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0d1e21686a
* Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability * Fix EC lint for unrelated hmmcopy module
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
process PICARD_COLLECTHSMETRICS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::picard=2.26.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.26.7--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.7--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam)
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path fasta
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path fai
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path bait_intervals
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path target_intervals
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output:
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tuple val(meta), path("*collecthsmetrics.txt"), emit: hs_metrics
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def reference = fasta ? "-R $fasta" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard CollectHsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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-Xmx${avail_mem}g \\
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CollectHsMetrics \\
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$args \\
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$reference \\
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-BAIT_INTERVALS $bait_intervals \\
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-TARGET_INTERVALS $target_intervals \\
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-INPUT $bam \\
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-OUTPUT ${prefix}_collecthsmetrics.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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}
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