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https://github.com/MillironX/nf-core_modules.git
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c5235a983d
* Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
49 lines
1.7 KiB
Text
49 lines
1.7 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 PICARD_COLLECTWGSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? 'bioconda::picard=2.25.7' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/picard:2.25.7--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/picard:2.25.7--hdfd78af_0"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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path fasta
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output:
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tuple val(meta), path("*_metrics"), emit: metrics
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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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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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-Xmx${avail_mem}g \\
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CollectWgsMetrics \\
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$options.args \\
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INPUT=$bam \\
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OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
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REFERENCE_SEQUENCE=$fasta
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echo \$(picard CollectWgsMetrics --version 2>&1) | grep -o 'Version.*' | cut -f2- -d: > ${software}.version.txt
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"""
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}
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