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https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
35 lines
1.2 KiB
Text
35 lines
1.2 KiB
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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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), publish_id: '') }
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conda (params.enable_conda ? "bioconda::multiqc=1.9" : 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:1.9--pyh9f0ad1d_0"
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} else {
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container "quay.io/biocontainers/multiqc:1.9--pyh9f0ad1d_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 "*.version.txt" , 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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multiqc --version | sed -e "s/multiqc, version //g" > ${software}.version.txt
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"""
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}
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