From 64bdd3d3592aa2db7203fc118fb713983ff42179 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 19 Dec 2023 18:36:47 +0000 Subject: [PATCH 1/6] Template update for nf-core/tools version 2.11 --- .github/CONTRIBUTING.md | 3 + .github/PULL_REQUEST_TEMPLATE.md | 1 + .github/workflows/ci.yml | 2 +- .github/workflows/fix-linting.yml | 4 +- .github/workflows/linting.yml | 12 +- .gitpod.yml | 4 +- CHANGELOG.md | 2 +- README.md | 17 +-- assets/multiqc_config.yml | 6 +- assets/slackreport.json | 2 +- conf/modules.config | 2 +- docs/usage.md | 4 +- lib/NfcoreTemplate.groovy | 32 ++--- modules.json | 6 +- .../dumpsoftwareversions/environment.yml | 7 ++ .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 7 +- .../dumpsoftwareversions/tests/main.nf.test | 38 ++++++ .../tests/main.nf.test.snap | 27 +++++ .../dumpsoftwareversions/tests/tags.yml | 2 + modules/nf-core/fastqc/environment.yml | 7 ++ modules/nf-core/fastqc/main.nf | 10 +- modules/nf-core/fastqc/meta.yml | 5 + modules/nf-core/fastqc/tests/main.nf.test | 109 ++++++++++++++++++ .../nf-core/fastqc/tests/main.nf.test.snap | 10 ++ modules/nf-core/fastqc/tests/tags.yml | 2 + modules/nf-core/multiqc/environment.yml | 7 ++ modules/nf-core/multiqc/main.nf | 8 +- modules/nf-core/multiqc/meta.yml | 11 +- modules/nf-core/multiqc/tests/main.nf.test | 63 ++++++++++ modules/nf-core/multiqc/tests/tags.yml | 2 + nextflow.config | 12 +- 32 files changed, 361 insertions(+), 69 deletions(-) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml create mode 100644 modules/nf-core/fastqc/environment.yml create mode 100644 modules/nf-core/fastqc/tests/main.nf.test create mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap create mode 100644 modules/nf-core/fastqc/tests/tags.yml create mode 100644 modules/nf-core/multiqc/environment.yml create mode 100644 modules/nf-core/multiqc/tests/main.nf.test create mode 100644 modules/nf-core/multiqc/tests/tags.yml diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index a66c8d8b..597c854d 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to +receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. + When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index e66587f6..073b2953 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/scrn - [ ] If necessary, also make a PR on the nf-core/scrnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d466269a..de0c4594 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ jobs: - "latest-everything" steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 9adbb159..05b700e4 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -24,7 +24,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b8bdd214..905c58e4 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -27,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @@ -40,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Check code lints with Black uses: psf/black@stable @@ -71,7 +71,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.gitpod.yml b/.gitpod.yml index 25488dcc..acf72695 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,7 +4,9 @@ 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 - codezombiech.gitignore # Language support for .gitignore files diff --git a/CHANGELOG.md b/CHANGELOG.md index 6d0db033..8839e0f7 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). -## v2.4.1 - [date] +## v2.5.0dev - [date] Initial release of nf-core/scrnaseq, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index 3f35dfd8..4736c821 100644 --- a/README.md +++ b/README.md @@ -30,11 +30,8 @@ ## Usage -:::note -If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -with `-profile test` before running the workflow on actual data. -::: +> [!NOTE] +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - + diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f550a97b..051ed54e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,9 +1,7 @@ report_comment: > - - This report has been generated by the nf-core/scrnaseq + This report has been generated by the nf-core/scrnaseq analysis pipeline. For information about how to interpret these results, please see the - documentation. - + documentation. report_section_order: "nf-core-scrnaseq-methods-description": order: -1000 diff --git a/assets/slackreport.json b/assets/slackreport.json index f6ba6baf..9538f235 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/scrnaseq v${version} - ${runName}", + "author_name": "nf-core/scrnaseq ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules.config b/conf/modules.config index 39e81386..d91c6aba 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -39,7 +39,7 @@ process { } withName: 'MULTIQC' { - ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, mode: params.publish_dir_mode, diff --git a/docs/usage.md b/docs/usage.md index 03ade981..e9b83795 