From 4475b7e334a6eca6b65bf999c5ce0f3f65dba919 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 19 Dec 2023 19:47:00 +0000 Subject: [PATCH] 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 +- .nf-core.yml | 2 +- README.md | 17 +-- assets/multiqc_config.yml | 2 +- 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 | 8 +- nextflow_schema.json | 16 +-- 33 files changed, 361 insertions(+), 77 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 1189151..cde3aa6 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 b716bb3..775ca31 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/rang - [ ] If necessary, also make a PR on the nf-core/rangeland _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 b65ba9a..226bce4 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 c57b539..6286d83 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 b8bdd21..905c58e 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 25488dc..acf7269 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/.nf-core.yml b/.nf-core.yml index 96b0d30..af643f6 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,4 +2,4 @@ repository_type: pipeline template: prefix: nf-core skip: - - igenomes + - igenomes diff --git a/README.md b/README.md index eb73b46..37605da 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 3bf0482..2d0c6ee 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/rangeland + This report has been generated by the nf-core/rangeland analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: diff --git a/assets/slackreport.json b/assets/slackreport.json index af53fb9..50d914f 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/rangeland v${version} - ${runName}", + "author_name": "nf-core/rangeland ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules.config b/conf/modules.config index 39e8138..d91c6ab 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -39,7 +39,7 @@ process { } withName: 'MULTIQC' { - ext.args = params.multiqc_title ? "--title \"$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 286718c..a4ed357 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 01b8653..e248e4c 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 f2f2a26..93e746a 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 0000000..f0c63f6 --- /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 ebc8727..7685b33 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 c32657d..5f15a5f 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 0000000..eec1db1 --- /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 0000000..4274ed5 --- /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 0000000..405aa24 --- /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 0000000..1787b38 --- /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 249f906..9e19a74 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 4da5bb5..ee5507e 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 0000000..b9e8f92 --- /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 0000000..636a32c --- /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 0000000..7834294 --- /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 0000000..bc0bdb5 --- /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 1fc387b..00cc48d 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 f93b5ee..f1aa660 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: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 0000000..c2dad21 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,63 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + when { + params { + outdir = "$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 0000000..bea6c0d --- /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 3c2b52b..9410428 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,6 +78,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -100,13 +101,13 @@ 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' @@ -177,7 +178,7 @@ 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 } // Export these variables to prevent local Python/R libraries from conflicting with those in the container @@ -194,6 +195,9 @@ 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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 34856c4..b418065 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,10 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input", - "outdir" - ], + "required": ["input", "outdir"], "properties": { "input": { "type": "string", @@ -171,14 +168,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email_on_fail": { @@ -282,4 +272,4 @@ "$ref": "#/definitions/generic_options" } ] -} \ No newline at end of file +}