\ - -tax ${kmerfinder_db}/bacteria.name \\ + --db_path ${kmerfinderdb_path}/${tax_group}/bacteria.ATG \\ + -tax ${kmerfinderdb_path}/${tax_group}/bacteria.name \\ -x mv results.txt ${prefix}_results.txt @@ -34,6 +36,7 @@ process KMERFINDER { cat <<-END_VERSIONS > versions.yml "${task.process}": kmerfinder: \$(echo "${kmerfinder_version}") + kmerfinderdb: \$(echo "${kmerfinderdb_version}") END_VERSIONS """ } diff --git a/nextflow_schema.json b/nextflow_schema.json index 8eec000..c5dc6ce 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -83,7 +83,7 @@ }, "kmerfinderdb": { "type": "string", - "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz " + "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz" }, "reference_fasta": { "type": "string", @@ -95,7 +95,7 @@ }, "ncbi_assembly_metadata": { "type": "string", - "description": "Master file (*.txt) containing a summary of assemblies available in GeneBank or RefSeq. See: https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt" + "description": "Master file (*.txt) containing a summary of assemblies available in GeneBank or RefSeq. See: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt" } } }, diff --git a/subworkflows/local/kmerfinder_subworkflow.nf b/subworkflows/local/kmerfinder_subworkflow.nf index ef777eb..9b27f08 100644 --- a/subworkflows/local/kmerfinder_subworkflow.nf +++ b/subworkflows/local/kmerfinder_subworkflow.nf @@ -33,7 +33,8 @@ workflow KMERFINDER_SUBWORKFLOW { .set{ ch_to_kmerfinder } KMERFINDER ( - ch_to_kmerfinder + ch_to_kmerfinder, // Channel: [ meta, reads, path_to_kmerfinderdb ] + 'bacteria' // Val: 'tax_group' ) ch_kmerfinder_report = KMERFINDER.out.report ch_kmerfinder_json = KMERFINDER.out.json From 82adb62370621390050d19370ae2d0f681e63a32 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 10:20:04 +0200 Subject: [PATCH 13/70] update changelog in #157 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 583e1d8..7c1b9b1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues. - [#153](https://github.com/nf-core/bacass/pull/153) Update `.nf-core.yml` to fix files_unchanged section for accurate linting checks. From 04def18c8d2669a9dbeccfd3c4621edca83b6efd Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 11:53:14 +0200 Subject: [PATCH 14/70] enhance KmerFinder support parsing multiple file format versions --- modules/local/kmerfinder.nf | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/local/kmerfinder.nf b/modules/local/kmerfinder.nf index 38532de..18a0f52 100644 --- a/modules/local/kmerfinder.nf +++ b/modules/local/kmerfinder.nf @@ -19,15 +19,17 @@ process KMERFINDER { script: def prefix = task.ext.prefix ?: "${meta.id}" def in_reads = reads[0] && reads[1] ? "${reads[0]} ${reads[1]}" : "${reads}" - // WARNING: Ensure to update software or database version in this line if you modify the container/environment. + def dbpath_file = file("${kmerfinder_db}/bacteria/bacteria.ATG").exists() ?: "${kmerfinder_db}/bacteria/bacteria.ATG" + def tax_file = file("${kmerfinder_db}/bacteria/bacteria.name").exists() ? "${kmerfinder_db}/bacteria/bacteria.name" : "${kmerfinder_db}/bacteria/bacteria.tax" + // WARNING: Ensure to update software version in this line if you modify the container/environment. def kmerfinder_version = "3.0.2" def kmerfinderdb_version = "20190108" """ kmerfinder.py \\ --infile $in_reads \\ --output_folder . \\ - --db_path ${kmerfinderdb_path}/${tax_group}/bacteria.ATG \\ - -tax ${kmerfinderdb_path}/${tax_group}/bacteria.name \\ + --db_path $dbpath_file \\ + -tax $tax_file \\ -x mv results.txt ${prefix}_results.txt From 9280f8975a8b3e92929923c53a66edaeb0ab761c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 15:50:16 +0200 Subject: [PATCH 15/70] update kmerfinderdb description --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index c5dc6ce..e7dfb12 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -83,7 +83,7 @@ }, "kmerfinderdb": { "type": "string", - "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz" + "description": "Path to the Kmerfinder bacteria database. See database installation (guidelines)[https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/] for details. The latest version can be downloaded from the KmerFinder Database FTP site or directly during pipeline execution with. Example:\n\n```--kmerfinder_db 'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz'```\n(Note: Downloading the KmerFinder database (~30GB) via FTP can be time-consuming. It's recommended to pre-download the database and provide the *.tar.gz file using this parameter instead of URL site.).\nAn older version is available on (Zenodo)[https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz]." }, "reference_fasta": { "type": "string", From b5b0407ff1e18e0cc8a82214f36d50c4746882fe Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 30 Aug 2024 15:52:41 +0200 Subject: [PATCH 16/70] update kmerfinder module --- modules/local/kmerfinder.nf | 10 ++++------ nextflow_schema.json | 2 +- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/modules/local/kmerfinder.nf b/modules/local/kmerfinder.nf index 18a0f52..0159e74 100644 --- a/modules/local/kmerfinder.nf +++ b/modules/local/kmerfinder.nf @@ -19,17 +19,16 @@ process KMERFINDER { script: def prefix = task.ext.prefix ?: "${meta.id}" def in_reads = reads[0] && reads[1] ? "${reads[0]} ${reads[1]}" : "${reads}" - def dbpath_file = file("${kmerfinder_db}/bacteria/bacteria.ATG").exists() ?: "${kmerfinder_db}/bacteria/bacteria.ATG" - def tax_file = file("${kmerfinder_db}/bacteria/bacteria.name").exists() ? "${kmerfinder_db}/bacteria/bacteria.name" : "${kmerfinder_db}/bacteria/bacteria.tax" + def db_atg = "${kmerfinderdb_path}/${tax_group}.ATG" + def db_tax = file("${kmerfinderdb_path}/${tax_group}.name").exists() ? "${kmerfinderdb_path}/${tax_group}.name" : "${kmerfinderdb_path}/${tax_group}.tax" // WARNING: Ensure to update software version in this line if you modify the container/environment. def kmerfinder_version = "3.0.2" - def kmerfinderdb_version = "20190108" """ kmerfinder.py \\ --infile $in_reads \\ --output_folder . \\ - --db_path $dbpath_file \\ - -tax $tax_file \\ + --db_path $db_atg \\ + -tax $db_tax \\ -x mv results.txt ${prefix}_results.txt @@ -38,7 +37,6 @@ process KMERFINDER { cat <<-END_VERSIONS > versions.yml "${task.process}": kmerfinder: \$(echo "${kmerfinder_version}") - kmerfinderdb: \$(echo "${kmerfinderdb_version}") END_VERSIONS """ } diff --git a/nextflow_schema.json b/nextflow_schema.json index e7dfb12..5c40fdd 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -83,7 +83,7 @@ }, "kmerfinderdb": { "type": "string", - "description": "Path to the Kmerfinder bacteria database. See database installation (guidelines)[https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/] for details. The latest version can be downloaded from the KmerFinder Database FTP site or directly during pipeline execution with. Example:\n\n```--kmerfinder_db 'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz'```\n(Note: Downloading the KmerFinder database (~30GB) via FTP can be time-consuming. It's recommended to pre-download the database and provide the *.tar.gz file using this parameter instead of URL site.).\nAn older version is available on (Zenodo)[https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz]." + "description": "Path to the Kmerfinder bacteria database (ie: '/path_to/kmerfinder/bacteria/ or '/path_to/kmerfinder/bacteria.tar.gz'). Only taxonomic group 'bacteria' is allowed. See database installation (guidelines)[https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/] for details. The latest version can be downloaded from the KmerFinder Database FTP site or directly during pipeline execution with. Example:\n\n```--kmerfinder_db 'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz'```\n(Note: Downloading the KmerFinder database (~30GB) via FTP can be time-consuming. It's recommended to pre-download the database and provide the *.tar.gz file using this parameter instead of URL site.).\nAn older version is available on (Zenodo)[https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz]." }, "reference_fasta": { "type": "string", From fd7dd01eaa5e9a0e1d6450bf53c31e5db6366f95 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 30 Aug 2024 16:01:20 +0200 Subject: [PATCH 17/70] update kmerfinder module dir structure --- modules/local/kmerfinder/environment.yml | 7 +++++++ modules/local/{kmerfinder.nf => kmerfinder/main.nf} | 1 - modules/local/kmerfinder_summary/environment.yml | 7 +++++++ .../{kmerfinder_summary.nf => kmerfinder_summary/main.nf} | 1 - 4 files changed, 14 insertions(+), 2 deletions(-) create mode 100644 modules/local/kmerfinder/environment.yml rename modules/local/{kmerfinder.nf => kmerfinder/main.nf} (97%) create mode 100644 modules/local/kmerfinder_summary/environment.yml rename modules/local/{kmerfinder_summary.nf => kmerfinder_summary/main.nf} (96%) diff --git a/modules/local/kmerfinder/environment.yml b/modules/local/kmerfinder/environment.yml new file mode 100644 index 0000000..bcb28a9 --- /dev/null +++ b/modules/local/kmerfinder/environment.yml @@ -0,0 +1,7 @@ +name: kmerfinder +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::kmerfinder=3.0.2 diff --git a/modules/local/kmerfinder.nf b/modules/local/kmerfinder/main.nf similarity index 97% rename from modules/local/kmerfinder.nf rename to modules/local/kmerfinder/main.nf index 0159e74..cd0b88e 100644 --- a/modules/local/kmerfinder.nf +++ b/modules/local/kmerfinder/main.nf @@ -2,7 +2,6 @@ process KMERFINDER { tag "$meta.id" label 'process_high' - conda "bioconda::kmerfinder=3.0.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kmerfinder:3.0.2--hdfd78af_0' : 'biocontainers/kmerfinder:3.0.2--hdfd78af_0' }" diff --git a/modules/local/kmerfinder_summary/environment.yml b/modules/local/kmerfinder_summary/environment.yml new file mode 100644 index 0000000..ebf6fb5 --- /dev/null +++ b/modules/local/kmerfinder_summary/environment.yml @@ -0,0 +1,7 @@ +name: kmerfinder_summary +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/local/kmerfinder_summary.nf b/modules/local/kmerfinder_summary/main.nf similarity index 96% rename from modules/local/kmerfinder_summary.nf rename to modules/local/kmerfinder_summary/main.nf index 8e5fe45..5b22205 100644 --- a/modules/local/kmerfinder_summary.nf +++ b/modules/local/kmerfinder_summary/main.nf @@ -2,7 +2,6 @@ process KMERFINDER_SUMMARY { tag "kmerfinder_summary" label 'process_low' - conda "bioconda::multiqc=1.19" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" From c2a94d7e3a9fb4567b54c6161df74336cdb33680 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 30 Aug 2024 16:23:59 +0200 Subject: [PATCH 18/70] update module paths and handle memory-errors in kmerfinder --- CHANGELOG.md | 1 + conf/modules.config | 4 ++++ modules/local/kmerfinder/main.nf | 2 +- subworkflows/local/kmerfinder_subworkflow.nf | 4 ++-- 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7c1b9b1..ceda150 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#159](https://github.com/nf-core/bacass/pull/159) Updated Kmerfinder module and increased memory. - [#150](https://github.com/nf-core/bacass/pull/150) Replace local unicycler module with nf-core module + bump version ### `Added` diff --git a/conf/modules.config b/conf/modules.config index 78bd92b..b751620 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -291,6 +291,10 @@ if (!params.skip_fastp) { if (!params.skip_kmerfinder) { process { withName: '.*:.*:KMERFINDER_SUBWORKFLOW:KMERFINDER' { + errorStrategy = { task.exitStatus in [1, 137, 139] ? 'retry' : 'finish'} + maxRetries = 3 + memory = { task.memory * task.attempt } + ext.args = '' publishDir = [ path: { "${params.outdir}/Kmerfinder/${meta.id}" }, diff --git a/modules/local/kmerfinder/main.nf b/modules/local/kmerfinder/main.nf index cd0b88e..37439da 100644 --- a/modules/local/kmerfinder/main.nf +++ b/modules/local/kmerfinder/main.nf @@ -1,6 +1,6 @@ process KMERFINDER { tag "$meta.id" - label 'process_high' + label 'process_medium' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kmerfinder:3.0.2--hdfd78af_0' : diff --git a/subworkflows/local/kmerfinder_subworkflow.nf b/subworkflows/local/kmerfinder_subworkflow.nf index 9b27f08..54d4e23 100644 --- a/subworkflows/local/kmerfinder_subworkflow.nf +++ b/subworkflows/local/kmerfinder_subworkflow.nf @@ -2,8 +2,8 @@ // Kmerfinder subworkflow for species identification & QC // include { UNTAR } from '../../modules/nf-core/untar/main' -include { KMERFINDER } from '../../modules/local/kmerfinder' -include { KMERFINDER_SUMMARY } from '../../modules/local/kmerfinder_summary' +include { KMERFINDER } from '../../modules/local/kmerfinder/main' +include { KMERFINDER_SUMMARY } from '../../modules/local/kmerfinder_summary/main' include { FIND_DOWNLOAD_REFERENCE } from '../../modules/local/find_download_reference' workflow KMERFINDER_SUBWORKFLOW { From 6250ad3b5a13c45a7d2b6ee1c880b0b453bae611 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 3 Sep 2024 11:11:01 +0200 Subject: [PATCH 19/70] fix memory issues due to config in kmerfinder --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index b751620..35248e4 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -293,7 +293,6 @@ if (!params.skip_kmerfinder) { withName: '.*:.*:KMERFINDER_SUBWORKFLOW:KMERFINDER' { errorStrategy = { task.exitStatus in [1, 137, 139] ? 'retry' : 'finish'} maxRetries = 3 - memory = { task.memory * task.attempt } ext.args = '' publishDir = [ From 09a1eb68c69ba6256ea8b12f5d3523a37697ca4b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 3 Sep 2024 12:06:55 +0200 Subject: [PATCH 20/70] Handle KmerFinder results when no species hit is detected --- subworkflows/local/kmerfinder_subworkflow.nf | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/kmerfinder_subworkflow.nf b/subworkflows/local/kmerfinder_subworkflow.nf index 54d4e23..2c0bf70 100644 --- a/subworkflows/local/kmerfinder_subworkflow.nf +++ b/subworkflows/local/kmerfinder_subworkflow.nf @@ -53,7 +53,9 @@ workflow KMERFINDER_SUBWORKFLOW { .join(consensus, by:0) .map{ meta, report_json, report_txt, fasta -> - specie = report_json.splitJson(path:"kmerfinder.results.species_hits").value.get(0)["Species"] + species_hits = report_json.splitJson(path:"kmerfinder.results.species_hits").value + def specie = species_hits.size() > 0 ? species_hits.get(0)["Species"] : "Unknown Species" + return tuple(specie, meta, report_txt, fasta) } .groupTuple(by:0) // Group by the "Species" field @@ -61,7 +63,9 @@ workflow KMERFINDER_SUBWORKFLOW { // SUBWORKFLOW: For each species target, this subworkflow collects reference genome assemblies ('GCF*') and subsequently downloads the best matching reference assembly. FIND_DOWNLOAD_REFERENCE ( - ch_reports_byreference.map{ specie, meta, report_txt, fasta-> tuple(specie, report_txt) }, + ch_reports_byreference + .map{ specie, meta, report_txt, fasta-> tuple(specie, report_txt) } + .filter{ specie, report_txt -> specie != "Unknown Species" }, ch_ncbi_assembly_metadata ) ch_versions = ch_versions.mix(FIND_DOWNLOAD_REFERENCE.out.versions) From ae525c05e23c1012f19fd7ebf4a461214422b1f5 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 3 Sep 2024 12:07:52 +0200 Subject: [PATCH 21/70] handle prokka/bakkta channel when fasta file is empty --- workflows/bacass.