diff --git a/.nf-core.yml b/.nf-core.yml new file mode 100644 index 0000000..3805dc8 --- /dev/null +++ b/.nf-core.yml @@ -0,0 +1 @@ +repository_type: pipeline diff --git a/CHANGELOG.md b/CHANGELOG.md index fa8d993..b4620ea 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,9 +9,13 @@ Initial release of nf-core/dragen, created with the [nf-core](https://nf-co.re/) ### `Added` +- Publish csv outputs from `DRAGEN` for `multiQC` module +- Stub runs for `DRAGEN`, including creation of a file recognised by the `multiQC` module + ### `Fixed` - Fixed error `Access to 'FASTQC.out' is undefined since the workflow 'FASTQC' has not been invoked before accessing the output attribute` when `-skip_fastqc` enabled by adjusting channel generation +- Added `arm` profile for docker runs on Mac OS ### `Dependencies` diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml new file mode 100644 index 0000000..1c7c313 --- /dev/null +++ b/assets/methods_description_template.yml @@ -0,0 +1,25 @@ +id: "seqeralabs-dragen-methods-description" +description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." +section_name: "seqeralabs/nf-dragen Methods Description" +section_href: "https://github.com/seqeralabs/nf-dragen" +plot_type: "html" +## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## You inject any metadata in the Nextflow '${workflow}' object +data: | +

Methods

+

Data was processed using seqeralabs/nf-dragen v${workflow.manifest.version}.

