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48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process PICARD_COLLECTMULTIPLEMETRICS {
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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:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/picard:2.23.2--0"
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//container "https://depot.galaxyproject.org/singularity/picard:2.23.2--0"
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conda (params.conda ? "bioconda::picard=2.23.2" : null)
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input:
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tuple val(meta), path(bam)
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path fasta
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val options
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output:
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tuple val(meta), path("*_metrics"), emit: metrics
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tuple val(meta), path("*.pdf"), emit: pdf
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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 ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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-Xmx${avail_mem}g \\
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CollectMultipleMetrics \\
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$ioptions.args \\
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INPUT=$bam \\
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OUTPUT=${prefix}.CollectMultipleMetrics \\
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REFERENCE_SEQUENCE=$fasta
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echo \$(picard CollectMultipleMetrics --version 2>&1) | awk -F' ' '{print \$NF}' > ${software}.version.txt
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"""
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}
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