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index faa9524..df41750 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -460,7 +460,7 @@ workflow BACASS { ch_versions = ch_versions.mix( GUNZIP.out.versions ) PROKKA ( - ch_to_prokka, + ch_to_prokka.filter{ meta, fasta -> !fasta.isEmpty() }, [], [] ) @@ -479,7 +479,7 @@ workflow BACASS { ch_versions = ch_versions.mix( GUNZIP.out.versions ) BAKTA_DBDOWNLOAD_RUN ( - ch_to_bakta, + ch_to_bakta.filter{ meta, fasta -> !fasta.isEmpty() }, params.baktadb, params.baktadb_download ) From fcf0ab93d0bf3023b6355d2f7f855011382679ae Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 3 Sep 2024 13:46:46 +0200 Subject: [PATCH 22/70] update changelog in #160 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ceda150..4ae6d43 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues. - [#153](https://github.com/nf-core/bacass/pull/153) Update `.nf-core.yml` to fix files_unchanged section for accurate linting checks. From 41fd8c9a023f360383f178c09ad54619a2ff9680 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 5 Sep 2024 16:36:55 +0200 Subject: [PATCH 23/70] fix saving merged fastq files in fastp module --- conf/modules.config | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 35248e4..0304051 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -270,6 +270,12 @@ if (!params.skip_fastp) { mode: params.publish_dir_mode, pattern: "*.fail.fastq.gz", enabled: params.save_trimmed_fail + ], + [ + path: { "${params.outdir}/trimming/shortreads" }, + mode: params.publish_dir_mode, + pattern: "*.merged.fastq.gz", + enabled: params.save_merged ] ] } From 7f438ecda52aa6838e9c5692930a9111f3499ddd Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 5 Sep 2024 17:17:43 +0200 Subject: [PATCH 24/70] #163 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4ae6d43..5e2ef25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues. From f1f915cb2fc3cc48a8f060d02a9f5ffdf99d8f40 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 6 Sep 2024 13:58:02 +0200 Subject: [PATCH 25/70] extend description on save_merged param --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5c40fdd..a058d28 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -56,7 +56,7 @@ }, "save_merged": { "type": "boolean", - "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`" + "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`. This option enables read merging and saves all merged reads to a file ending in `*.merged.fastq.gz`; these reads will be won't be passed to the assembly process." }, "skip_fastqc": { "type": "boolean", From 6e0d781e8ff61135b70d9f674d1ec06c8e103797 Mon Sep 17 00:00:00 2001 From: Daniel VM <69470278+Daniel-VM@users.noreply.github.com> Date: Fri, 6 Sep 2024 14:02:20 +0200 Subject: [PATCH 26/70] Fix CHANGELOG.md #163 Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5e2ef25..ad1c58c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files +- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files. - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues. From 488b5abda410eb0f2de98a0868a1e9cb706698e4 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 13 Sep 2024 17:37:03 +0200 Subject: [PATCH 27/70] append fastqc trim section to multiqc report --- conf/modules.config | 8 ++++++++ modules/local/multiqc_custom.nf | 1 + workflows/bacass.nf | 7 ++++--- 3 files changed, 13 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 0304051..064f4a2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -241,6 +241,14 @@ if (!params.skip_fastqc) { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } + withName: '.*:.*:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM' { + ext.args = '--quiet' + publishDir = [ + path: { "${params.outdir}/FastQC/trim" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } } } if (!params.skip_fastp) { diff --git a/modules/local/multiqc_custom.nf b/modules/local/multiqc_custom.nf index 5c0cc9f..bc0a8e6 100644 --- a/modules/local/multiqc_custom.nf +++ b/modules/local/multiqc_custom.nf @@ -14,6 +14,7 @@ process MULTIQC_CUSTOM { path methods_description path software_versions path ('fastqc/*') + path ('fastqc_trim/*') path ('fastp/*') path ('nanoplot/*') path ('porechop/*') diff --git a/workflows/bacass.nf b/workflows/bacass.nf index df41750..3aeb476 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -127,7 +127,7 @@ workflow BACASS { // ch_fastqc_raw_multiqc = Channel.empty() ch_fastqc_trim_multiqc = Channel.empty() - ch_trim_json_multiqc = Channel.empty() + ch_fastp_json_multiqc = Channel.empty() if (params.assembly_type != 'long'){ FASTQ_TRIM_FASTP_FASTQC ( ch_shortreads, @@ -139,7 +139,7 @@ workflow BACASS { ) ch_fastqc_raw_multiqc = FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip ch_fastqc_trim_multiqc = FASTQ_TRIM_FASTP_FASTQC.out.fastqc_trim_zip - ch_trim_json_multiqc = FASTQ_TRIM_FASTP_FASTQC.out.trim_json + ch_fastp_json_multiqc = FASTQ_TRIM_FASTP_FASTQC.out.trim_json ch_versions = ch_versions.mix(FASTQ_TRIM_FASTP_FASTQC.out.versions) } @@ -527,7 +527,8 @@ workflow BACASS { ch_multiqc_custom_methods_description.ifEmpty([]), ch_collated_versions.ifEmpty([]), ch_fastqc_raw_multiqc.collect{it[1]}.ifEmpty([]), - ch_trim_json_multiqc.collect{it[1]}.ifEmpty([]), + ch_fastqc_trim_multiqc.collect{it[1]}.ifEmpty([]), + ch_fastp_json_multiqc.collect{it[1]}.ifEmpty([]), ch_nanoplot_txt_multiqc.collect{it[1]}.ifEmpty([]), ch_porechop_log_multiqc.collect{it[1]}.ifEmpty([]), ch_pycoqc_multiqc.collect{it[1]}.ifEmpty([]), From b308a95e28c38c4f2a24a2a319939951877c9856 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 13 Sep 2024 17:37:40 +0200 Subject: [PATCH 28/70] update multiqc config files to arrange preprocessing sections --- assets/multiqc_config.yml | 21 +++++++++++++++++++++ assets/multiqc_config_hybrid.yml | 5 +++++ assets/multiqc_config_short.yml | 5 +++++ 3 files changed, 31 insertions(+) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e647ad5..d1c1e07 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -2,6 +2,27 @@ report_comment: > This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the documentation. + + +max_table_rows: 10000 + +module_order: + - fastqc: + name: "PREPROCESS: FastQC (raw reads)" + info: "This section of the report shows FastQC results for the raw reads before adapter trimming." + path_filters: + - "./fastqc/*.zip" + - fastqc: + name: "PREPROCESS: FastQC (trimmed reads)" + info: "This section of the report shows FastQC results for the processed and trimmed reads." + path_filters: + - "./fastqc_trim/*.zip" + - fastp: + name: "PREPROCESS: fastp (adapter trimming)" + info: "This section of the report shows fastp results for reads after adapter and quality trimming." + path_filters: + - "./fastp/*.json" + report_section_order: "nf-core-bacass-methods-description": order: -1000 diff --git a/assets/multiqc_config_hybrid.yml b/assets/multiqc_config_hybrid.yml index 4c03626..190f5a6 100644 --- a/assets/multiqc_config_hybrid.yml +++ b/assets/multiqc_config_hybrid.yml @@ -28,6 +28,11 @@ module_order: info: "This section of the report shows FastQC results for the raw reads before adapter trimming." path_filters: - "./fastqc/*.zip" + - fastqc: + name: "PREPROCESS: FastQC (trimmed reads)" + info: "This section of the report shows FastQC results for the processed and trimmed reads." + path_filters: + - "./fastqc_trim/*.zip" - fastp: name: "PREPROCESS: fastp (adapter trimming)" info: "This section of the report shows fastp results for reads after adapter and quality trimming." diff --git a/assets/multiqc_config_short.yml b/assets/multiqc_config_short.yml index 2ce2eca..fdb1563 100644 --- a/assets/multiqc_config_short.yml +++ b/assets/multiqc_config_short.yml @@ -25,6 +25,11 @@ module_order: info: "This section of the report shows FastQC results for the raw reads before adapter trimming." path_filters: - "./fastqc/*.zip" + - fastqc: + name: "PREPROCESS: FastQC (trimmed reads)" + info: "This section of the report shows FastQC results for the processed and trimmed reads." + path_filters: + - "./fastqc_trim/*.zip" - fastp: name: "PREPROCESS: fastp (adapter trimming)" info: "This section of the report shows fastp results for reads after adapter and quality trimming." From 235bf18e1ce327435de5982f767374580e9198f1 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 13 Sep 2024 17:45:43 +0200 Subject: [PATCH 29/70] update changelog #166 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ad1c58c..deb9df0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- [#166](https://github.com/nf-core/bacass/pull/166) Added FastQC after-trimming section to MultiQC report. + ### `Fixed` - [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files. From 7842632882d5d805b28daf890e6a9df3decbc17b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 13 Sep 2024 17:46:10 +0200 Subject: [PATCH 30/70] fix prettier #166 --- assets/multiqc_config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d1c1e07..6f6ef07 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,7 +3,6 @@ report_comment: > analysis pipeline. For information about how to interpret these results, please see the documentation. - max_table_rows: 10000 module_order: From 3045163cc61ff7727f1782127d1a6bf3fb02361d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 10 Sep 2024 16:29:26 +0200 Subject: [PATCH 31/70] remove prams.save_merged from this pipeline --- conf/modules.config | 6 ------ nextflow.config | 1 - nextflow_schema.json | 4 ---- workflows/bacass.nf | 2 +- 4 files changed, 1 insertion(+), 12 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 064f4a2..0324168 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -278,12 +278,6 @@ if (!params.skip_fastp) { mode: params.publish_dir_mode, pattern: "*.fail.fastq.gz", enabled: params.save_trimmed_fail - ], - [ - path: { "${params.outdir}/trimming/shortreads" }, - mode: params.publish_dir_mode, - pattern: "*.merged.fastq.gz", - enabled: params.save_merged ] ] } diff --git a/nextflow.config b/nextflow.config index ad40756..a312f4c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,6 @@ params { fastp_args = "" save_trimmed = false save_trimmed_fail = false - save_merged = false // Contamination_screening kraken2db = '' diff --git a/nextflow_schema.json b/nextflow_schema.json index a058d28..610ec52 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -54,10 +54,6 @@ "type": "boolean", "description": "save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`" }, - "save_merged": { - "type": "boolean", - "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`. This option enables read merging and saves all merged reads to a file ending in `*.merged.fastq.gz`; these reads will be won't be passed to the assembly process." - }, "skip_fastqc": { "type": "boolean", "description": "Skip FastQC" diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 3aeb476..270aabb 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -133,7 +133,7 @@ workflow BACASS { ch_shortreads, [], params.save_trimmed_fail, - params.save_merged, + [], params.skip_fastp, params.skip_fastqc ) From 8adff80adc51ec725556eab6e28bd864d343ba49 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 17 Sep 2024 12:04:20 +0200 Subject: [PATCH 32/70] update CHANGELOG in #167 --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index deb9df0..2081c65 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,8 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#167](https://github.com/nf-core/bacass/pull/167) Remove params.save_merged as merged reads are not used in downstream analysis. - [#159](https://github.com/nf-core/bacass/pull/159) Updated Kmerfinder module and increased memory. -- [#150](https://github.com/nf-core/bacass/pull/150) Replace local unicycler module with nf-core module + bump version +- [#150](https://github.com/nf-core/bacass/pull/150) Replace local unicycler module with nf-core module + bump version. ### `Added` From 37488ee5ef6c342e99b2e1e2233de653804f4338 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 17 Sep 2024 12:56:19 +0200 Subject: [PATCH 33/70] fix wrong metadata in canu input channel --- workflows/bacass.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 270aabb..2846600 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -231,7 +231,7 @@ workflow BACASS { CANU ( ch_for_assembly.map { meta, reads, lr -> tuple( meta, lr ) }, params.canu_mode, - ch_for_assembly.map { meta, reads, lr -> meta.genome_size } + ch_for_assembly.map { meta, reads, lr -> meta.gsize } ) ch_assembly = ch_assembly.mix( CANU.out.assembly.dump(tag: 'canu') ) ch_versions = ch_versions.mix(CANU.out.versions) From a65648e428a2760ee22d0a40b32fb86b7f0317c9 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 17 Sep 2024 13:38:00 +0200 Subject: [PATCH 34/70] updated changelog in #168 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2081c65..ab4eeef 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#168](https://github.com/nf-core/bacass/pull/168) Fix wrong metadata in canu input channel. - [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files. - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database. From 8bf71a8dd8b738629f6b010bd9dd3a78fe689581 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 17 Sep 2024 15:10:44 +0200 Subject: [PATCH 35/70] fixed input channel to minimap2_align --- workflows/bacass.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 2846600..8c1221e 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -302,8 +302,8 @@ workflow BACASS { .set { ch_for_polish } MINIMAP2_POLISH ( - ch_for_polish.map { meta, sr, lr, fasta -> tuple(meta, lr) }, - ch_for_polish.map { meta, sr, lr, fasta -> fasta }, + ch_for_polish.map { meta, sr, lr, fasta -> tuple(meta, lr) }, + ch_for_polish.map { meta, sr, lr, fasta -> tuple(meta, fasta) }, true, false, false From 663a7706f5a72942bf9fc18436c4f15f3bbbb3c6 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 18 Sep 2024 16:38:11 +0200 Subject: [PATCH 36/70] refactor longread polishing and update medaka --- modules/local/medaka/main.nf | 6 ++- workflows/bacass.nf | 97 ++++++++++++++++++++---------------- 2 files changed, 59 insertions(+), 44 deletions(-) diff --git a/modules/local/medaka/main.nf b/modules/local/medaka/main.nf index 7cc540b..656f88a 100644 --- a/modules/local/medaka/main.nf +++ b/modules/local/medaka/main.nf @@ -8,7 +8,7 @@ process MEDAKA { 'biocontainers/medaka:1.4.3--py38h130def0_0' }" input: - tuple val(meta), file(longreads), file(assembly) + tuple val(meta), path(longreads), path(assembly) output: tuple val(meta), path('*_polished_genome.fa') , emit: assembly @@ -33,9 +33,11 @@ process MEDAKA { medaka_consensus $args \ -i ${ reads_bgzip_out ?: longreads } \ -d ${ assembly_bgzip_out ?: assembly } \ - -o "${prefix}_polished_genome.fa" \ + -o "${prefix}_out" \ -t $task.cpus + mv ${prefix}_out/* . + mv consensus.fasta ${prefix}_polished_genome.fa cat <<-END_VERSIONS > versions.yml "${task.process}": medaka: \$( medaka --version 2>&1 | sed 's/medaka //g' ) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 8c1221e..e339689 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -294,51 +294,64 @@ workflow BACASS { } // - // MODULE: Nanopolish, polishes assembly using FAST5 files - should take either miniasm, canu, or unicycler consensus sequence + // SUBWORKFLOW: Long reads polishing. Uses medaka or Nanopolish (this last requires Fast5 files available in input samplesheet). // - if ( !params.skip_polish && params.assembly_type == 'long' && params.polish_method != 'medaka' ) { + if ( (params.assembly_type != 'short' && !params.skip_polish) || ( params.assembly_type != 'short' && params.polish_method) ){ + // Set channel for polishing long reads ch_for_assembly .join( ch_assembly ) - .set { ch_for_polish } - - MINIMAP2_POLISH ( - ch_for_polish.map { meta, sr, lr, fasta -> tuple(meta, lr) }, - ch_for_polish.map { meta, sr, lr, fasta -> tuple(meta, fasta) }, - true, - false, - false - ) - ch_versions = ch_versions.mix(MINIMAP2_POLISH.out.versions) - - SAMTOOLS_INDEX ( - MINIMAP2_POLISH.out.bam.dump(tag: 'samtools_sort') - ) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) - - ch_for_polish // tuple val(meta), val(reads), file(longreads), file(assembly) - .join( MINIMAP2_POLISH.out.bam ) // tuple val(meta), file(bam) - .join( SAMTOOLS_INDEX.out.bai ) // tuple val(meta), file(bai) - .join( ch_fast5 ) // tuple val(meta), file(fast5) - .set { ch_for_nanopolish } // tuple val(meta), val(reads), file(longreads), file(assembly), file(bam), file(bai), file(fast5) - - // TODO: 'nanopolish index' couldn't be tested. No fast5 provided in test datasets. - NANOPOLISH ( - ch_for_nanopolish.dump(tag: 'into_nanopolish') - ) - ch_versions = ch_versions.mix(NANOPOLISH.out.versions) - } - - // - // MODULE: Medaka, polishes assembly - should take either miniasm, canu, or unicycler consensus sequence - // - if ( !params.skip_polish && params.assembly_type == 'long' && params.polish_method == 'medaka' ) { - ch_for_assembly - .join( ch_assembly ) - .map { meta, sr, lr, assembly -> tuple(meta, lr, assembly) } - .set { ch_for_medaka } - - MEDAKA ( ch_for_medaka.dump(tag: 'into_medaka') ) - ch_versions = ch_versions.mix(MEDAKA.out.versions) + .set { ch_polish_long } // channel: [ val(meta), path(sr), path(lr), path(fasta) ] + if (params.polish_method == 'medaka'){ + // + // MODULE: Medaka, polishes assembly - should take either miniasm, canu, or unicycler consensus sequence + // + ch_polish_long + .map { meta, sr, lr, fasta -> tuple(meta, lr, fasta) } + .set { ch_for_medaka } + MEDAKA ( ch_for_medaka.dump(tag: 'into_medaka') ) + ch_assembly = ch_assembly.mix( MEDAKA.out.assembly ) + ch_versions = ch_versions.mix(MEDAKA.out.versions) + } else if (params.polish_method == 'nanopolish') { + // + // MODULE: Nanopolish, polishes assembly using FAST5 files + // + if (!ch_fast5){ + log.error "ERROR: FAST5 files are required for Nanopolish but none were provided. Please supply FAST5 files or choose another polishing method. Available options are: medaka, nanopolish" + } else { + // + // MODULE: Minimap2 polish + // + MINIMAP2_POLISH ( + ch_polish_long.map { meta, sr, lr, fasta -> tuple(meta, lr) }, + ch_polish_long.map { meta, sr, lr, fasta -> tuple(meta, fasta) }, + true, + false, + false + ) + ch_versions = ch_versions.mix(MINIMAP2_POLISH.out.versions) + // + // MODULE: Samtools index + // + SAMTOOLS_INDEX ( + MINIMAP2_POLISH.out.bam.dump(tag: 'samtools_sort') + ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + // + // MODULE: Nanopolish + // + ch_polish_long // tuple val(meta), val(reads), file(longreads), file(assembly) + .join( MINIMAP2_POLISH.out.bam ) // tuple val(meta), file(bam) + .join( SAMTOOLS_INDEX.out.bai ) // tuple val(meta), file(bai) + .join( ch_fast5 ) // tuple val(meta), file(fast5) + .set { ch_for_nanopolish } // tuple val(meta), val(reads), file(longreads), file(assembly), file(bam), file(bai), file(fast5) + // TODO: 'nanopolish index' couldn't be tested. No fast5 provided in test datasets. + NANOPOLISH ( + ch_for_nanopolish.dump(tag: 'into_nanopolish') + ) + ch_assembly = ch_assembly.mix( NANOPOLISH.out.assembly ) + ch_versions = ch_versions.mix( NANOPOLISH.out.versions ) + } + } } // From 92bcfdecee9a2de7be0675d316e21a082d600cbf Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 18 Sep 2024 16:38:47 +0200 Subject: [PATCH 37/70] add condition to run miniasm on long/hybrid mode only --- workflows/bacass.