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -20,7 +20,7 @@ You will need to create a samplesheet with information about the samples you wou The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz @@ -33,7 +33,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. -```console +```csv title="samplesheet.csv" sample,fastq_1,fastq_2 CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..e248e4c3 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -4,6 +4,7 @@ import org.yaml.snakeyaml.Yaml import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -141,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -155,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -227,15 +232,14 @@ class NfcoreTemplate { // Dump pipeline parameters in a json file // public static void dump_parameters(workflow, params) { - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def output_pf = new File(output_d, "params_${timestamp}.json") + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() } // diff --git a/modules.json b/modules.json index 13919f04..47755872 100644 --- a/modules.json +++ b/modules.json @@ -7,17 +7,17 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] } } diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..f0c63f69 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..eec1db10 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..4274ed57 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ], + "1": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "2": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "versions": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "yml": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ] + } + ], + "timestamp": "2023-11-03T14:43:22.157011" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..1787b38a --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..9e19a74c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..b9e8f926 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process FASTQC" + script "../main.nf" + process "FASTQC" + tag "modules" + tag "modules_nfcore" + tag "fastqc" + + test("Single-Read") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) + } + } +// TODO +// // +// // Test with paired-end data +// // +// workflow test_fastqc_paired_end { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with interleaved data +// // +// workflow test_fastqc_interleaved { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with bam data +// // +// workflow test_fastqc_bam { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with multiple samples +// // +// workflow test_fastqc_multiple { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with custom prefix +// // +// workflow test_fastqc_custom_prefix { +// input = [ +// [ id:'mysample', single_end:true ], // meta map +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } +} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..636a32ce --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 00000000..7834294b --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..bc0bdb5b --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..c2dad217 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } + + test("MULTIQC: FASTQC and a config file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index 0d250ffd..41b7daba 100644 --- a/nextflow.config +++ b/nextflow.config @@ -14,7 +14,7 @@ params { input = null // References genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false @@ -82,6 +82,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -104,13 +105,13 @@ profiles { } docker { docker.enabled = true - docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + runOptions = '-u $(id -u):$(id -g)' } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -181,7 +182,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -204,6 +205,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -229,7 +233,7 @@ manifest { description = """Pipeline for processing 10x Genomics single cell rnaseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.4.1' + version = '2.5.0dev' doi = '' } From 4a3231abf6b66dbd425a6d0056f5d48c9e475619 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Wed, 20 Dec 2023 17:05:31 +0000 Subject: [PATCH 2/6] Template update for nf-core/tools version 2.11.1 --- .../{release-announcments.yml => release-announcements.yml} | 0 nextflow.config | 4 ++-- 2 files changed, 2 insertions(+), 2 deletions(-) rename .github/workflows/{release-announcments.yml => release-announcements.yml} (100%) diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcements.yml similarity index 100% rename from .github/workflows/release-announcments.yml rename to .github/workflows/release-announcements.yml diff --git a/nextflow.config b/nextflow.config index 41b7daba..68563110 100644 --- a/nextflow.config +++ b/nextflow.config @@ -111,10 +111,10 @@ profiles { shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false - runOptions = '-u $(id -u):$(id -g)' + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true From 7f4a70c23ce540326782ce4fce621549a34543d1 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 22 Dec 2023 08:25:06 +0100 Subject: [PATCH 3/6] Modulese updates --- modules.json | 24 ++-- .../nf-core/cellranger/count/environment.yml | 5 + modules/nf-core/cellranger/count/meta.yml | 4 +- .../count/templates/cellranger_count.py | 4 +- .../nf-core/cellranger/mkgtf/environment.yml | 5 + modules/nf-core/cellranger/mkgtf/meta.yml | 4 +- .../nf-core/cellranger/mkref/environment.yml | 5 + modules/nf-core/cellranger/mkref/meta.yml | 3 +- .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 7 +- modules/nf-core/fastqc/main.nf | 10 +- modules/nf-core/fastqc/meta.yml | 5 + modules/nf-core/fastqc/tests/main.nf.test | 89 ++++++++++++- modules/nf-core/gffread/environment.yml | 7 ++ modules/nf-core/gffread/main.nf | 12 +- modules/nf-core/gffread/meta.yml | 11 +- modules/nf-core/gffread/tests/main.nf.test | 61 +++++++++ .../nf-core/gffread/tests/main.nf.test.snap | 52 ++++++++ modules/nf-core/gffread/tests/nextflow.config | 5 + modules/nf-core/gffread/tests/tags.yml | 2 + modules/nf-core/gunzip/environment.yml | 7 ++ modules/nf-core/gunzip/main.nf | 2 +- modules/nf-core/gunzip/meta.yml | 4 + modules/nf-core/gunzip/tests/main.nf.test | 35 ++++++ .../nf-core/gunzip/tests/main.nf.test.snap | 31 +++++ modules/nf-core/gunzip/tests/tags.yml | 2 + .../kallistobustools/count/environment.yml | 7 ++ .../nf-core/kallistobustools/count/main.nf | 2 +- .../nf-core/kallistobustools/count/meta.yml | 5 +- .../kallistobustools/ref/environment.yml | 8 ++ modules/nf-core/kallistobustools/ref/main.nf | 2 +- modules/nf-core/kallistobustools/ref/meta.yml | 13 +- modules/nf-core/multiqc/main.nf | 8 +- modules/nf-core/multiqc/meta.yml | 11 +- .../star/genomegenerate/environment.yml | 11 ++ modules/nf-core/star/genomegenerate/main.nf | 89 ++++++++----- modules/nf-core/star/genomegenerate/meta.yml | 5 +- .../star/genomegenerate/tests/main.nf.test | 117 ++++++++++++++++++ .../genomegenerate/tests/main.nf.test.snap | 22 ++++ .../star/genomegenerate/tests/tags.yml | 2 + modules/nf-core/universc/environment.yml | 5 + modules/nf-core/universc/meta.yml | 6 +- 42 files changed, 616 insertions(+), 99 deletions(-) create mode 100644 modules/nf-core/cellranger/count/environment.yml create mode 100644 modules/nf-core/cellranger/mkgtf/environment.yml create mode 100644 modules/nf-core/cellranger/mkref/environment.yml create mode 100644 modules/nf-core/gffread/environment.yml create mode 100644 modules/nf-core/gffread/tests/main.nf.test create mode 100644 modules/nf-core/gffread/tests/main.nf.test.snap create mode 100644 modules/nf-core/gffread/tests/nextflow.config create mode 100644 modules/nf-core/gffread/tests/tags.yml create mode 100644 modules/nf-core/gunzip/environment.yml create mode 100644 modules/nf-core/gunzip/tests/main.nf.test create mode 100644 modules/nf-core/gunzip/tests/main.nf.test.snap create mode 100644 modules/nf-core/gunzip/tests/tags.yml create mode 100644 modules/nf-core/kallistobustools/count/environment.yml create mode 100644 modules/nf-core/kallistobustools/ref/environment.yml create mode 100644 modules/nf-core/star/genomegenerate/environment.yml create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/genomegenerate/tests/tags.yml create mode 100644 modules/nf-core/universc/environment.yml diff --git a/modules.json b/modules.json index 5b4e4a3f..a05f65d8 100644 --- a/modules.json +++ b/modules.json @@ -7,62 +7,62 @@ "nf-core": { "cellranger/count": { "branch": "master", - "git_sha": "5df79e0383386a9e43462a6e81bf978ce0a6db09", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "cellranger/mkgtf": { "branch": "master", - "git_sha": "716ef3019b66772a817b417078edce2f7b337858", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "cellranger/mkref": { "branch": "master", - "git_sha": "716ef3019b66772a817b417078edce2f7b337858", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", + "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53", "installed_by": ["modules"] }, "gffread": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8", "installed_by": ["modules"] }, "gunzip": { "branch": "master", - "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "kallistobustools/count": { "branch": "master", - "git_sha": "de204d3c950f091336539ad74f0e47ddffe69ed4", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "kallistobustools/ref": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", + "git_sha": "4ab13872435962dadc239979554d13709e20bf29", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", + "git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a", "installed_by": ["modules"] }, "universc": { "branch": "master", - "git_sha": "cf67a6d7d043e2bd6a3099be84c72046fc71508f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } diff --git a/modules/nf-core/cellranger/count/environment.yml b/modules/nf-core/cellranger/count/environment.yml new file mode 100644 index 00000000..662f747d --- /dev/null +++ b/modules/nf-core/cellranger/count/environment.yml @@ -0,0 +1,5 @@ +name: cellranger_count +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index c7d82bbc..a672180e 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -10,7 +10,6 @@ tools: homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - licence: 10x Genomics EULA input: - meta: @@ -47,3 +46,6 @@ output: authors: - "@ggabernet" - "@Emiller88" +maintainers: + - "@ggabernet" + - "@Emiller88" diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py index 4bfb9f4f..1527ba76 100644 --- a/modules/nf-core/cellranger/count/templates/cellranger_count.py +++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py @@ -34,11 +34,11 @@ def chunk_iter(seq, size): # Match R1 in the filename, but only if it is followed by a non-digit or non-character # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but # do not match "SRR12345", "file_INFIXR12", etc -filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])" +filename_pattern = r'([^a-zA-Z0-9])R1([^a-zA-Z0-9])' for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)): # double escapes are required because nextflow processes this python 'template' - if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name: + if re.sub(filename_pattern, r'\\1R2\\2', r1.name) != r2.name: raise AssertionError( dedent( f"""\ diff --git a/modules/nf-core/cellranger/mkgtf/environment.yml b/modules/nf-core/cellranger/mkgtf/environment.yml new file mode 100644 index 00000000..c81ef3e4 --- /dev/null +++ b/modules/nf-core/cellranger/mkgtf/environment.yml @@ -0,0 +1,5 @@ +name: cellranger_mkgtf +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml index e226e42d..7ec0e0a3 100644 --- a/modules/nf-core/cellranger/mkgtf/meta.yml +++ b/modules/nf-core/cellranger/mkgtf/meta.yml @@ -10,7 +10,6 @@ tools: homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - licence: 10x Genomics EULA input: - gtf: @@ -29,3 +28,6 @@ output: authors: - "@ggabernet" - "@Emiller88" +maintainers: + - "@ggabernet" + - "@Emiller88" diff --git a/modules/nf-core/cellranger/mkref/environment.yml b/modules/nf-core/cellranger/mkref/environment.yml new file mode 100644 index 00000000..9ca3e88c --- /dev/null +++ b/modules/nf-core/cellranger/mkref/environment.yml @@ -0,0 +1,5 @@ +name: cellranger_mkref +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index 1ad5d6e3..4cd9091c 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -10,7 +10,6 @@ tools: homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - licence: 10x Genomics EULA input: - fasta: @@ -35,3 +34,5 @@ output: pattern: "versions.yml" authors: - "@ggabernet" +maintainers: + - "@ggabernet" diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..9e19a74c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 3961de60..b9e8f926 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -1,13 +1,18 @@ nextflow_process { name "Test Process FASTQC" - script "modules/nf-core/fastqc/main.nf" + script "../main.nf" process "FASTQC" + tag "modules" + tag "modules_nfcore" tag "fastqc" test("Single-Read") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = [ @@ -21,12 +26,84 @@ nextflow_process { } then { - assert process.success - assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" - assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") - assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) } - } +// TODO +// // +// // Test with paired-end data +// // +// workflow test_fastqc_paired_end { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with interleaved data +// // +// workflow test_fastqc_interleaved { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with bam data +// // +// workflow test_fastqc_bam { +// input = [ +// [id: 'test', single_end: false], // meta map +// file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with multiple samples +// // +// workflow test_fastqc_multiple { +// input = [ +// [id: 'test', single_end: false], // meta map +// [ +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), +// file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) +// ] +// ] + +// FASTQC ( input ) +// } + +// // +// // Test with custom prefix +// // +// workflow test_fastqc_custom_prefix { +// input = [ +// [ id:'mysample', single_end:true ], // meta map +// file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) +// ] +// FASTQC ( input ) +// } } diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml new file mode 100644 index 00000000..5398f71c --- /dev/null +++ b/modules/nf-core/gffread/environment.yml @@ -0,0 +1,7 @@ +name: gffread +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gffread=0.12.1 diff --git a/modules/nf-core/gffread/main.nf b/modules/nf-core/gffread/main.nf index f4472b0e..d8a473e0 100644 --- a/modules/nf-core/gffread/main.nf +++ b/modules/nf-core/gffread/main.nf @@ -2,7 +2,7 @@ process GFFREAD { tag "$gff" label 'process_low' - conda "bioconda::gffread=0.12.