+

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

+ 
${workflow.commandLine}
+

References

+ +
+
Notes:
+ +
diff --git a/conf/modules.config b/conf/modules.config index f84d881..0a0ddfe 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -65,7 +65,7 @@ if (!params.skip_dragen) { withName: 'DRAGEN_FASTQ_TO_BAM_DNA' { publishDir = [ - path: { "${params.outdir}/dragen/dna_fastq_to_bam" }, + path: { "${params.outdir}/dragen/dna_fastq_to_bam/${meta.id}/" }, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -74,7 +74,7 @@ if (!params.skip_dragen) { withName: 'DRAGEN_FASTQ_TO_VCF_DNA' { ext.args = '--enable-variant-caller true' publishDir = [ - path: { "${params.outdir}/dragen/dna_fastq_to_vcf" }, + path: { "${params.outdir}/dragen/dna_fastq_to_vcf/${meta.id}/" }, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -83,7 +83,7 @@ if (!params.skip_dragen) { withName: 'DRAGEN_FASTQ_TO_BAM_RNA' { ext.args = '--enable-rna true' publishDir = [ - path: { "${params.outdir}/dragen/rna_fastq_to_bam" }, + path: { "${params.outdir}/dragen/rna_fastq_to_bam/${meta.id}/" }, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/lib/WorkflowDragen.groovy b/lib/WorkflowDragen.groovy index 9dce044..e8a6dcc 100755 --- a/lib/WorkflowDragen.groovy +++ b/lib/WorkflowDragen.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the workflow/dragen.nf in the nf-core/dragen pipeline // +import groovy.text.SimpleTemplateEngine + class WorkflowDragen { // @@ -43,6 +45,23 @@ class WorkflowDragen { return yaml_file_text } + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + def meta = [:] + meta.workflow = run_workflow.toMap() + meta["manifest_map"] = run_workflow.manifest.toMap() + + meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" + meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + + def methods_text = mqc_methods_yaml.text + + def engine = new SimpleTemplateEngine() + def description_html = engine.createTemplate(methods_text).make(meta) + + return description_html + } + // // Exit pipeline if incorrect --genome key provided // diff --git a/modules.json b/modules.json index 3d97359..1a4abe6 100644 --- a/modules.json +++ b/modules.json @@ -1,17 +1,31 @@ { - "name": "nf-core/dragen", - "homePage": "https://github.com/nf-core/dragen", + "name": "nf-dragen", + "homePage": "https://github.com/drpatelh/nf-dragen", "repos": { - "nf-core/modules": { - "custom/dumpsoftwareversions": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "https://github.com/nf-core/modules.git": { + "modules": { + "nf-core": { + "custom/dumpsoftwareversions": { + "branch": "master", + "git_sha": "7101db4432d3268b7fcb5b8f75fa0a022dc5561b", + "installed_by": ["modules"] + }, + "fastqc": { + "branch": "master", + "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "installed_by": ["modules"] + }, + "multiqc": { + "branch": "master", + "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba", + "installed_by": ["modules"], + "patch": "modules/nf-core/multiqc/multiqc.diff" + } + } }, - "fastqc": { - "git_sha": "9d0cad583b9a71a6509b754fdf589cbfbed08961" - }, - "multiqc": { - "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" + "subworkflows": { + "nf-core": {} } } } -} \ No newline at end of file +} diff --git a/modules/local/dragen.nf b/modules/local/dragen.nf index 6363fdd..7f65ffb 100644 --- a/modules/local/dragen.nf +++ b/modules/local/dragen.nf @@ -16,6 +16,7 @@ process DRAGEN { tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: tbi , optional:true tuple val(meta), path("${prefix}.hard-filtered.vcf.gz") , emit: vcf_filtered, optional:true tuple val(meta), path("${prefix}.hard-filtered.vcf.gz.tbi"), emit: tbi_filtered, optional:true + tuple val(meta), path("${prefix}.*.csv") , emit: csv , optional:true path "versions.yml" , emit: versions script: @@ -52,4 +53,33 @@ process DRAGEN { dragen: \$(echo \$(/opt/edico/bin/dragen --version 2>&1) | sed -e "s/dragen Version //g") END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + // Generate stub files + // Include one possible csv file, and faked data to prompt multiqc + """ + touch ${prefix}.bam + touch ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + touch ${prefix}.hard-filtered.vcf.gz + touch ${prefix}.hard-filtered.vcf.gz.tbi + + # Define the header row of the CSV file + echo "RUN TIME,,Time loading reference,00:00.1,0.09" > ${prefix}.time_metrics.csv + echo "RUN TIME,,Time aligning reads,00:00.5,0.53" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time sorting,00:00.4,0.38" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time DRAGStr calibration,00:00.0,0" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time saving map/align output,00:05.6,5.57" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time variant calling,00:05.5,5.45" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time partitioning,00:00.1,0.12" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time structural variant calling,00:02.8,2.83" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Time accessing license server,00:13.2,13.21" >> ${prefix}.time_metrics.csv + echo "RUN TIME,,Total runtime,00:27.2,27.17" >> ${prefix}.time_metrics.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + dragen: \$(echo "vSTUB") + END_VERSIONS + """ } diff --git a/modules/local/dragen_buildhashtable.nf b/modules/local/dragen_buildhashtable.nf index 7f6d27f..9b1ac9d 100644 --- a/modules/local/dragen_buildhashtable.nf +++ b/modules/local/dragen_buildhashtable.nf @@ -30,4 +30,15 @@ process DRAGEN_BUILDHASHTABLE { dragen: \$(echo \$(/opt/edico/bin/dragen --version 2>&1) | sed -e "s/dragen Version //g") END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: 'dragen' + """ + mkdir -p $prefix + touch $prefix/dragen.ht + cat <<-END_VERSIONS > versions.yml + "${task.process}": + dragen: \$(echo "v3.4.12") + END_VERSIONS + """ } diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf similarity index 75% rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf rename to modules/nf-core/custom/dumpsoftwareversions/main.nf index 934bb46..800a609 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -1,11 +1,11 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { - label 'process_low' + label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda (params.enable_conda ? "bioconda::multiqc=1.11" : null) + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions @@ -15,6 +15,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { path "software_versions_mqc.yml", emit: mqc_yml path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' template 