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index e339689..4b2b0ed 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -240,7 +240,7 @@ workflow BACASS { // // MODULE: Miniasm, genome assembly, long reads // - if ( params.assembler == 'miniasm' ) { + if ( params.assembly_type != 'short' && params.assembler == 'miniasm' ) { MINIMAP2_ALIGN ( ch_for_assembly.map{ meta,sr,lr -> tuple(meta,lr) }, [[:],[]], @@ -280,6 +280,8 @@ workflow BACASS { ) ch_assembly = ch_assembly.mix( RACON.out.improved_assembly.dump(tag: 'miniasm') ) ch_versions = ch_versions.mix( RACON.out.versions ) + } else if (params.assembly_type == 'short' && params.assembler == 'miniasm') { + exit("Selected assembler ${params.assembler} cannot run on short reads") } // From fc6c0b91bbfbe067bd6317e1b13c2272052e446b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 20 Sep 2024 16:20:35 +0200 Subject: [PATCH 38/70] Refined polishing step by 1-removing short reads; 2- selecting the polished genome for downstream analysis --- workflows/bacass.nf | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 4b2b0ed..9f70e78 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -302,16 +302,14 @@ workflow BACASS { // Set channel for polishing long reads ch_for_assembly .join( ch_assembly ) - .set { ch_polish_long } // channel: [ val(meta), path(sr), path(lr), path(fasta) ] + .map { meta, sr, lr, fasta -> tuple(meta, lr, fasta) } + .set { ch_polish_long } // channel: [ val(meta), path(lr), path(fasta) ] if (params.polish_method == 'medaka'){ // // MODULE: Medaka, polishes assembly - should take either miniasm, canu, or unicycler consensus sequence // - ch_polish_long - .map { meta, sr, lr, fasta -> tuple(meta, lr, fasta) } - .set { ch_for_medaka } - MEDAKA ( ch_for_medaka.dump(tag: 'into_medaka') ) - ch_assembly = ch_assembly.mix( MEDAKA.out.assembly ) + MEDAKA ( ch_polish_long ) + ch_assembly = MEDAKA.out.assembly ch_versions = ch_versions.mix(MEDAKA.out.versions) } else if (params.polish_method == 'nanopolish') { // @@ -324,8 +322,8 @@ workflow BACASS { // MODULE: Minimap2 polish // MINIMAP2_POLISH ( - ch_polish_long.map { meta, sr, lr, fasta -> tuple(meta, lr) }, - ch_polish_long.map { meta, sr, lr, fasta -> tuple(meta, fasta) }, + ch_polish_long.map { meta, lr, fasta -> tuple(meta, lr) }, + ch_polish_long.map { meta, lr, fasta -> tuple(meta, fasta) }, true, false, false @@ -350,7 +348,7 @@ workflow BACASS { NANOPOLISH ( ch_for_nanopolish.dump(tag: 'into_nanopolish') ) - ch_assembly = ch_assembly.mix( NANOPOLISH.out.assembly ) + ch_assembly = NANOPOLISH.out.assembly ch_versions = ch_versions.mix( NANOPOLISH.out.versions ) } } From c5c32d5593a8878ab75cc9e911177b3c56fb337f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 20 Sep 2024 16:21:33 +0200 Subject: [PATCH 39/70] restricted the polishing step to long reads mode --- workflows/bacass.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 9f70e78..17c3573 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -298,7 +298,7 @@ workflow BACASS { // // SUBWORKFLOW: Long reads polishing. Uses medaka or Nanopolish (this last requires Fast5 files available in input samplesheet). // - if ( (params.assembly_type != 'short' && !params.skip_polish) || ( params.assembly_type != 'short' && params.polish_method) ){ + if ( (params.assembly_type == 'long' && !params.skip_polish) || ( params.assembly_type != 'short' && params.polish_method) ){ // Set channel for polishing long reads ch_for_assembly .join( ch_assembly ) From 0917bda1c8cd13ec6a16905a57ca55d0b57e2083 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 23 Sep 2024 09:15:40 +0200 Subject: [PATCH 40/70] update changelog in #169 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ab4eeef..923df4d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#169](https://github.com/nf-core/bacass/pull/169) Refactored long-reads polishing step. - [#167](https://github.com/nf-core/bacass/pull/167) Remove params.save_merged as merged reads are not used in downstream analysis. - [#159](https://github.com/nf-core/bacass/pull/159) Updated Kmerfinder module and increased memory. - [#150](https://github.com/nf-core/bacass/pull/150) Replace local unicycler module with nf-core module + bump version. @@ -17,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel. - [#168](https://github.com/nf-core/bacass/pull/168) Fix wrong metadata in canu input channel. - [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files. - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel. From db3eb59762dcdd20ce5f71746fdadd3fed2c77b6 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 8 Oct 2024 12:28:58 +0000 Subject: [PATCH 41/70] Template update for nf-core/tools version 3.0.0 --- .editorconfig | 4 + .github/CONTRIBUTING.md | 10 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- .github/workflows/awsfulltest.yml | 23 +- .github/workflows/ci.yml | 17 +- .github/workflows/download_pipeline.yml | 53 ++- .github/workflows/linting.yml | 23 +- .github/workflows/linting_comment.yml | 2 +- .github/workflows/release-announcements.yml | 2 +- .../workflows/template_version_comment.yml | 43 ++ .gitpod.yml | 7 +- .nf-core.yml | 21 +- .pre-commit-config.yaml | 2 +- .prettierignore | 1 + CHANGELOG.md | 2 +- CITATIONS.md | 4 +- README.md | 5 +- assets/schema_input.json | 2 +- conf/base.config | 34 +- conf/igenomes_ignored.config | 9 + conf/modules.config | 1 - conf/test.config | 13 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/output.md | 11 +- docs/usage.md | 12 +- main.nf | 10 +- modules.json | 12 +- modules/nf-core/fastqc/environment.yml | 2 - modules/nf-core/fastqc/main.nf | 5 +- modules/nf-core/fastqc/meta.yml | 57 +-- modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- modules/nf-core/multiqc/environment.yml | 4 +- modules/nf-core/multiqc/main.nf | 14 +- modules/nf-core/multiqc/meta.yml | 78 ++-- modules/nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 20 +- modules/nf-core/multiqc/tests/nextflow.config | 5 + nextflow.config | 148 ++++--- nextflow_schema.json | 85 +--- .../utils_nfcore_bacass_pipeline/main.nf | 56 +-- .../nf-core/utils_nextflow_pipeline/main.nf | 24 +- .../tests/nextflow.config | 2 +- .../nf-core/utils_nfcore_pipeline/main.nf | 45 ++- .../nf-core/utils_nfschema_plugin/main.nf | 46 +++ .../nf-core/utils_nfschema_plugin/meta.yml | 35 ++ .../utils_nfschema_plugin/tests/main.nf.test | 117 ++++++ .../tests/nextflow.config | 8 + .../tests/nextflow_schema.json | 8 +- .../nf-core/utils_nfvalidation_plugin/main.nf | 62 --- .../utils_nfvalidation_plugin/meta.yml | 44 --- .../tests/main.nf.test | 200 ---------- .../utils_nfvalidation_plugin/tests/tags.yml | 2 - workflows/bacass.nf | 23 +- 56 files changed, 1210 insertions(+), 808 deletions(-) create mode 100644 .github/workflows/template_version_comment.yml create mode 100644 conf/igenomes_ignored.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 modules/nf-core/multiqc/tests/nextflow.config create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/main.nf create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/meta.yml create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test create mode 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config rename subworkflows/nf-core/{utils_nfvalidation_plugin => utils_nfschema_plugin}/tests/nextflow_schema.json (95%) delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/main.nf delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test delete mode 100644 subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml diff --git a/.editorconfig b/.editorconfig index 72dda28..e105881 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,6 +11,7 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 + # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -25,9 +26,12 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset + + [/assets/email*] indent_size = unset + # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 24edde8..091001c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/bacass, the standard workflow is as 1. Check that there isn't already an issue about your idea in the [nf-core/bacass issues](https://github.com/nf-core/bacass/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/bacass repository](https://github.com/nf-core/bacass) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,7 +86,7 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 99d5b0f..a7d7f39 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/baca - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e11165d..60fbcf4 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,33 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/bacass' + if: github.repository == 'nf-core/bacass' && github.event.review.state == 'approved' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + run: | + JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' + CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') + test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f44d81d..a1eda2e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,6 +7,7 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false @@ -24,7 +25,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" steps: - name: Check out pipeline code @@ -38,9 +39,21 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data + - name: Run pipeline with test data (docker) # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + + - name: Run pipeline with test data (singularity) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results + if: "${{ github.base_ref == 'master' }}" + + - name: Run pipeline with test data (conda) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results + if: "${{ github.base_ref == 'master' }}" diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d64..713dc3e 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -54,33 +56,64 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe8..b882838 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,32 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yaml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23..42e519b 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf..c6ba35d 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 0000000..9dea41f --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,43 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + + - name: Read template version from .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.0.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: pip list --outdated | grep nf-core + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + ## :warning: Newer version of the nf-core template is available. + + Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + Please update your pipeline to the latest version. + + For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitpod.yml b/.gitpod.yml index 105a182..4611863 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,14 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code + #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code - charliermarsh.ruff # Code linter Ruff diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a7..4149900 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,21 @@ +bump_version: null +lint: + files_exist: + - conf/igenomes.config + nextflow_config: + - config_defaults: + - params.dfast_config +nf_core_version: 3.0.0 +org_path: null repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: Andreas Wilm, Alexander Peltzer + description: Simple bacterial assembly and annotation + force: false + is_nfcore: true + name: bacass + org: nf-core + outdir: . + skip_features: null + version: 2.4.0dev +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1d..9e9f0e1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/.prettierignore b/.prettierignore index 437d763..610e506 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,3 +1,4 @@ + email_template.html adaptivecard.json slackreport.json diff --git a/CHANGELOG.md b/CHANGELOG.md index ef80463..86bfaf2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.3.0dev - [date] +## v2.4.0dev - [date] Initial release of nf-core/bacass, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 79501bc..69cdc73 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,11 +12,11 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index b04b8d1..8d92a18 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/bacass/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/bacass/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/bacass/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -67,8 +67,7 @@ nextflow run nf-core/bacass \ ``` > [!WARNING] -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/bacass/usage) and the [parameter documentation](https://nf-co.re/bacass/parameters). diff --git a/assets/schema_input.json b/assets/schema_input.json index 80a9231..f221d75 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/bacass/master/assets/schema_input.json", "title": "nf-core/bacass pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/conf/base.config b/conf/base.config index ae9bd1f..71dc2a4 100644 --- a/conf/base.config +++ b/conf/base.config @@ -11,9 +11,9 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -27,30 +27,30 @@ process { // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 0000000..b4034d8 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index d203d2b..d266a38 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -21,7 +21,6 @@ process { withName: FASTQC { ext.args = '--quiet' } - withName: 'MULTIQC' { ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ diff --git a/conf/test.config b/conf/test.config index 686fa02..3d189cd 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Give any required params for the test so that command line flags are not needed diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 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zXwhtT%ei{n#FzEH|C;yZ>+$!u_x#*+`=L8{b9SH^9&27u3G_Gxqxe`L2UJtdxghk z&-wzDFvLvW{chK5u3{n6GSKKy!P&C6w^IFpbD0bcp^A{{2lcLh_DXj@ybtYvc^;(2 M)78&qol`;+0Fu7JivR!s diff --git a/docs/output.md b/docs/output.md index 87f26cc..0feb2b1 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,6 +14,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline + - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC @@ -29,16 +30,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: - ### MultiQC
