nf-core_modules/modules/multiqc/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process MULTIQC {
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label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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) {
container "https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0"
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} else {
container "quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0"
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}
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input:
path multiqc_files
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output:
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path "*multiqc_report.html", emit: report
path "*_data" , emit: data
path "*_plots" , optional:true, emit: plots
path "*.version.txt" , emit: version
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script:
def software = getSoftwareName(task.process)
"""
multiqc -f $options.args .
multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
"""
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}