'dumpsoftwareversions.py' diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml similarity index 97% rename from modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml rename to modules/nf-core/custom/dumpsoftwareversions/meta.yml index 5b5b8a6..60b546a 100644 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -8,7 +8,7 @@ tools: description: Custom module used to dump software versions within the nf-core pipeline template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools - licence: ['MIT'] + licence: ["MIT"] input: - versions: type: file diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py new file mode 100644 index 0000000..da03340 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python + + +"""Provide functions to merge multiple versions.yml files.""" + + +import yaml +import platform +from textwrap import dedent + + +def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" + html = [ + dedent( + """\\ + + + + + + + + + + """ + ) + ] + for process, tmp_versions in sorted(versions.items()): + html.append("") + for i, (tool, version) in enumerate(sorted(tmp_versions.items())): + html.append( + dedent( + f"""\\ + + + + + + """ + ) + ) + html.append("") + html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") + return "\\n".join(html) + + +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf new file mode 100644 index 0000000..9ae5838 --- /dev/null +++ b/modules/nf-core/fastqc/main.nf @@ -0,0 +1,51 @@ +process FASTQC { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::fastqc=0.11.9" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : + 'quay.io/biocontainers/fastqc:0.11.9--0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip") , emit: zip + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // Make list of old name and new name pairs to use for renaming in the bash while loop + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + """ + printf "%s %s\\n" $rename_to | while read old_name new_name; do + [ -f "\${new_name}" ] || ln -s \$old_name \$new_name + done + fastqc $args --threads $task.cpus $renamed_files + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.html + touch ${prefix}.zip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml new file mode 100644 index 0000000..4da5bb5 --- /dev/null +++ b/modules/nf-core/fastqc/meta.yml @@ -0,0 +1,52 @@ +name: fastqc +description: Run FastQC on sequenced reads +keywords: + - quality control + - qc + - adapters + - fastq +tools: + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py deleted file mode 100644 index d139039..0000000 --- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env python - -import yaml -import platform -from textwrap import dedent - - -def _make_versions_html(versions): - html = [ - dedent( - """\\ - - - - - - - - - - """ - ) - ] - for process, tmp_versions in sorted(versions.items()): - html.append("") - for i, (tool, version) in enumerate(sorted(tmp_versions.items())): - html.append( - dedent( - f"""\\ - - - - - - """ - ) - ) - html.append("") - html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") - return "\\n".join(html) - - -versions_this_module = {} -versions_this_module["${task.process}"] = { - "python": platform.python_version(), - "yaml": yaml.__version__, -} - -with open("$versions") as f: - versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module - -# aggregate versions by the module name (derived from fully-qualified process name) -versions_by_module = {} -for process, process_versions in versions_by_process.items(): - module = process.split(":")[-1] - try: - assert versions_by_module[module] == process_versions, ( - "We assume that software versions are the same between all modules. " - "If you see this error-message it means you discovered an edge-case " - "and should open an issue in nf-core/tools. " - ) - except KeyError: - versions_by_module[module] = process_versions - -versions_by_module["Workflow"] = { - "Nextflow": "$workflow.nextflow.version", - "$workflow.manifest.name": "$workflow.manifest.version", -} - -versions_mqc = { - "id": "software_versions", - "section_name": "${workflow.manifest.name} Software Versions", - "section_href": "https://github.com/${workflow.manifest.name}", - "plot_type": "html", - "description": "are collected at run time from the software output.", - "data": _make_versions_html(versions_by_module), -} - -with open("software_versions.yml", "w") as f: - yaml.dump(versions_by_module, f, default_flow_style=False) -with open("software_versions_mqc.yml", "w") as f: - yaml.dump(versions_mqc, f, default_flow_style=False) - -with open("versions.yml", "w") as f: - yaml.dump(versions_this_module, f, default_flow_style=False) diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/modules/fastqc/main.nf deleted file mode 100644 index d250eca..0000000 --- a/modules/nf-core/modules/fastqc/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - script: - def args = task.ext.args ?: '' - // Add soft-links to original FastQs for consistent naming in pipeline - def prefix = task.ext.prefix ?: "${meta.id}" - if (meta.single_end) { - """ - [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz - fastqc $args --threads $task.cpus ${prefix}.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } else { - """ - [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz - [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz - fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) - END_VERSIONS - """ - } -} diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/modules/fastqc/meta.yml deleted file mode 100644 index b09553a..0000000 --- a/modules/nf-core/modules/fastqc/meta.yml +++ /dev/null @@ -1,52 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ['GPL-2.0-only'] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/modules/multiqc/meta.yml deleted file mode 100644 index 63c75a4..0000000 --- a/modules/nf-core/modules/multiqc/meta.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: MultiQC -description: Aggregate results from bioinformatics analyses across many samples into a single report -keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report -tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ['GPL-3.0-or-later'] -input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC -output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/multiqc/main.nf similarity index 52% rename from modules/nf-core/modules/multiqc/main.nf rename to modules/nf-core/multiqc/main.nf index 3dceb16..b65b8f0 100644 --- a/modules/nf-core/modules/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,13 +1,16 @@ process MULTIQC { - label 'process_medium' + label 'process_single' - conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null) + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: - path multiqc_files + path multiqc_files, stageAs: "?