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' : 'biocontainers/gffread:0.12.1--h8b12597_0' }" @@ -11,20 +11,22 @@ process GFFREAD { path gff output: - path "*.gtf" , emit: gtf + path "*.gtf" , emit: gtf , optional: true + path "*.gff3" , emit: gffread_gff , optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${gff.baseName}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${gff.baseName}" + def extension = args.contains("-T") ? 'gtf' : 'gffread.gff3' """ gffread \\ $gff \\ $args \\ - -o ${prefix}.gtf + -o ${prefix}.${extension} cat <<-END_VERSIONS > versions.yml "${task.process}": gffread: \$(gffread --version 2>&1) diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index 20335747..27ac3105 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -12,22 +12,25 @@ tools: tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] - input: - gff: type: file description: A reference file in either the GFF3, GFF2 or GTF format. pattern: "*.{gff, gtf}" - output: - gtf: type: file - description: GTF file resulting from the conversion of the GFF input file + description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present pattern: "*.{gtf}" + - gffread_gff: + type: file + description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent + pattern: "*.{gff3}" - versions: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@emiller88" +maintainers: + - "@emiller88" diff --git a/modules/nf-core/gffread/tests/main.nf.test b/modules/nf-core/gffread/tests/main.nf.test new file mode 100644 index 00000000..3c064b31 --- /dev/null +++ b/modules/nf-core/gffread/tests/main.nf.test @@ -0,0 +1,61 @@ +nextflow_process { + + name "Test Process GFFREAD" + script "../main.nf" + process "GFFREAD" + + tag "gffread" + tag "modules_nfcore" + tag "modules" + + test("sarscov2-gff3-gtf") { + + config "./nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf != null }, + { assert process.out.gffread_gff == [] } + ) + } + + } + + test("sarscov2-gff3-gff3") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.gtf == [] }, + { assert process.out.gffread_gff != null }, + ) + } + + } + +} diff --git a/modules/nf-core/gffread/tests/main.nf.test.snap b/modules/nf-core/gffread/tests/main.nf.test.snap new file mode 100644 index 00000000..1f1342e1 --- /dev/null +++ b/modules/nf-core/gffread/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "sarscov2-gff3-gtf": { + "content": [ + { + "0": [ + "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3" + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + ], + "gffread_gff": [ + + ], + "gtf": [ + "genome.gtf:md5,2394072d7d31530dfd590c4a117bf6e3" + ], + "versions": [ + "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + ] + } + ], + "timestamp": "2023-11-29T15:39:30.006985" + }, + "sarscov2-gff3-gff3": { + "content": [ + { + "0": [ + + ], + "1": [ + "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d" + ], + "2": [ + "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + ], + "gffread_gff": [ + "genome.gffread.gff3:md5,a7d40d99dcddac23ac673c473279ea2d" + ], + "gtf": [ + + ], + "versions": [ + "versions.yml:md5,a71b6cdfa528dd206a238ec64bae13d6" + ] + } + ], + "timestamp": "2023-11-29T15:39:34.636061" + } +} \ No newline at end of file diff --git a/modules/nf-core/gffread/tests/nextflow.config b/modules/nf-core/gffread/tests/nextflow.config new file mode 100644 index 00000000..74b25094 --- /dev/null +++ b/modules/nf-core/gffread/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GFFREAD { + ext.args = '-T' + } +} diff --git a/modules/nf-core/gffread/tests/tags.yml b/modules/nf-core/gffread/tests/tags.yml new file mode 100644 index 00000000..05576065 --- /dev/null +++ b/modules/nf-core/gffread/tests/tags.yml @@ -0,0 +1,2 @@ +gffread: + - modules/nf-core/gffread/** diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 00000000..25910b34 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +name: gunzip +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index 73bf08cd..468a6f28 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -2,7 +2,7 @@ process GUNZIP { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7" + 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' }" diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 4cdcdf4c..231034f2 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -33,3 +33,7 @@ authors: - "@joseespinosa" - "@drpatelh" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 00000000..d0317922 --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,35 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [], + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 00000000..720fd9ff --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,31 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "timestamp": "2023-10-17T15:35:37.690477896" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 00000000..fd3f6915 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/kallistobustools/count/environment.yml b/modules/nf-core/kallistobustools/count/environment.yml new file mode 100644 index 00000000..7ff8a2da --- /dev/null +++ b/modules/nf-core/kallistobustools/count/environment.yml @@ -0,0 +1,7 @@ +name: kallistobustools_count +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::kb-python=0.27.2 diff --git a/modules/nf-core/kallistobustools/count/main.nf b/modules/nf-core/kallistobustools/count/main.nf index b7942fc2..036bb35d 100644 --- a/modules/nf-core/kallistobustools/count/main.nf +++ b/modules/nf-core/kallistobustools/count/main.nf @@ -2,7 +2,7 @@ process KALLISTOBUSTOOLS_COUNT { tag "$meta.id" label 'process_medium' - conda "bioconda::kb-python=0.27.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : 'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }" diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml index f25b7bc4..7491248c 100644 --- a/modules/nf-core/kallistobustools/count/meta.yml +++ b/modules/nf-core/kallistobustools/count/meta.yml @@ -13,7 +13,6 @@ tools: documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python licence: MIT License - input: - meta: type: map @@ -49,7 +48,6 @@ input: type: string description: String value defining the sequencing technology used. pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" - output: - meta: type: map @@ -64,6 +62,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@flowuenne" +maintainers: + - "@flowuenne" diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml new file mode 100644 index 00000000..acbd0e0a --- /dev/null +++ b/modules/nf-core/kallistobustools/ref/environment.yml @@ -0,0 +1,8 @@ +name: kallistobustools_ref +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::kb-python=0.27.2 + - conda-forge::requests>=2.23.0 diff --git a/modules/nf-core/kallistobustools/ref/main.nf b/modules/nf-core/kallistobustools/ref/main.nf index 9d7f1741..68d72ca9 100644 --- a/modules/nf-core/kallistobustools/ref/main.nf +++ b/modules/nf-core/kallistobustools/ref/main.nf @@ -2,7 +2,7 @@ process KALLISTOBUSTOOLS_REF { tag "$fasta" label 'process_medium' - conda "bioconda::kb-python=0.27.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kb-python:0.27.2--pyhdfd78af_0' : 'biocontainers/kb-python:0.27.2--pyhdfd78af_0' }" diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml index aca61082..00be5143 100644 --- a/modules/nf-core/kallistobustools/ref/meta.yml +++ b/modules/nf-core/kallistobustools/ref/meta.yml @@ -1,7 +1,11 @@ name: kallistobustools_ref description: index creation for kb count quantification of single-cell data. keywords: - - kallisto-bustools + - scRNA-seq + - count + - single-cell + - kallisto + - bustools - index tools: - kb: @@ -11,7 +15,6 @@ tools: tool_dev_url: https://github.com/pachterlab/kb_python doi: "10.22002/D1.1876" licence: MIT License - input: - fasta: type: file @@ -22,10 +25,9 @@ input: description: Genomic gtf file pattern: "*.{gtf,gtf.gz}" - workflow_mode: - type: value + type: string description: String value defining workflow to use, can be one of "standard", "lamanno", "nucleus" pattern: "{standard,lamanno,nucleus}" - output: - versions: type: file @@ -55,6 +57,7 @@ output: type: file description: intron transcript to capture file pattern: "*intron_t2c.{txt}" - authors: - "@flowuenne" +maintainers: + - "@flowuenne" diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 65d7dd0d..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml new file mode 100644 index 00000000..93e4476a --- /dev/null +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -0,0 +1,11 @@ +name: star_genomegenerate + +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - bioconda::samtools=1.18 + - bioconda::star=2.7.10a + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 43424042..b8855715 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -2,10 +2,10 @@ process STAR_GENOMEGENERATE { tag "$fasta" label 'process_high' - conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }" input: tuple val(meta), path(fasta) @@ -19,9 +19,10 @@ process STAR_GENOMEGENERATE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def args_list = args.tokenize() - def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + