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32 lines
982 B
Text
32 lines
982 B
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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def options = initOptions(params.options)
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process MULTIQC {
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tag "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), publish_id: '') }
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conda(params.enable_conda ? "bioconda::multiqc=1.9" : null)
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container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_0"
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input:
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// path multiqc_config
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// path multiqc_custom_config
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path('fastqc/*')
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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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script:
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// def custom_config = params.multiqc_config ? "--config $multiqc_custom_config" : ''
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"""
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multiqc -f $options.args $custom_config .
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"""
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}
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