/*" + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) output: path "*multiqc_report.html", emit: report @@ -15,14 +18,25 @@ process MULTIQC { path "*_plots" , optional:true, emit: plots path "versions.yml" , emit: versions + when: + task.ext.when == null || task.ext.when + script: def args = task.ext.args ?: '' + def config = multiqc_config ? "--config $multiqc_config" : '' + def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' """ - multiqc -f $args . + multiqc \\ + --force \\ + $args \\ + $config \\ + $extra_config \\ + . cat <<-END_VERSIONS > versions.yml "${task.process}": multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) END_VERSIONS """ + } diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml new file mode 100644 index 0000000..ebc29b2 --- /dev/null +++ b/modules/nf-core/multiqc/meta.yml @@ -0,0 +1,55 @@ +name: MultiQC +description: Aggregate results from bioinformatics analyses across many samples into a single report +keywords: + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report +tools: + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] + +input: + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. + pattern: "*.{yml,yaml}" + - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + +output: + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff new file mode 100644 index 0000000..1c798fb --- /dev/null +++ b/modules/nf-core/multiqc/multiqc.diff @@ -0,0 +1,21 @@ +Changes in module 'nf-core/multiqc' +--- modules/nf-core/multiqc/main.nf ++++ modules/nf-core/multiqc/main.nf +@@ -39,15 +39,4 @@ + END_VERSIONS + """ + +- stub: +- """ +- touch multiqc_data +- touch multiqc_plots +- touch multiqc_report.html +- +- cat <<-END_VERSIONS > versions.yml +- "${task.process}": +- multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) +- END_VERSIONS +- """ + } + +************************************************************ diff --git a/nextflow.config b/nextflow.config index ec79952..98c886b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -23,9 +23,11 @@ params { igenomes_ignore = false // MultiQC options - multiqc_config = null - multiqc_title = null - max_multiqc_email_size = '25.MB' + multiqc_config = null + multiqc_title = null + max_multiqc_email_size = '25.MB' + multiqc_logo = null + multiqc_methods_description = null // Boilerplate options outdir = './results' @@ -84,6 +86,9 @@ profiles { shifter.enabled = false charliecloud.enabled = false } + arm { + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + } singularity { singularity.enabled = true singularity.autoMounts = true diff --git a/nextflow_schema.json b/nextflow_schema.json index 26b21bd..e40bf9d 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -226,6 +226,17 @@ "fa_icon": "fas fa-cog", "hidden": true }, + "multiqc_logo": { + "type": "string", + "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", + "fa_icon": "fas fa-image", + "hidden": true + }, + "multiqc_methods_description": { + "type": "string", + "description": "Custom MultiQC yaml file containing HTML including a methods description.", + "fa_icon": "fas fa-cog" + }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", diff --git a/workflows/dragen.nf b/workflows/dragen.nf index be28045..c99edc1 100644 --- a/workflows/dragen.nf +++ b/workflows/dragen.nf @@ -24,8 +24,10 @@ if (params.fasta) { ch_fasta = file(params.fasta) } else { exit 1, 'Genome fasta ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config) : Channel.empty() +ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) +ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true ) : Channel.empty() +ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() +ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -56,9 +58,9 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check' // // MODULE: Installed directly from nf-core/modules // -include { FASTQC } from '../modules/nf-core/modules/fastqc/main' -include { MULTIQC } from '../modules/nf-core/modules/multiqc/main' -include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' +include { FASTQC } from '../modules/nf-core/fastqc/main' +include { MULTIQC } from '../modules/nf-core/multiqc/main' +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -93,6 +95,10 @@ workflow DRAGEN { ch_multiqc_fastqc = FASTQC.out.zip } + // + // SUBWORKFLOW: Build index and run DRAGEN + // + ch_multiqc_dragen = Channel.empty() if (!params.skip_dragen) { // @@ -119,6 +125,7 @@ workflow DRAGEN { DRAGEN_BUILDHASHTABLE_DNA.out.index ) ch_versions = ch_versions.mix(DRAGEN_FASTQ_TO_BAM_DNA.out.versions.first()) + ch_multiqc_dragen = ch_multiqc_dragen.mix(DRAGEN_FASTQ_TO_BAM_DNA.out.csv) // // MODULE: Run DRAGEN on DNA samples to generate VCF from FastQ @@ -128,6 +135,7 @@ workflow DRAGEN { DRAGEN_BUILDHASHTABLE_DNA.out.index ) ch_versions = ch_versions.mix(DRAGEN_FASTQ_TO_VCF_DNA.out.versions.first()) + ch_multiqc_dragen = ch_multiqc_dragen.mix(DRAGEN_FASTQ_TO_VCF_DNA.out.csv) // // MODULE: Run DRAGEN on RNA samples to generate BAM from FastQ @@ -137,6 +145,7 @@ workflow DRAGEN { DRAGEN_BUILDHASHTABLE_RNA.out.index ) ch_versions = ch_versions.mix(DRAGEN_FASTQ_TO_BAM_RNA.out.versions.first()) + ch_multiqc_dragen = ch_multiqc_dragen.mix(DRAGEN_FASTQ_TO_BAM_RNA.out.csv) } // @@ -152,15 +161,21 @@ workflow DRAGEN { workflow_summary = WorkflowDragen.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) + methods_description = WorkflowDragen.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + ch_methods_description = Channel.value(methods_description) + ch_multiqc_files = Channel.empty() - ch_multiqc_files = ch_multiqc_files.mix(Channel.from(ch_multiqc_config)) - ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_custom_config.collect().ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) + ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_fastqc.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(ch_multiqc_dragen.collect{it[1]}.ifEmpty([])) MULTIQC ( - ch_multiqc_files.collect() + ch_multiqc_files.collect(), + ch_multiqc_config.toList(), + ch_multiqc_custom_config.toList(), + ch_multiqc_logo.toList() ) multiqc_report = MULTIQC.out.report.toList() ch_versions = ch_versions.mix(MULTIQC.out.versions)