def args = task.ext.args ?: '' + def args_list = args.tokenize() + def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : '' + def include_gtf = gtf ? "--sjdbGTFfile $gtf" : '' if (args_list.contains('--genomeSAindexNbases')) { """ mkdir star @@ -29,7 +30,7 @@ process STAR_GENOMEGENERATE { --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ - --sjdbGTFfile $gtf \\ + $include_gtf \\ --runThreadN $task.cpus \\ $memory \\ $args @@ -51,7 +52,7 @@ process STAR_GENOMEGENERATE { --runMode genomeGenerate \\ --genomeDir star/ \\ --genomeFastaFiles $fasta \\ - --sjdbGTFfile $gtf \\ + $include_gtf \\ --runThreadN $task.cpus \\ --genomeSAindexNbases \$NUM_BASES \\ $memory \\ @@ -67,30 +68,52 @@ process STAR_GENOMEGENERATE { } stub: - """ - mkdir star - touch star/Genome - touch star/Log.out - touch star/SA - touch star/SAindex - touch star/chrLength.txt - touch star/chrName.txt - touch star/chrNameLength.txt - touch star/chrStart.txt - touch star/exonGeTrInfo.tab - touch star/exonInfo.tab - touch star/geneInfo.tab - touch star/genomeParameters.txt - touch star/sjdbInfo.txt - touch star/sjdbList.fromGTF.out.tab - touch star/sjdbList.out.tab - touch star/transcriptInfo.tab + if (gtf) { + """ + mkdir star + touch star/Genome + touch star/Log.out + touch star/SA + touch star/SAindex + touch star/chrLength.txt + touch star/chrName.txt + touch star/chrNameLength.txt + touch star/chrStart.txt + touch star/exonGeTrInfo.tab + touch star/exonInfo.tab + touch star/geneInfo.tab + touch star/genomeParameters.txt + touch star/sjdbInfo.txt + touch star/sjdbList.fromGTF.out.tab + touch star/sjdbList.out.tab + touch star/transcriptInfo.tab - cat <<-END_VERSIONS > versions.yml - "${task.process}": - star: \$(STAR --version | sed -e "s/STAR_//g") - samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') - gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') - END_VERSIONS - """ + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + } else { + """ + mkdir star + touch star/Genome + touch star/Log.out + touch star/SA + touch star/SAindex + touch star/chrLength.txt + touch star/chrName.txt + touch star/chrNameLength.txt + touch star/chrStart.txt + touch star/genomeParameters.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + star: \$(STAR --version | sed -e "s/STAR_//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//') + END_VERSIONS + """ + } } diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index eba2d9cf..1061e1b8 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -31,7 +31,6 @@ input: - gtf: type: file description: GTF file of the reference genome - output: - meta: type: map @@ -46,7 +45,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@kevinmenden" - "@drpatelh" +maintainers: + - "@kevinmenden" + - "@drpatelh" diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test new file mode 100644 index 00000000..af0c9421 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_process { + + name "Test Process STAR_GENOMEGENERATE" + script "../main.nf" + process "STAR_GENOMEGENERATE" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/genomegenerate" + + test("homo_sapiens") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_with_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-without_gtf") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ [], [] ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("homo_sapiens-without_gtf-stub") { + + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ [], [] ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).listFiles().collect { it.getName() }.sort().toString()).match("index_without_gtf") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap new file mode 100644 index 00000000..9de08c74 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -0,0 +1,22 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,46b8f1f34bb7f23892cd1eb249ed4d7f" + ] + ], + "timestamp": "2023-12-19T11:05:51.741109" + }, + "index_with_gtf": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, exonGeTrInfo.tab, exonInfo.tab, geneInfo.tab, genomeParameters.txt, sjdbInfo.txt, sjdbList.fromGTF.out.tab, sjdbList.out.tab, transcriptInfo.tab]" + ], + "timestamp": "2023-12-19T11:38:14.551548" + }, + "index_without_gtf": { + "content": [ + "[Genome, Log.out, SA, SAindex, chrLength.txt, chrName.txt, chrNameLength.txt, chrStart.txt, genomeParameters.txt]" + ], + "timestamp": "2023-12-19T11:38:22.382905" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml new file mode 100644 index 00000000..79f619bf --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/tags.yml @@ -0,0 +1,2 @@ +star/genomegenerate: + - modules/nf-core/star/genomegenerate/** diff --git a/modules/nf-core/universc/environment.yml b/modules/nf-core/universc/environment.yml new file mode 100644 index 