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https://github.com/MillironX/nf-core_modules.git
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e751e5040a
* Bump software versions for viralrecon modules * Remove custom params.save_unaligned from bowtie2_align * Unify samtools modules and error if input and output names are the same * Fix ALL the tests
42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
process PICARD_MARKDUPLICATES {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.bai") , optional:true, emit: bai
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tuple val(meta), path("*.metrics.txt"), emit: 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 ?: "${meta.id}"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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-Xmx${avail_mem}g \\
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MarkDuplicates \\
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$args \\
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I=$bam \\
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O=${prefix}.bam \\
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M=${prefix}.MarkDuplicates.metrics.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(echo \$(picard MarkDuplicates --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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