diff --git a/docs/usage.md b/docs/usage.md index bb10023..d80916b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -85,9 +85,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/bacass -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' @@ -199,14 +199,6 @@ See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs). -## Azure Resource Requests - -To be used with the `azurebatch` profile by specifying the `-profile azurebatch`. -We recommend providing a compute `params.vm_type` of `Standard_D16_v3` VMs by default but these options can be changed if required. - -Note that the choice of VM size depends on your quota and the overall workload during the analysis. -For a thorough list, please refer the [Azure Sizes for virtual machines in Azure](https://docs.microsoft.com/en-us/azure/virtual-machines/sizes). - ## Running in the background Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished. diff --git a/main.nf b/main.nf index 4111c7c..6402f62 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,7 +18,6 @@ nextflow.enable.dsl = 2 include { BACASS } from './workflows/bacass' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_bacass_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_bacass_pipeline' - include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_bacass_pipeline' /* @@ -56,10 +53,8 @@ workflow NFCORE_BACASS { BACASS ( samplesheet ) - emit: multiqc_report = BACASS.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -70,27 +65,24 @@ workflow NFCORE_BACASS { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // NFCORE_BACASS ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index 3a43051..dcbf627 100644 --- a/modules.json +++ b/modules.json @@ -7,12 +7,12 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -21,17 +21,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38..691d4c7 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c8..d8989f4 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e..4827da7 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4..e9d79a0 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c31..d5db309 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb6..f1cd99b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352..b9ccebd 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc3..b16c187 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242..33316a7 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd80..b779e46 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 0000000..c537a6a --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/nextflow.config b/nextflow.config index 6ed459c..d2b37ed 100644 --- a/nextflow.config +++ b/nextflow.config @@ -16,7 +16,6 @@ params { genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false - // MultiQC options multiqc_config = null multiqc_title = null @@ -33,48 +32,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' - // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true + } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/bacass custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/bacass.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/bacass profiles: ${params.custom_config_base}/pipeline/bacass.config") -} profiles { debug { dumpHashes = true @@ -89,7 +66,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -178,25 +155,23 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/bacass custom profiles from different institutions. +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null" +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -208,8 +183,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +set -C # No clobber - prevent output redirection from overwriting files. +""" // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false @@ -238,43 +220,47 @@ manifest { homePage = 'https://github.com/nf-core/bacass' description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '2.3.0dev' + nextflowVersion = '!>=24.04.2' + version = '2.4.0dev' doi = '' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} + +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m +\033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m + \033[0;32m`._,._,\'\033[0m +\033[0;35m ${manifest.name} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} +* The nf-core framework + https://doi.org/10.1038/s41587-020-0439-x -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +* Software dependencies + https://github.com/${manifest.name}/blob/master/CITATIONS.md +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' + diff --git a/nextflow_schema.json b/nextflow_schema.json index 9fcff48..6c25907 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/bacass/master/nextflow_schema.json", "title": "nf-core/bacass pipeline parameters", "description": "Simple bacterial assembly and annotation", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -71,6 +71,14 @@ "fa_icon": "fas fa-ban", "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -122,41 +130,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fab fa-acquisitions-incorporated", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -164,12 +137,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -245,27 +212,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -278,19 +224,16 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" - }, - { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf index 5d43bdd..68dab7d 100644 --- a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf @@ -8,17 +8,14 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* ======================================================================================== @@ -30,7 +27,6 @@ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -51,20 +47,16 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) + // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) + // // Check config provided to the pipeline @@ -80,8 +72,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // + Channel - .fromSamplesheet("input") + .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) .map { meta, fastq_1, fastq_2 -> if (!fastq_2) { @@ -91,8 +84,8 @@ workflow PIPELINE_INITIALISATION { } } .groupTuple() - .map { - validateInputSamplesheet(it) + .map { samplesheet -> + validateInputSamplesheet(samplesheet) } .map { meta, fastqs -> @@ -117,13 +110,13 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML + outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -131,11 +124,18 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -165,7 +165,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -197,7 +197,6 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // @@ -239,8 +238,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +262,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28..28e32b2 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,10 +2,6 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) { def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') def filename = "params_${timestamp}.json" def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) @@ -102,14 +98,16 @@ def checkCondaChannels() { // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) + + required_channels_in_order.eachWithIndex { channel, index -> + if (index < required_channels_in_order.size() - 1) { + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + } } if (channels_missing | channel_priority_violation) { diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926b..a09572e 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c3..cbd8495 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,9 +2,6 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* ======================================================================================== SUBWORKFLOW DEFINITION @@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE { // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + @@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") + def manifest_doi = workflow.manifest.doi.tokenize(",") // Using a loop to handle multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + manifest_doi.each { doi_ref -> + temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" + } return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + @@ -84,7 +83,7 @@ def workflowCitation() { // Generate workflow version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +101,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } return yaml.dumpAsMap(versions).trim() } @@ -124,7 +123,7 @@ def workflowVersionToYAML() { def softwareVersionsToYAML(ch_versions) { return ch_versions .unique() - .map { processVersionsFromYAML(it) } + .map { version -> processVersionsFromYAML(version) } .unique() .mix(Channel.of(workflowVersionToYAML())) } @@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { + summary_params.keySet().each { group -> def group_params = summary_params.get(group) // This gets the parameters of that particular group if (group_params) { summary_section += "

    $group

    \n" summary_section += "
    \n" - for (param in group_params.keySet()) { + group_params.keySet().sort().each { param -> summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" } summary_section += "
    \n" } } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" @@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi } def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } @@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } @@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); output_tf.delete() } @@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" @@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { + summary_params.keySet().sort().each { group -> summary << summary_params[group] } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 0000000..4994303 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 0000000..f7d9f02 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 0000000..842dc43 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 0000000..0907ac5 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c..331e0d2 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b0..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cff..0000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/bacass.nf b/workflows/bacass.nf index eb5b309..297525d 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -3,10 +3,9 @@ IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - include { FASTQC } from '../modules/nf-core/fastqc/main' include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryMap } from 'plugin/nf-schema' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_bacass_pipeline' @@ -21,12 +20,10 @@ workflow BACASS { take: ch_samplesheet // channel: samplesheet read in from --input - main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() - // // MODULE: Run FastQC // @@ -42,11 +39,12 @@ workflow BACASS { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } + // // MODULE: MultiQC // @@ -59,18 +57,19 @@ workflow BACASS { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() + summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - + ch_multiqc_files = ch_multiqc_files.mix( + ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) ch_methods_description = Channel.value( methodsDescriptionText(ch_multiqc_custom_methods_description)) - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) ch_multiqc_files = ch_multiqc_files.mix( ch_methods_description.collectFile( @@ -83,12 +82,14 @@ workflow BACASS { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) - emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + emit:multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] + } /* From 75ef2ec10269a562563635b41e9b44c61f8abe56 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 9 Oct 2024 11:01:33 +0000 Subject: [PATCH 42/70] Template update for nf-core/tools version 3.0.1 --- .editorconfig | 4 - .github/CONTRIBUTING.md | 2 +- .github/workflows/awsfulltest.yml | 6 +- .github/workflows/linting.yml | 4 +- .nf-core.yml | 2 +- .prettierignore | 1 - docs/output.md | 1 - modules.json | 6 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- .../nf-core/multiqc/tests/main.nf.test.snap | 26 +- nextflow.config | 8 +- .../utils_nfcore_bacass_pipeline/main.nf | 12 +- .../nf-core/utils_nextflow_pipeline/main.nf | 46 ++- .../nf-core/utils_nfcore_pipeline/main.nf | 279 ++++++++++-------- 15 files changed, 209 insertions(+), 194 deletions(-) diff --git a/.editorconfig b/.editorconfig index e105881..72dda28 100644 --- a/.editorconfig +++ b/.editorconfig @@ -11,7 +11,6 @@ indent_style = space [*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 - # These files are edited and tested upstream in nf-core/modules [/modules/nf-core/**] charset = unset @@ -26,12 +25,9 @@ insert_final_newline = unset trim_trailing_whitespace = unset indent_style = unset - - [/assets/email*] indent_size = unset - # ignore python and markdown [*.{py,md}] indent_style = unset diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 091001c..07c8e1d 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -90,7 +90,7 @@ Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 60fbcf4..597d186 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,16 +14,18 @@ on: jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/bacass' && github.event.review.state == 'approved' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/bacass' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: - uses: octokit/request-action@v2.x id: check_approvals with: - route: GET /repos/${{ github.repository }}/pulls/${{ github.event.review.number }}/reviews + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - id: test_variables + if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b882838..a502573 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -42,10 +42,10 @@ jobs: architecture: "x64" - name: read .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: pietrobolcato/action-read-yaml@1.1.0 id: read_yml with: - config: ${{ github.workspace }}/.nf-core.yaml + config: ${{ github.workspace }}/.nf-core.yml - name: Install dependencies run: | diff --git a/.nf-core.yml b/.nf-core.yml index 4149900..b424086 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -5,7 +5,7 @@ lint: nextflow_config: - config_defaults: - params.dfast_config -nf_core_version: 3.0.0 +nf_core_version: 3.0.1 org_path: null repository_type: pipeline template: diff --git a/.prettierignore b/.prettierignore index 610e506..437d763 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,4 +1,3 @@ - email_template.html adaptivecard.json slackreport.json diff --git a/docs/output.md b/docs/output.md index 0feb2b1..58328ac 100644 --- a/docs/output.md +++ b/docs/output.md @@ -14,7 +14,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [FastQC](#fastqc) - Raw read QC - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution ### FastQC diff --git a/modules.json b/modules.json index dcbf627..57aba29 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", + "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", + "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b..6f5b867 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index b9ccebd..9724d2f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index b779e46..2fcbb5f 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-10-02T17:52:09.185842" } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index d2b37ed..85f547d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,10 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false + // MultiQC options multiqc_config = null multiqc_title = null @@ -36,6 +38,7 @@ params { show_hidden = false version = false pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/' + // Config options config_profile_name = null config_profile_description = null @@ -44,9 +47,9 @@ params { custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null + // Schema validation default options validate_params = true - } // Load base.config by default for all pipelines @@ -161,6 +164,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load nf-core/bacass custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null" + // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled // Set to your registry if you have a mirror of containers @@ -172,6 +176,7 @@ charliecloud.registry = 'quay.io' // Load igenomes.config if required includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -263,4 +268,3 @@ validation { // Load modules.config for DSL2 module specific options includeConfig 'conf/modules.config' - diff --git a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf index 68dab7d..9d079a6 100644 --- a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf @@ -18,9 +18,9 @@ include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { @@ -99,9 +99,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -147,9 +147,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 28e32b2..2b0dc67 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -72,11 +71,11 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() @@ -91,9 +90,14 @@ def checkCondaChannels() { try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present @@ -106,19 +110,13 @@ def checkCondaChannels() { required_channels_in_order.eachWithIndex { channel, index -> if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) } } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn( + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index cbd8495..b78273c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE { def checkConfigProvided() { def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -49,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -70,13 +68,7 @@ def workflowCitation() { manifest_doi.each { doi_ref -> temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // @@ -102,7 +94,7 @@ def getWorkflowVersion() { // def processVersionsFromYAML(yaml_file) { def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -121,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { version -> processVersionsFromYAML(version) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - summary_params.keySet().each { group -> - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