00000000..e9cdf650 --- /dev/null +++ b/modules/nf-core/universc/environment.yml @@ -0,0 +1,5 @@ +name: universc +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/universc/meta.yml b/modules/nf-core/universc/meta.yml index 681bb849..92a46bc6 100644 --- a/modules/nf-core/universc/meta.yml +++ b/modules/nf-core/universc/meta.yml @@ -15,7 +15,6 @@ tools: tool_dev_url: "https://github.com/minoda-lab/universc" doi: "10.1101/2021.01.19.427209" licence: ["GPL-3.0-or-later"] - input: - meta: type: map @@ -26,7 +25,6 @@ input: type: file description: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - output: - outs: type: file @@ -36,7 +34,9 @@ output: type: file description: File containing software version pattern: "versions.yml" - authors: - "@kbattenb" - "@tomkellygenetics" +maintainers: + - "@kbattenb" + - "@tomkellygenetics" From 29eab6b46806f162d8da27c428894d023f22960e Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 22 Dec 2023 08:32:40 +0100 Subject: [PATCH 4/6] Fix numba cache dir --- bin/concat_h5ad.py | 5 +++++ bin/mtx_to_h5ad.py | 6 +++++- modules/local/simpleaf_index.nf | 1 + 3 files changed, 11 insertions(+), 1 deletion(-) diff --git a/bin/concat_h5ad.py b/bin/concat_h5ad.py index e38ca80e..6ecc17fd 100755 --- a/bin/concat_h5ad.py +++ b/bin/concat_h5ad.py @@ -1,4 +1,9 @@ #!/usr/bin/env python + +# Set numba chache dir to current working directory (which is a writable mount also in containers) +import os +os.environ["NUMBA_CACHE_DIR"] = "." + import scanpy as sc, anndata as ad, pandas as pd from pathlib import Path import argparse diff --git a/bin/mtx_to_h5ad.py b/bin/mtx_to_h5ad.py index 40e1e025..62449f5f 100755 --- a/bin/mtx_to_h5ad.py +++ b/bin/mtx_to_h5ad.py @@ -1,8 +1,12 @@ #!/usr/bin/env python + +# Set numba chache dir to current working directory (which is a writable mount also in containers) +import os +os.environ["NUMBA_CACHE_DIR"] = "." + import scanpy as sc import pandas as pd import argparse -import os from scipy import io from anndata import AnnData diff --git a/modules/local/simpleaf_index.nf b/modules/local/simpleaf_index.nf index 5e8f5c42..8e8bd519 100644 --- a/modules/local/simpleaf_index.nf +++ b/modules/local/simpleaf_index.nf @@ -27,6 +27,7 @@ process SIMPLEAF_INDEX { """ # export required var export ALEVIN_FRY_HOME=. + export NUMBA_CACHE_DIR=. # prep simpleaf simpleaf set-paths From 06c79d3b34b0d7a5b922559d9eaa314570afe18b Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 22 Dec 2023 08:35:47 +0100 Subject: [PATCH 5/6] Fix numba cache dir in simpleaf quant --- modules/local/simpleaf_quant.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/local/simpleaf_quant.nf b/modules/local/simpleaf_quant.nf index f350acf3..abb58404 100644 --- a/modules/local/simpleaf_quant.nf +++ b/modules/local/simpleaf_quant.nf @@ -53,6 +53,7 @@ process SIMPLEAF_QUANT { """ # export required var export ALEVIN_FRY_HOME=. + export NUMBA_CACHE_DIR=. # prep simpleaf simpleaf set-paths From 5e2273b9aa490ad8a3537dd138acd616e6d83a90 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Fri, 22 Dec 2023 08:37:57 +0100 Subject: [PATCH 6/6] black --- bin/concat_h5ad.py | 1 + bin/mtx_to_h5ad.py | 1 + .../nf-core/cellranger/count/templates/cellranger_count.py | 4 ++-- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/bin/concat_h5ad.py b/bin/concat_h5ad.py index 6ecc17fd..43ea071a 100755 --- a/bin/concat_h5ad.py +++ b/bin/concat_h5ad.py @@ -2,6 +2,7 @@ # Set numba chache dir to current working directory (which is a writable mount also in containers) import os + os.environ["NUMBA_CACHE_DIR"] = "." import scanpy as sc, anndata as ad, pandas as pd diff --git a/bin/mtx_to_h5ad.py b/bin/mtx_to_h5ad.py index 62449f5f..3282122d 100755 --- a/bin/mtx_to_h5ad.py +++ b/bin/mtx_to_h5ad.py @@ -2,6 +2,7 @@ # Set numba chache dir to current working directory (which is a writable mount also in containers) import os + os.environ["NUMBA_CACHE_DIR"] = "." import scanpy as sc diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py index 1527ba76..4bfb9f4f 100644 --- a/modules/nf-core/cellranger/count/templates/cellranger_count.py +++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py @@ -34,11 +34,11 @@ def chunk_iter(seq, size): # Match R1 in the filename, but only if it is followed by a non-digit or non-character # match "file_R1.fastq.gz", "file.R1_000.fastq.gz", etc. but # do not match "SRR12345", "file_INFIXR12", etc -filename_pattern = r'([^a-zA-Z0-9])R1([^a-zA-Z0-9])' +filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])" for i, (r1, r2) in enumerate(chunk_iter(fastqs, 2)): # double escapes are required because nextflow processes this python 'template' - if re.sub(filename_pattern, r'\\1R2\\2', r1.name) != r2.name: + if re.sub(filename_pattern, r"\\1R2\\2", r1.name) != r2.name: raise AssertionError( dedent( f"""\