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https://github.com/MillironX/nf-core_modules.git
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ab67a1d41b
* Update fastqc to produce multi-version versions.yml * Update readme and pull request template * Fix markdownlint * remove variable * Change publish dir to lowercase * Re-add getSoftwareName * Add custom pytest-workflow test to ensure versions.yml is valid * Add docstring * Remove __init__.py as it is not needed * Remove changes to README, since this part went to nf-co.re * Add NF_CORE_TEST env var * Fix editorconfig * Add additional consistency checks for versions.yml * Update multiqc module * Fix output channel
39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process MULTIQC {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
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} else {
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container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
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}
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input:
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path multiqc_files
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output:
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path "*multiqc_report.html", emit: report
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path "*_data" , emit: data
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path "*_plots" , optional:true, emit: plots
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path "versions.yml" , emit: version
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script:
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def software = getSoftwareName(task.process)
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"""
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multiqc -f $options.args .
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
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END_VERSIONS
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"""
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}
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