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

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() @@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) { def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } From 4a10f2ad990faa4e694649640dcbcdd849490897 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 11 Oct 2024 12:28:32 +0000 Subject: [PATCH 43/70] Template update for nf-core/tools version 3.0.2 --- .github/workflows/ci.yml | 60 +++++++++++++------ .../workflows/template_version_comment.yml | 21 ++++--- .gitignore | 1 + .nf-core.yml | 2 +- main.nf | 2 +- modules.json | 6 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 4 +- .../utils_nfcore_bacass_pipeline/main.nf | 4 +- .../nf-core/utils_nextflow_pipeline/main.nf | 30 +++++----- .../nf-core/utils_nfcore_pipeline/main.nf | 10 ++-- workflows/bacass.nf | 2 - 12 files changed, 86 insertions(+), 58 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a1eda2e..e1a51cd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,6 +11,8 @@ on: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -18,7 +20,7 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" # Only run on push if this is the nf-core dev branch (merged PRs) if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/bacass') }}" runs-on: ubuntu-latest @@ -27,33 +29,57 @@ jobs: NXF_VER: - "24.04.2" - "latest-everything" + profile: + - "conda" + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - name: Set up Apptainer + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-apptainer@main - - name: Run pipeline with test data (docker) - # TODO nf-core: You can customise CI pipeline run tests as required - # For example: adding multiple test runs with different parameters - # Remember that you can parallelise this by using strategy.matrix + - name: Set up Singularity + if: matrix.profile == 'singularity' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Set up Miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 + with: + miniconda-version: "latest" + auto-update-conda: true + conda-solver: libmamba + channels: conda-forge,bioconda - - name: Run pipeline with test data (singularity) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: Set up Conda + if: matrix.profile == 'conda' run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results - if: "${{ github.base_ref == 'master' }}" + echo $(realpath $CONDA)/condabin >> $GITHUB_PATH + echo $(realpath python) >> $GITHUB_PATH + + - name: Clean up Disk space + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data (conda) - # TODO nf-core: You can customise CI pipeline run tests as required + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results - if: "${{ github.base_ref == 'master' }}" + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index 9dea41f..e8aafe4 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -10,9 +10,11 @@ jobs: steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} - name: Read template version from .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: nichmor/minimal-read-yaml@v0.0.2 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml @@ -24,20 +26,21 @@ jobs: - name: Check nf-core outdated id: nf_core_outdated - run: pip list --outdated | grep nf-core + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} - name: Post nf-core template version comment uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 if: | - ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core' + contains(env.OUTPUT, 'nf-core') with: repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} allow-repeats: false message: | - ## :warning: Newer version of the nf-core template is available. - - Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. - Please update your pipeline to the latest version. - - For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). # diff --git a/.gitignore b/.gitignore index 5124c9a..a42ce01 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,4 @@ results/ testing/ testing* *.pyc +null/ diff --git a/.nf-core.yml b/.nf-core.yml index b424086..b089730 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -5,7 +5,7 @@ lint: nextflow_config: - config_defaults: - params.dfast_config -nf_core_version: 3.0.1 +nf_core_version: 3.0.2 org_path: null repository_type: pipeline template: diff --git a/main.nf b/main.nf index 6402f62..8f1827a 100644 --- a/main.nf +++ b/main.nf @@ -76,7 +76,7 @@ workflow { params.outdir, params.input ) - + // // WORKFLOW: Run main workflow // diff --git a/modules.json b/modules.json index 57aba29..387c0ed 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] } } @@ -21,12 +21,12 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 9724d2f..cc0643e 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -52,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/nextflow.config b/nextflow.config index 85f547d..5bb8caa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -254,10 +254,10 @@ validation { """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework - https://doi.org/10.1038/s41587-020-0439-x + https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/${manifest.name}/blob/master/CITATIONS.md """ } summary { diff --git a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf index 9d079a6..c3d50d2 100644 --- a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf @@ -47,7 +47,6 @@ workflow PIPELINE_INITIALISATION { workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1 ) - // // Validate parameters and generate parameter summary to stdout // @@ -56,7 +55,6 @@ workflow PIPELINE_INITIALISATION { validate_params, null ) - // // Check config provided to the pipeline @@ -64,6 +62,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -110,7 +109,6 @@ workflow PIPELINE_COMPLETION { email // string: email address email_on_fail // string: email address sent on pipeline failure plaintext_email // boolean: Send plain-text email instead of HTML - outdir // path: Path to output directory where results will be published monochrome_logs // boolean: Disable ANSI colour codes in log output hook_url // string: hook URL for notifications diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67..0fcbf7b 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -106,17 +106,19 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273c..5cb7baf 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 297525d..d42bdeb 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -57,13 +57,11 @@ workflow BACASS { Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty() - summary_params = paramsSummaryMap( workflow, parameters_schema: "nextflow_schema.json") ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) ch_multiqc_files = ch_multiqc_files.mix( ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) From efbade0b9e96a24d1446376bec880f922180aab9 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 11 Oct 2024 16:34:53 +0200 Subject: [PATCH 44/70] mv fastp to older version due to inconsistency with fastq_trim_fastp_fastqc subworkflow --- modules.json | 8 +- modules/nf-core/fastp/environment.yml | 2 + modules/nf-core/fastp/main.nf | 21 +- modules/nf-core/fastp/meta.yml | 134 +- modules/nf-core/fastp/tests/main.nf.test | 823 ++++++---- modules/nf-core/fastp/tests/main.nf.test.snap | 1361 +++-------------- modules/nf-core/fastqc/environment.yml | 2 + modules/nf-core/fastqc/main.nf | 9 - modules/nf-core/fastqc/meta.yml | 57 +- modules/nf-core/fastqc/tests/main.nf.test | 225 +-- .../nf-core/fastqc/tests/main.nf.test.snap | 370 +---- .../nf-core/fastq_trim_fastp_fastqc/main.nf | 1 - .../nf-core/fastq_trim_fastp_fastqc/meta.yml | 2 +- 13 files changed, 852 insertions(+), 2163 deletions(-) diff --git a/modules.json b/modules.json index 0facb65..ba06f0a 100644 --- a/modules.json +++ b/modules.json @@ -28,12 +28,12 @@ }, "fastp": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["fastq_trim_fastp_fastqc"] + "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080", + "installed_by": ["fastq_trim_fastp_fastqc", "modules"] }, "fastqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080", "installed_by": ["fastq_trim_fastp_fastqc"] }, "gunzip": { @@ -113,7 +113,7 @@ "nf-core": { "fastq_trim_fastp_fastqc": { "branch": "master", - "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", + "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080", "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 26d4aca..70389e6 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,5 +1,7 @@ +name: fastp channels: - conda-forge - bioconda + - defaults dependencies: - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index e1b9f56..4fc19b7 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -10,7 +10,6 @@ process FASTP { input: tuple val(meta), path(reads) path adapter_fasta - val discard_trimmed_pass val save_trimmed_fail val save_merged @@ -19,9 +18,9 @@ process FASTP { tuple val(meta), path('*.json') , emit: json tuple val(meta), path('*.html') , emit: html tuple val(meta), path('*.log') , emit: log + path "versions.yml" , emit: versions tuple val(meta), path('*.fail.fastq.gz') , optional:true, emit: reads_fail tuple val(meta), path('*.merged.fastq.gz'), optional:true, emit: reads_merged - path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -31,8 +30,6 @@ process FASTP { 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 ? "--failed_out ${prefix}.paired.fail.fastq.gz --unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : '' - def out_fq1 = discard_trimmed_pass ?: ( meta.single_end ? "--out1 ${prefix}.fastp.fastq.gz" : "--out1 ${prefix}_1.fastp.fastq.gz" ) - def out_fq2 = discard_trimmed_pass ?: "--out2 ${prefix}_2.fastp.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') ) { @@ -62,7 +59,7 @@ process FASTP { fastp \\ --in1 ${prefix}.fastq.gz \\ - $out_fq1 \\ + --out1 ${prefix}.fastp.fastq.gz \\ --thread $task.cpus \\ --json ${prefix}.fastp.json \\ --html ${prefix}.fastp.html \\ @@ -84,8 +81,8 @@ process FASTP { fastp \\ --in1 ${prefix}_1.fastq.gz \\ --in2 ${prefix}_2.fastq.gz \\ - $out_fq1 \\ - $out_fq2 \\ + --out1 ${prefix}_1.fastp.fastq.gz \\ + --out2 ${prefix}_2.fastp.fastq.gz \\ --json ${prefix}.fastp.json \\ --html ${prefix}.fastp.html \\ $adapter_list \\ @@ -106,16 +103,14 @@ process FASTP { stub: def prefix = task.ext.prefix ?: "${meta.id}" def is_single_output = task.ext.args?.contains('--interleaved_in') || meta.single_end - def touch_reads = (discard_trimmed_pass) ? "" : (is_single_output) ? "echo '' | gzip > ${prefix}.fastp.fastq.gz" : "echo '' | gzip > ${prefix}_1.fastp.fastq.gz ; echo '' | gzip > ${prefix}_2.fastp.fastq.gz" - def touch_merged = (!is_single_output && save_merged) ? "echo '' | gzip > ${prefix}.merged.fastq.gz" : "" - def touch_fail_fastq = (!save_trimmed_fail) ? "" : meta.single_end ? "echo '' | gzip > ${prefix}.fail.fastq.gz" : "echo '' | gzip > ${prefix}.paired.fail.fastq.gz ; echo '' | gzip > ${prefix}_1.fail.fastq.gz ; echo '' | gzip > ${prefix}_2.fail.fastq.gz" + def touch_reads = is_single_output ? "${prefix}.fastp.fastq.gz" : "${prefix}_1.fastp.fastq.gz ${prefix}_2.fastp.fastq.gz" + def touch_merged = (!is_single_output && save_merged) ? "touch ${prefix}.merged.fastq.gz" : "" """ - $touch_reads - $touch_fail_fastq - $touch_merged + touch $touch_reads touch "${prefix}.fastp.json" touch "${prefix}.fastp.html" touch "${prefix}.fastp.log" + $touch_merged cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 159404d..c22a16a 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -11,100 +11,62 @@ tools: documentation: https://github.com/OpenGene/fastp doi: 10.1093/bioinformatics/bty560 licence: ["MIT"] - identifier: biotools:fastp input: - - - meta: - type: map - description: | - Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. - 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. If you wish to run interleaved paired-end data, supply as single-end data - but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. - | This can be used to use fastp for the output report only. - - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds - ending in `*.fail.fastq.gz` - - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + - meta: + type: map + description: | + Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. + 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. If you wish to run interleaved paired-end data, supply as single-end data + but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. + - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` + - save_merged: + type: boolean + description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz` output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - reads: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.fastp.fastq.gz": - type: file - description: The trimmed/modified/unmerged fastq reads - pattern: "*fastp.fastq.gz" + type: file + description: The trimmed/modified/unmerged fastq reads + pattern: "*fastp.fastq.gz" - json: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.json": - type: file - description: Results in JSON format - pattern: "*.json" + type: file + description: Results in JSON format + pattern: "*.json" - html: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.html": - type: file - description: Results in HTML format - pattern: "*.html" + type: file + description: Results in HTML format + pattern: "*.html" - log: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.log": - type: file - description: fastq log file - pattern: "*.log" + type: file + description: fastq log file + pattern: "*.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" - reads_fail: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.fail.fastq.gz": - type: file - description: Reads the failed the preprocessing - pattern: "*fail.fastq.gz" + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" - reads_merged: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.merged.fastq.gz": - type: file - description: Reads that were successfully merged - pattern: "*.{merged.fastq.gz}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: Reads that were successfully merged + pattern: "*.{merged.fastq.gz}" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test index 30dbb8a..6f1f489 100644 --- a/modules/nf-core/fastp/tests/main.nf.test +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -10,290 +10,221 @@ nextflow_process { test("test_fastp_single_end") { when { - + params { + outdir = "$outputDir" + } process { """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)" ] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { file(it[1]).getName() } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_single_end-_match") + }, + { assert snapshot(process.out.versions).match("versions_single_end") } ) } } - test("test_fastp_paired_end") { + test("test_fastp_single_end-stub") { - when { + options '-stub' + when { + params { + outdir = "$outputDir" + } process { """ adapter_fasta = [] - save_trimmed_pass = true save_trimmed_fail = false save_merged = false 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) ] + [ id:'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { - assertAll( - { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") }, - { assert snapshot( - process.out.json, - process.out.reads, - process.out.reads_fail, - process.out.reads_merged, - process.out.versions).match() } - ) - } - } - test("fastp test_fastp_interleaved") { - - config './nextflow.interleaved.config' - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] - ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false - """ - } - } - - then { assertAll( { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("paired end (151 cycles + 151 cycles)") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 162") }, - { assert process.out.reads_fail == [] }, - { assert process.out.reads_merged == [] }, - { assert snapshot( - process.out.reads, - process.out.json, - process.out.versions).match() } + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { file(it[1]).getName() } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_single_end-for_stub_match") + }, + { assert snapshot(process.out.versions).match("versions_single_end_stub") } ) } } - test("test_fastp_single_end_trim_fail") { + test("test_fastp_paired_end") { when { - - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll( - { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") }, - { assert snapshot( - process.out.json, - process.out.reads, - process.out.reads_fail, - process.out.reads_merged, - process.out.versions).match() } - ) - } - } - - test("test_fastp_paired_end_trim_fail") { - - config './nextflow.save_failed.config' - when { process { """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] - ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 162") }, - { assert snapshot( - process.out.reads, - process.out.reads_fail, - process.out.reads_merged, - process.out.json, - process.out.versions).match() } - ) - } - } - - test("test_fastp_paired_end_merged") { + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false - when { - process { - """ input[0] = Channel.of([ [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = true + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { it[1].collect { item -> file(item).getName() } } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_paired_end_match") + }, + { assert snapshot(process.out.versions).match("versions_paired_end") } ) } } - test("test_fastp_paired_end_merged_adapterlist") { + test("test_fastp_paired_end-stub") { - when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:false ], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - input[1] = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ]) - input[2] = false - input[3] = false - input[4] = true - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("
    ") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("total bases: 13683") }, - { assert snapshot( - process.out.json, - process.out.reads, - process.out.reads_fail, - process.out.reads_merged, - process.out.versions).match() } - ) - } - } - - test("test_fastp_single_end_qc_only") { + options '-stub' when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - input[1] = [] - input[2] = true - input[3] = false - input[4] = false - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll( - { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("single end (151 cycles)") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("reads passed filter: 99") }, - { assert snapshot( - process.out.json, - process.out.reads, - process.out.reads, - process.out.reads_fail, - process.out.reads_fail, - process.out.reads_merged, - process.out.reads_merged, - process.out.versions).match() } - ) - } - } - - test("test_fastp_paired_end_qc_only") { - - when { process { """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + 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] = [] - input[2] = true - input[3] = false - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -301,99 +232,114 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.html.get(0).get(1)).getText().contains("The input has little adapter percentage (~0.000000%), probably it's trimmed before.") }, - { assert path(process.out.log.get(0).get(1)).getText().contains("Q30 bases: 12281(88.3716%)") }, - { assert snapshot( - process.out.json, - process.out.reads, - process.out.reads, - process.out.reads_fail, - process.out.reads_fail, - process.out.reads_merged, - process.out.reads_merged, - process.out.versions).match() } + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { it[1].collect { item -> file(item).getName() } } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_paired_end-for_stub_match") + }, + { assert snapshot(process.out.versions).match("versions_paired_end-stub") } ) } } - test("test_fastp_single_end - stub") { - - options "-stub" + test("fastp test_fastp_interleaved") { + config './nextflow.interleaved.config' when { - - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_fastp_paired_end - stub") { - - options "-stub" - - when { - process { """ adapter_fasta = [] - save_trimmed_pass = true save_trimmed_fail = false save_merged = false 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) ] + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + 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: 162"] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("fastp test_fastp_interleaved_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { file(it[1]).getName() } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_interleaved-_match") + }, + { assert snapshot(process.out.versions).match("versions_interleaved") } ) } } - test("fastp - stub test_fastp_interleaved") { + test("fastp test_fastp_interleaved-stub") { - options "-stub" + options '-stub' config './nextflow.interleaved.config' when { + params { + outdir = "$outputDir" + } process { """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) ] ]) - input[1] = [] - input[2] = false - input[3] = false - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -401,112 +347,277 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { file(it[1]).getName() } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_interleaved-for_stub_match") + }, + { assert snapshot(process.out.versions).match("versions_interleaved-stub") } ) } } - test("test_fastp_single_end_trim_fail - stub") { - - options "-stub" + test("test_fastp_single_end_trim_fail") { when { - + params { + outdir = "$outputDir" + } process { """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + input[0] = Channel.of([ [ id:'test', single_end:true ], // meta map [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ]) - input[1] = [] - input[2] = false - input[3] = true - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { failed_read_lines.each { failed_read_line -> + { assert path(process.out.reads_fail.get(0).get(1)).linesGzip.contains(failed_read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_trim_fail_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions_single_end_trim_fail") } ) } } - test("test_fastp_paired_end_trim_fail - stub") { - - options "-stub" + test("test_fastp_paired_end_trim_fail") { config './nextflow.save_failed.config' when { + params { + outdir = "$outputDir" + } process { """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + 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] = [] - input[2] = false - input[3] = true - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 162'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { failed_read2_lines.each { 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 -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions_paired_end_trim_fail") } ) } } - test("test_fastp_paired_end_merged - stub") { - - options "-stub" + test("test_fastp_paired_end_merged") { when { + params { + outdir = "$outputDir" + } process { """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true 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] = [] - input[2] = false - input[3] = false - input[4] = true + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + def html_text = [ "
    "] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683'] + def read1_lines = [ "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { it[1].collect { item -> file(item).getName() } } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_paired_end_merged_match") + }, + { assert snapshot(process.out.versions).match("versions_paired_end_merged") } ) } } - test("test_fastp_paired_end_merged_adapterlist - stub") { + test("test_fastp_paired_end_merged-stub") { - options "-stub" + options '-stub' when { + params { + outdir = "$outputDir" + } process { """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true + 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] = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ]) - input[2] = false - input[3] = false - input[4] = true + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } @@ -514,63 +625,101 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { + assert snapshot( + ( + [process.out.reads[0][0].toString()] + // meta + process.out.reads.collect { it[1].collect { item -> file(item).getName() } } + + process.out.json.collect { file(it[1]).getName() } + + process.out.html.collect { file(it[1]).getName() } + + process.out.log.collect { file(it[1]).getName() } + + process.out.reads_fail.collect { file(it[1]).getName() } + + process.out.reads_merged.collect { file(it[1]).getName() } + ).sort() + ).match("test_fastp_paired_end_merged-for_stub_match") + }, + { assert snapshot(process.out.versions).match("versions_paired_end_merged_stub") } ) } } - test("test_fastp_single_end_qc_only - stub") { - - options "-stub" + test("test_fastp_paired_end_merged_adapterlist") { when { - process { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - input[1] = [] - input[2] = true - input[3] = false - input[4] = false - """ + params { + outdir = "$outputDir" } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("test_fastp_paired_end_qc_only - stub") { - - options "-stub" - - when { process { """ + adapter_fasta = Channel.of([ file(params.modules_testdata_base_path + 'delete_me/fastp/adapters.fasta', checkIfExists: true) ]) + save_trimmed_fail = false + save_merged = true + 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] = [] - input[2] = true - input[3] = false - input[4] = false + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged """ } } then { + def html_text = [ "
    "] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683',"--adapter_fasta"] + def read1_lines = ["@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions_paired_end_merged_adapterlist") } ) } } -} \ No newline at end of file +} diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap index 54be7e4..3e87628 100644 --- a/modules/nf-core/fastp/tests/main.nf.test.snap +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -1,178 +1,55 @@ { - "test_fastp_single_end_qc_only - stub": { + "fastp test_fastp_interleaved_json": { "content": [ - { - "0": [ - - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "json": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "reads": [ - - ], - "reads_fail": [ - - ], - "reads_merged": [ - - ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,b24e0624df5cc0b11cd5ba21b726fb22" ] - } + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T14:31:10.841098" + "timestamp": "2024-03-18T16:19:15.063001" }, - "test_fastp_paired_end": { + "test_fastp_paired_end_merged-for_stub_match": { "content": [ [ [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,1e0f8e27e71728e2b63fc64086be95cd" - ] - ], - [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastp.fastq.gz:md5,67b2bbae47f073e05a97a9c2edce23c7", - "test_2.fastp.fastq.gz:md5,25cbdca08e2083dbd4f0502de6b62f39" - ] - ] - ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + "test_1.fastp.fastq.gz", + "test_2.fastp.fastq.gz" + ], + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "test.merged.fastq.gz", + "{id=test, single_end=false}" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T13:43:28.665779" + "timestamp": "2024-01-17T18:10:13.467574" }, - "test_fastp_paired_end_merged_adapterlist": { + "versions_interleaved": { "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,5914ca3f21ce162123a824e33e8564f6" - ] - ], - [ - [ - { - "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.merged.fastq.gz:md5,c873bb1ab3fa859dcc47306465e749d5" - ] - ], [ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T13:44:18.210375" + "timestamp": "2024-02-01T11:56:24.615634793" }, - "test_fastp_single_end_qc_only": { + "test_fastp_single_end_json": { "content": [ [ [ @@ -180,1152 +57,274 @@ "id": "test", "single_end": true }, - "test.fastp.json:md5,5cc5f01e449309e0e689ed6f51a2294a" + "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" ] - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - - ], - [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T13:44:27.380974" + "timestamp": "2024-03-18T16:18:43.526412" }, - "test_fastp_paired_end_trim_fail": { + "versions_paired_end": { "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.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 - }, - "test.fastp.json:md5,4c3268ddb50ea5b33125984776aa3519" - ] - ], [ "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T13:43:58.749589" + "timestamp": "2024-02-01T11:55:42.333545689" }, - "fastp - stub test_fastp_interleaved": { + "test_fastp_paired_end_match": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "json": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "reads_fail": [ - - ], - "reads_merged": [ - + [ + [ + "test_1.fastp.fastq.gz", + "test_2.fastp.fastq.gz" ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] - } + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "{id=test, single_end=false}" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T13:50:00.270029" + "timestamp": "2024-02-01T12:03:06.431833729" }, - "test_fastp_single_end - stub": { + "test_fastp_interleaved-_match": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "json": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "reads": [ - [ - { - "id": "test", - "single_end": true - }, - "test.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "reads_fail": [ - - ], - "reads_merged": [ - - ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" - ] - } + [ + "test.fastp.fastq.gz", + "test.fastp.html", + "test.fastp.json", + "test.fastp.log", + "{id=test, single_end=true}" + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T13:49:42.502789" + "timestamp": "2024-03-18T16:19:15.111894" }, - "test_fastp_paired_end_merged_adapterlist - stub": { + "test_fastp_paired_end_merged_match": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - [ - "test_1.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test_2.fastp.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - 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], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "json": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "log": [ - [ - { - "id": "test", - "single_end": false - }, - "test.fastp.log:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "reads": [ - - ], - "reads_fail": [ - - ], - "reads_merged": [ - - ], - "versions": [ - "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5" ] - } + ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "23.10.1" }, - "timestamp": "2024-07-05T14:31:27.096468" + "timestamp": "2024-01-17T18:08:41.942317" } } \ No newline at end of file diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 691d4c7..1787b38 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,5 +1,7 @@ +name: fastqc channels: - conda-forge - bioconda + - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d8989f4..9e19a74 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -25,14 +25,6 @@ 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(' ') - - // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) - // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus - // FastQC memory value allowed range (100 - 10000) - def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) - """ printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name @@ -41,7 +33,6 @@ process FASTQC { fastqc \\ $args \\ --threads $task.cpus \\ - --memory $fastqc_memory \\ $renamed_files cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4827da7..ee5507e 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,44 +16,35 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] - identifier: biotools:fastqc input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - html: - - 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}" + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - "*.zip": - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index e9d79a0..70edae4 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,14 +23,17 @@ nextflow_process { then { assertAll ( - { assert process.success }, - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
    Mon 2 Oct 2023
    test.gz
    - // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_single") } ) } } @@ -51,14 +54,16 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_paired") } ) } } @@ -78,11 +83,13 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } ) } } @@ -102,11 +109,13 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_bam") } ) } } @@ -129,20 +138,22 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + + { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } ) } } @@ -162,116 +173,27 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - { assert snapshot(process.out.versions).match() } - ) - } - } + { assert process.success }, - test("sarscov2 single-end [fastq] - stub") { + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } ) } } - test("sarscov2 paired-end [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 interleaved [fastq] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("sarscov2 paired-end [bam] - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } + test("sarscov2 single-end [fastq] - stub") { - test("sarscov2 multiple [fastq] - stub") { + options "-stub" - options "-stub" when { process { """ input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + [ id: 'test', single_end:true ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] ]) """ } @@ -279,31 +201,12 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match("fastqc_stub") } ) } } - test("sarscov2 custom_prefix - stub") { - - options "-stub" - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index d5db309..86f7c31 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,392 +1,88 @@ { - "sarscov2 custom_prefix": { + "fastqc_versions_interleaved": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:16.374038" + "timestamp": "2024-01-31T17:40:07.293713" }, - "sarscov2 single-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": true - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": true - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:02:24.993809" - }, - "sarscov2 custom_prefix - stub": { - "content": [ - { - "0": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "mysample", - "single_end": true - }, - "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:10.93942" - }, - "sarscov2 interleaved [fastq]": { + "fastqc_stub": { "content": [ [ + "test.html", + "test.zip", "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:01:42.355718" + "timestamp": "2024-01-31T17:31:01.425198" }, - "sarscov2 paired-end [bam]": { + "fastqc_versions_multiple": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:01:53.276274" + "timestamp": "2024-01-31T17:40:55.797907" }, - "sarscov2 multiple [fastq]": { + "fastqc_versions_bam": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:05.527626" + "timestamp": "2024-01-31T17:40:26.795862" }, - "sarscov2 paired-end [fastq]": { + "fastqc_versions_single": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:31.188871" - }, - "sarscov2 paired-end [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:34.273566" + "timestamp": "2024-01-31T17:39:27.043675" }, - "sarscov2 multiple [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:03:02.304411" - }, - "sarscov2 single-end [fastq]": { + "fastqc_versions_paired": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" - }, - "timestamp": "2024-07-22T11:01:19.095607" - }, - "sarscov2 interleaved [fastq] - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:44.640184" + "timestamp": "2024-01-31T17:39:47.584191" }, - "sarscov2 paired-end [bam] - stub": { + "fastqc_versions_custom_prefix": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "html": [ - [ - { - "id": "test", - "single_end": false - }, - "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ], - "zip": [ - [ - { - "id": "test", - "single_end": false - }, - "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-22T11:02:53.550742" + "timestamp": "2024-01-31T17:41:14.576531" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf b/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf index a7b856b..4f1c84f 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf @@ -52,7 +52,6 @@ workflow FASTQ_TRIM_FASTP_FASTQC { FASTP ( ch_reads, ch_adapter_fasta, - false, val_save_trimmed_fail, val_save_merged ) diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml index fb2d12f..9f4e12e 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml @@ -46,7 +46,7 @@ input: skip the fastp process if true output: - meta: - type: string + type: value description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file From b86a1a8493568d3fab073ebd6886318294ddc6cc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 11 Oct 2024 16:41:10 +0200 Subject: [PATCH 45/70] update CHANGELOG in #176 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 923df4d..e314323 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` +- [#176](https://github.com/nf-core/bacass/pull/176) Update nf-core/bacass to nf-core-tools v3.0.2 `TEMPLATE`. - [#166](https://github.com/nf-core/bacass/pull/166) Added FastQC after-trimming section to MultiQC report. ### `Fixed` From 2083999ef317d9a52ef578072505726e82644035 Mon Sep 17 00:00:00 2001 From: Daniel VM <69470278+Daniel-VM@users.noreply.github.com> Date: Tue, 15 Oct 2024 15:28:09 +0200 Subject: [PATCH 46/70] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- .nf-core.yml | 3 ++- CITATIONS.md | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index b089730..38f44e0 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,6 +16,7 @@ template: name: bacass org: nf-core outdir: . - skip_features: null + skip_features: + - igenomes version: 2.4.0dev update: null diff --git a/CITATIONS.md b/CITATIONS.md index aa5481f..9d2ab88 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [FastP](https://github.com/OpenGene/fastp) From 8a8182a4917f9513370b3c07525e7048e11060c1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Oct 2024 13:31:59 +0000 Subject: [PATCH 47/70] [automated] Fix code linting --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index 38f44e0..84c59be 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -16,7 +16,7 @@ template: name: bacass org: nf-core outdir: . - skip_features: + skip_features: - igenomes version: 2.4.0dev update: null From cc0ae3a303465788305c771796a1a6e6732aaf9f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 14:12:20 +0200 Subject: [PATCH 48/70] added module cat_fastq --- assets/schema_input.json | 2 +- modules.json | 5 + modules/nf-core/cat/fastq/environment.yml | 7 + modules/nf-core/cat/fastq/main.nf | 79 ++++ modules/nf-core/cat/fastq/meta.yml | 42 ++ modules/nf-core/cat/fastq/tests/main.nf.test | 248 ++++++++++++ .../nf-core/cat/fastq/tests/main.nf.test.snap | 376 ++++++++++++++++++ modules/nf-core/cat/fastq/tests/tags.yml | 2 + .../utils_nfcore_bacass_pipeline/main.nf | 2 +- workflows/bacass.nf | 38 +- 10 files changed, 789 insertions(+), 12 deletions(-) create mode 100644 modules/nf-core/cat/fastq/environment.yml create mode 100644 modules/nf-core/cat/fastq/main.nf create mode 100644 modules/nf-core/cat/fastq/meta.yml create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/fastq/tests/tags.yml diff --git a/assets/schema_input.json b/assets/schema_input.json index 3cf372d..a2681a4 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,7 +10,7 @@ "ID": { "type": "string", "pattern": "^\\S+$", - "unique": true, + "unique": false, "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] }, diff --git a/modules.json b/modules.json index ba06f0a..065534e 100644 --- a/modules.json +++ b/modules.json @@ -20,6 +20,11 @@ "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, + "cat/fastq": { + "branch": "master", + "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7", + "installed_by": ["modules"] + }, "dragonflye": { "branch": "master", "git_sha": "a3ae45e99f68e513b0feb8d5f27e2fdd0d0f083d", diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 0000000..8c69b12 --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,7 @@ +name: cat_fastq +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf new file mode 100644 index 0000000..b68e5f9 --- /dev/null +++ b/modules/nf-core/cat/fastq/main.nf @@ -0,0 +1,79 @@ +process CAT_FASTQ { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + + output: + tuple val(meta), path("*.merged.fastq.gz"), emit: reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] + if (meta.single_end) { + if (readList.size >= 1) { + """ + cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } else { + if (readList.size >= 2) { + def read1 = [] + def read2 = [] + readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v } + """ + cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz + cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] + if (meta.single_end) { + if (readList.size >= 1) { + """ + echo '' | gzip > ${prefix}.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } else { + if (readList.size >= 2) { + """ + echo '' | gzip > ${prefix}_1.merged.fastq.gz + echo '' | gzip > ${prefix}_2.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } +} diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml new file mode 100644 index 0000000..db4ac3c --- /dev/null +++ b/modules/nf-core/cat/fastq/meta.yml @@ -0,0 +1,42 @@ +name: cat_fastq +description: Concatenates fastq files +keywords: + - cat + - 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"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. +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" +authors: + - "@joseespinosa" + - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 0000000..f88a78b --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,248 @@ +// NOTE The version snaps may not be consistant +// https://github.com/nf-core/modules/pull/4087#issuecomment-1767948035 +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 0000000..aec119a --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,376 @@ +{ + "test_cat_fastq_single_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-01-17T17:30:39.816981" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-01-17T17:32:35.229332" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-01-17T17:34:00.058829" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-01-17T17:33:33.031555" + }, + "test_cat_fastq_single_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:28.244999" + }, + "test_cat_fastq_paired_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:57.070911" + }, + "test_cat_fastq_single_end_same_name - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:46.796254" + }, + "test_cat_fastq_paired_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-01-17T17:32:02.270935" + }, + "test_cat_fastq_paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_2.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:07:37.807553" + }, + "test_cat_fastq_single_end_single_file - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-07-05T12:14:51.861264" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml new file mode 100644 index 0000000..6ac4361 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/tags.yml @@ -0,0 +1,2 @@ +cat/fastq: + - modules/nf-core/cat/fastq/** diff --git a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf index 3cdbca3..c1febf3 100644 --- a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf @@ -88,7 +88,7 @@ workflow PIPELINE_INITIALISATION { } .map { meta, fastqs, longread, fast5 -> - return [ meta, fastqs.flatten(), longread, fast5 ] + return [ meta, fastqs, longread[0], fast5[0] ] } .set { ch_samplesheet } diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 01d17f9..c6d07aa 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -20,7 +20,7 @@ include { MULTIQC_CUSTOM } from '../modules/local/multiqc_custom' // MODULE: Installed directly from nf-core/modules // include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../modules/nf-core/cat/fastq' include { NANOPLOT } from '../modules/nf-core/nanoplot/main' include { PORECHOP_PORECHOP } from '../modules/nf-core/porechop/porechop/main' include { CANU } from '../modules/nf-core/canu/main' @@ -77,21 +77,18 @@ workflow BACASS { main: ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() + // // SUBWORKFLOW: Read in samplesheet, validate and stage input files // def criteria = multiMapCriteria { - meta, fastq_1, fastq_2, long_fastq, fast5 -> - shortreads: fastq_1 != 'NA' ? tuple(meta, [file(fastq_1, checkIfExists: true), file(fastq_2, checkIfExists: true)]) : null - longreads: long_fastq != 'NA' ? tuple(meta, file(long_fastq, checkIfExists: true)) : null - fast5: fast5 != 'NA' ? tuple(meta, file(fast5, checkIfExists: true)) : null + meta, fastqs, long_fastq, fast5 -> + shortreads: meta.single_end != 'NA' ? tuple(meta, fastqs) : null + longreads: long_fastq != 'NA' ? tuple(meta,long_fastq) : null + fast5: fast5 != 'NA' ? tuple(meta, fast5) : null } // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ ch_samplesheet - .map { - meta, fastqs, long_fastq, fast5 -> - return [meta, fastqs[0], fastqs[1], long_fastq[0], fast5[0]] - } .multiMap (criteria) .set { ch_input } @@ -99,7 +96,7 @@ workflow BACASS { ch_input .shortreads .filter{ it != null } - .set { ch_shortreads } + .set { ch_shortreads_cat } ch_input .longreads .filter{ it != null } @@ -109,6 +106,27 @@ workflow BACASS { .filter{ it != null } .set { ch_fast5 } + // + // MODULE: Concatenate FastQ files from same sample if required (shortreads) + // + ch_shortreads + .branch{ + meta, fastqs -> + single: fastqs.size() == 1 + return [meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [meta, fastqs.flatten() ] + } + .set { ch_shortreads_cat } + + CAT_FASTQ ( + ch_shortreads_cat.multiple + ) + .reads + .mix( ch_shortreads_cat.single ) + .set { ch_shortreads } + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + // // SUBWORKFLOW: Short reads QC and trim adapters // From b2ab59ce83378cd03b19fb1e7e49af54bb6ae0ea Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 15:56:02 +0200 Subject: [PATCH 49/70] fix wrong variable naming --- workflows/bacass.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index c6d07aa..8b23ab9 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -96,7 +96,7 @@ workflow BACASS { ch_input .shortreads .filter{ it != null } - .set { ch_shortreads_cat } + .set { ch_shortreads } ch_input .longreads .filter{ it != null } From 1f2b944a73e41eeb3de6c088a45e2c9a84e5a0af Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 16:06:30 +0200 Subject: [PATCH 50/70] update changelog #158 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e314323..f4ceb20 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#176](https://github.com/nf-core/bacass/pull/176) Update nf-core/bacass to nf-core-tools v3.0.2 `TEMPLATE`. - [#166](https://github.com/nf-core/bacass/pull/166) Added FastQC after-trimming section to MultiQC report. +- [#158](https://github.com/nf-core/bacass/pull/158) Support automatic concatenation of FastQ files for the same sample. ### `Fixed` From 2df4fca9a6da4f8e408789163af1eca2bafddb02 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 29 Aug 2024 16:38:31 +0200 Subject: [PATCH 51/70] fixed channel versions and rename variables --- workflows/bacass.nf | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 8b23ab9..85f400a 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -113,19 +113,19 @@ workflow BACASS { .branch{ meta, fastqs -> single: fastqs.size() == 1 - return [meta, fastqs.flatten() ] + return [ meta, fastqs.flatten() ] multiple: fastqs.size() > 1 - return [meta, fastqs.flatten() ] + return [ meta, fastqs.flatten() ] } - .set { ch_shortreads_cat } + .set { ch_shortreads_fastqs } - CAT_FASTQ ( - ch_shortreads_cat.multiple - ) - .reads - .mix( ch_shortreads_cat.single ) - .set { ch_shortreads } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + CAT_FASTQ ( + ch_shortreads_fastqs.multiple + ) + .reads + .mix( ch_shortreads_fastqs.single ) + .set { ch_shortreads_concat } + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) // // SUBWORKFLOW: Short reads QC and trim adapters @@ -135,7 +135,7 @@ workflow BACASS { ch_fastp_json_multiqc = Channel.empty() if (params.assembly_type != 'long'){ FASTQ_TRIM_FASTP_FASTQC ( - ch_shortreads, + ch_shortreads_concat, [], params.save_trimmed_fail, [], From cb0c18d6707c9ff57309ddbe287930ba831fd41b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 15 Oct 2024 17:11:34 +0200 Subject: [PATCH 52/70] align spaces --- workflows/bacass.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 85f400a..293056c 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -19,7 +19,7 @@ include { MULTIQC_CUSTOM } from '../modules/local/multiqc_custom' // // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/fastqc/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' include { CAT_FASTQ } from '../modules/nf-core/cat/fastq' include { NANOPLOT } from '../modules/nf-core/nanoplot/main' include { PORECHOP_PORECHOP } from '../modules/nf-core/porechop/porechop/main' From 890f44cca27169b91db63844501cae4acb133f86 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 24 Oct 2024 13:59:20 +0200 Subject: [PATCH 53/70] fix bakta running only for one sample --- subworkflows/local/bakta_dbdownload_run.nf | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/bakta_dbdownload_run.nf b/subworkflows/local/bakta_dbdownload_run.nf index 675adcb..6822ba6 100644 --- a/subworkflows/local/bakta_dbdownload_run.nf +++ b/subworkflows/local/bakta_dbdownload_run.nf @@ -43,9 +43,14 @@ workflow BAKTA_DBDOWNLOAD_RUN { // // MODULE: BAKTA, gene annotation // + // Setup input channel for Bakta process + ch_fasta + .combine(ch_baktadb) + .set{ ch_to_bakta } + ch_to_bakta.view() BAKTA_BAKTA ( - ch_fasta, - ch_baktadb, + ch_to_bakta.map{ meta, fasta, bakta_db -> [meta, fasta] }, + ch_to_bakta.map{ meta, fasta, bakta_db -> bakta_db }, [], [] ) From 9e622f147d3f2515741c8e219954e5e7704db653 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 24 Oct 2024 14:04:21 +0200 Subject: [PATCH 54/70] add changelog in #178 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e314323..33ee3cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample. - [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel. - [#168](https://github.com/nf-core/bacass/pull/168) Fix wrong metadata in canu input channel. - [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files. From 10a7df89e922cee689feaf04c57d075b34352f27 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 24 Oct 2024 15:42:19 +0200 Subject: [PATCH 55/70] include resequenced samples in test profile --- conf/test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test.config b/conf/test.config index 166c9b0..ea960ea 100644 --- a/conf/test.config +++ b/conf/test.config @@ -23,7 +23,7 @@ params { config_profile_description = 'Minimal test dataset to check pipeline function' // Input data - input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv' + input = params.pipelines_testdata_base_path + 'bacass/bacass_short_reseq.tsv' // some extra args to speed tests up prokka_args = " --fast" From 4ed19cbd9d17746a864d335c9148db11061d4e99 Mon Sep 17 00:00:00 2001 From: Daniel VM <69470278+Daniel-VM@users.noreply.github.com> Date: Thu, 24 Oct 2024 17:24:14 +0200 Subject: [PATCH 56/70] remove view operator Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com> --- subworkflows/local/bakta_dbdownload_run.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/subworkflows/local/bakta_dbdownload_run.nf b/subworkflows/local/bakta_dbdownload_run.nf index 6822ba6..d5fc41b 100644 --- a/subworkflows/local/bakta_dbdownload_run.nf +++ b/subworkflows/local/bakta_dbdownload_run.nf @@ -47,7 +47,6 @@ workflow BAKTA_DBDOWNLOAD_RUN { ch_fasta .combine(ch_baktadb) .set{ ch_to_bakta } - ch_to_bakta.view() BAKTA_BAKTA ( ch_to_bakta.map{ meta, fasta, bakta_db -> [meta, fasta] }, ch_to_bakta.map{ meta, fasta, bakta_db -> bakta_db }, From 5a9559c3c27123082048bc9f6953d12f763c247a Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 10:08:04 +0200 Subject: [PATCH 57/70] fix ambigous channel creation --- subworkflows/local/bakta_dbdownload_run.nf | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/bakta_dbdownload_run.nf b/subworkflows/local/bakta_dbdownload_run.nf index d5fc41b..8b3c1fd 100644 --- a/subworkflows/local/bakta_dbdownload_run.nf +++ b/subworkflows/local/bakta_dbdownload_run.nf @@ -25,16 +25,14 @@ workflow BAKTA_DBDOWNLOAD_RUN { // MODULE: untar database UNTAR( ch_baktadb_tar ) - ch_baktadb = UNTAR.out.untar.map{ meta, db -> db } + ch_path_baktadb = UNTAR.out.untar.map{ meta, db -> db } ch_versions = ch_versions.mix(UNTAR.out.versions) - } else { - ch_baktadb = Channel.from(ch_path_baktadb).map{ db -> db } } } else if (!ch_path_baktadb && val_baktadb_download){ // MODULE: Downlado Bakta database from zenodo BAKTA_BAKTADBDOWNLOAD() - ch_baktadb = BAKTA_BAKTADBDOWNLOAD.out.db - ch_versions = ch_versions.mix(BAKTA_BAKTADBDOWNLOAD.out.versions) + ch_path_baktadb = BAKTA_BAKTADBDOWNLOAD.out.db + ch_versions = ch_versions.mix(BAKTA_BAKTADBDOWNLOAD.out.versions) } else if (!ch_path_baktadb && !val_baktadb_download ){ exit 1, "The Bakta database argument is missing. To enable the workflow to access the Bakta database, please include the path using '--baktadb' or use '--bakdtadb_download true' to download the Bakta database." @@ -44,12 +42,9 @@ workflow BAKTA_DBDOWNLOAD_RUN { // MODULE: BAKTA, gene annotation // // Setup input channel for Bakta process - ch_fasta - .combine(ch_baktadb) - .set{ ch_to_bakta } BAKTA_BAKTA ( - ch_to_bakta.map{ meta, fasta, bakta_db -> [meta, fasta] }, - ch_to_bakta.map{ meta, fasta, bakta_db -> bakta_db }, + ch_fasta, + ch_path_baktadb, [], [] ) From 2bccce19bfc5880dd96cce5cc53cdb3fb8eb8070 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 10:24:55 +0200 Subject: [PATCH 58/70] fixed matrix.test_name in linting --- .github/workflows/ci.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b49a5fc..407121b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,6 +35,10 @@ jobs: - "singularity" test_name: - "test" + - "test_long" + - "test_long_miniasm" + - "test_hybrid" + - "test_dfast" isMaster: - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev From fd2b54e814f2d73961f8f288ae7c73159450a645 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 11:34:00 +0200 Subject: [PATCH 59/70] remove parameter section in git ci --- .github/workflows/ci.yml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 407121b..e234aaa 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -47,12 +47,6 @@ jobs: profile: "conda" - isMaster: false profile: "singularity" - parameters: - - "test" - - "test_long" - - "test_long_miniasm" - - "test_hybrid" - - "test_dfast" steps: - name: Check out pipeline code From 85bdf8540dc7fb2b1ae37cc353eaa5f3c500e068 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 11:57:56 +0200 Subject: [PATCH 60/70] implement missing features in memory set up from nf-core tools 3.0.2 --- assets/schema_input.json | 4 ---- conf/test_dfast.config | 14 +++++++++----- conf/test_full.config | 9 +++++++++ conf/test_hybrid.config | 14 +++++++++----- conf/test_hybrid_dragonflye.config | 14 +++++++++----- conf/test_long.config | 14 +++++++++----- conf/test_long_dragonflye.config | 8 ++++++++ conf/test_long_miniasm.config | 14 +++++++++----- 8 files changed, 62 insertions(+), 29 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 3cf372d..8758726 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -19,7 +19,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$" }, { @@ -33,7 +32,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$" }, { @@ -47,7 +45,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\S+\\.f(ast)?q\\.gz|NA)$" }, { @@ -61,7 +58,6 @@ "anyOf": [ { "type": ["string", "null"], - "exists": true, "pattern": "^(\\/[\\S\\s]*|NA)$" }, { diff --git a/conf/test_dfast.config b/conf/test_dfast.config index e2d0afe..ada68c6 100644 --- a/conf/test_dfast.config +++ b/conf/test_dfast.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test_dfast profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_short.tsv' diff --git a/conf/test_full.config b/conf/test_full.config index f3dc621..6535fd4 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,15 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config index a524de0..3ddad51 100644 --- a/conf/test_hybrid.config +++ b/conf/test_hybrid.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid.tsv' diff --git a/conf/test_hybrid_dragonflye.config b/conf/test_hybrid_dragonflye.config index 9cf3436..349c540 100644 --- a/conf/test_hybrid_dragonflye.config +++ b/conf/test_hybrid_dragonflye.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test hybrid-dragonflye profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_hybrid_dragonflye.tsv' diff --git a/conf/test_long.config b/conf/test_long.config index 3cc3a8b..3ebc421 100644 --- a/conf/test_long.config +++ b/conf/test_long.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test_long profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv' diff --git a/conf/test_long_dragonflye.config b/conf/test_long_dragonflye.config index 38301d4..07f1bf5 100644 --- a/conf/test_long_dragonflye.config +++ b/conf/test_long_dragonflye.config @@ -9,6 +9,14 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test_long_dragonfyle profile' diff --git a/conf/test_long_miniasm.config b/conf/test_long_miniasm.config index d6b5874..ab2dd10 100644 --- a/conf/test_long_miniasm.config +++ b/conf/test_long_miniasm.config @@ -10,15 +10,19 @@ ---------------------------------------------------------------------------------------- */ +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test_long_miniasm profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data input = params.pipelines_testdata_base_path + 'bacass/bacass_long_miniasm.tsv' From aa42f9517977013b6340a34a44ecdd42b61a3580 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 11:59:43 +0200 Subject: [PATCH 61/70] update changelog #179 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 33ee3cd..8ea7ef2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#179](https://github.com/nf-core/bacass/pull/179) Fixed matrix.test_name in linting and missing features from template 3.0.2. - [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample. - [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel. - [#168](https://github.com/nf-core/bacass/pull/168) Fix wrong metadata in canu input channel. From 8434c60edd9794c4bf8da1c8eabf3aeaab2cf886 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 24 Oct 2024 16:22:42 +0200 Subject: [PATCH 62/70] bump version 2.4.0 --- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index de65fe6..045d36f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0dev nf-core/bacass +## v2.4.0 nf-core/bacass: "Yellow Copper Crayfish" 2024/10/24 ### `Changed` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 6f6ef07..a247bc7 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/bacass + This report has been generated by the nf-core/bacass analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. max_table_rows: 10000 diff --git a/nextflow.config b/nextflow.config index 9131be6..e56b957 100644 --- a/nextflow.config +++ b/nextflow.config @@ -264,7 +264,7 @@ manifest { description = """Simple bacterial assembly and annotation""" mainScript = 'main.nf' nextflowVersion = '!>=24.04.2' - version = '2.4.0dev' + version = '2.4.0' doi = '10.5281/zenodo.2669428' } From f1809cec9f740f586da0736366273ff0b3c9e55e Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 25 Oct 2024 12:11:26 +0200 Subject: [PATCH 63/70] update changelog #180 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 045d36f..fd8dc21 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` +- [#180](https://github.com/nf-core/bacass/pull/180) Bump version 2.4.0. - [#169](https://github.com/nf-core/bacass/pull/169) Refactored long-reads polishing step. - [#167](https://github.com/nf-core/bacass/pull/167) Remove params.save_merged as merged reads are not used in downstream analysis. - [#159](https://github.com/nf-core/bacass/pull/159) Updated Kmerfinder module and increased memory. From 9c95fb780bb92728a47ffe1de662152e36122bdc Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 5 Nov 2024 12:04:47 +0100 Subject: [PATCH 64/70] fix release date in #180 --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fd8dc21..e0bb118 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0 nf-core/bacass: "Yellow Copper Crayfish" 2024/10/24 +## v2.4.0 nf-core/bacass: "Yellow Copper Crayfish" 2024/11/05 ### `Changed` From 262f74105d2ba63dd93b5db9464d9f7aea4a4887 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 5 Nov 2024 15:21:44 +0100 Subject: [PATCH 65/70] uncomment required line for linting in --release mode --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index e56b957..ff9faed 100644 --- a/nextflow.config +++ b/nextflow.config @@ -204,7 +204,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load nf-core/bacass custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null" +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/bacass.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled From e241ff879de1d36644c8e3d90e78a828003f0816 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Tue, 5 Nov 2024 15:29:37 +0100 Subject: [PATCH 66/70] update changelog in #182 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0bb118..f160d6a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#182](https://github.com/nf-core/bacass/pull/182) Uncommented required line to pass linting test in `--release` mode. - [#179](https://github.com/nf-core/bacass/pull/179) Fixed matrix.test_name in linting and missing features from template 3.0.2. - [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample. - [#169](https://github.com/nf-core/bacass/pull/169) Fixed long reads polishing input channel. From ad68b1f1cd0cdc067f159cd2fc8f302ec6044735 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 6 Nov 2024 13:07:42 +0100 Subject: [PATCH 67/70] fix dfast conda issue by updating version --- modules/local/dfast/environment.yml | 2 +- modules/local/dfast/main.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/dfast/environment.yml b/modules/local/dfast/environment.yml index f554259..f532ca2 100644 --- a/modules/local/dfast/environment.yml +++ b/modules/local/dfast/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::dfast=1.2.20 + - bioconda::dfast=1.3.2 diff --git a/modules/local/dfast/main.nf b/modules/local/dfast/main.nf index 3d82b66..1dacc33 100644 --- a/modules/local/dfast/main.nf +++ b/modules/local/dfast/main.nf @@ -4,8 +4,8 @@ process DFAST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/dfast:1.2.20--h43eeafb_0' : - 'biocontainers/dfast:1.2.20--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/dfast:1.3.2--h43eeafb_0' : + 'biocontainers/dfast:1.3.2--h43eeafb_0' }" input: tuple val(meta), path(fasta) From 0f7646a742a7fe470edd9a5b2cfd85943e5f8a7c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 6 Nov 2024 13:50:50 +0100 Subject: [PATCH 68/70] update changelog in #183 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f160d6a..950287d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#183](https://github.com/nf-core/bacass/pull/183) Fix DFAST issue in conda environment by updating its version. - [#182](https://github.com/nf-core/bacass/pull/182) Uncommented required line to pass linting test in `--release` mode. - [#179](https://github.com/nf-core/bacass/pull/179) Fixed matrix.test_name in linting and missing features from template 3.0.2. - [#178](https://github.com/nf-core/bacass/pull/178) Fixed bakta running only for one sample. From bf367e40c29be8ae608c32eb1db1d2134e9b133d Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 18 Nov 2024 12:39:07 +0100 Subject: [PATCH 69/70] added code review from #181 --- .github/workflows/awsfulltest.yml | 1 + .nf-core.yml | 2 +- CHANGELOG.md | 5 +++++ conf/base.config | 2 +- conf/modules.config | 3 --- workflows/bacass.nf | 3 --- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index dd5acbf..3d60a62 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -20,6 +20,7 @@ jobs: steps: - uses: octokit/request-action@v2.x id: check_approvals + if: github.event_name != 'workflow_dispatch' with: route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews env: diff --git a/.nf-core.yml b/.nf-core.yml index 84c59be..875c078 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,5 +18,5 @@ template: outdir: . skip_features: - igenomes - version: 2.4.0dev + version: 2.4.0 update: null diff --git a/CHANGELOG.md b/CHANGELOG.md index 950287d..df87f3c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -35,6 +35,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` +| Tool | Previous version | New version | +| ---------- | ---------------- | ----------- | +| Dfast | 1.2.20 | 1.3.2 | +| Unicycler | 0.4.8 | 0.5.0 | + ### `Deprecated` ## v2.3.1 nf-core/bacass: "Navy Iron Oyster" 2024/06/24 diff --git a/conf/base.config b/conf/base.config index 5dc3f9e..bad115d 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } - maxRetries = 1 + maxRetries = 3 maxErrors = '-1' // Process-specific resource requirements diff --git a/conf/modules.config b/conf/modules.config index 0324168..7b0bc4a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -299,9 +299,6 @@ if (!params.skip_fastp) { if (!params.skip_kmerfinder) { process { withName: '.*:.*:KMERFINDER_SUBWORKFLOW:KMERFINDER' { - errorStrategy = { task.exitStatus in [1, 137, 139] ? 'retry' : 'finish'} - maxRetries = 3 - ext.args = '' publishDir = [ path: { "${params.outdir}/Kmerfinder/${meta.id}" }, diff --git a/workflows/bacass.nf b/workflows/bacass.nf index 293056c..fed8253 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -60,9 +60,6 @@ include { methodsDescriptionText } from '../subworkflows/local/ut def checkPathParamList = [ params.input, params.multiqc_config, params.kraken2db, params.dfast_config ] for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } -// Place config files here - - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RUN MAIN WORKFLOW From cd1bf3e18d11aadec996265140562196fa07edc8 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 18 Nov 2024 12:46:04 +0100 Subject: [PATCH 70/70] fix linting in #184 --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index df87f3c..7594ac2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -35,10 +35,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Dependencies` -| Tool | Previous version | New version | -| ---------- | ---------------- | ----------- | -| Dfast | 1.2.20 | 1.3.2 | -| Unicycler | 0.4.8 | 0.5.0 | +| Tool | Previous version | New version | +| --------- | ---------------- | ----------- | +| Dfast | 1.2.20 | 1.3.2 | +| Unicycler | 0.4.8 | 0.5.0 | ### `Deprecated`