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a0d91e4a93
* add picard-addorreplacereadgroups * add picard_addorreplacereadgroups * add new line to main.nf * remove trailing whitespaces * remove trailing whitespaces * change to output in test yml * add when directive * picard 2.26.10 -> 2.26.9 * picard 2.26.10 -> 2.26.9 test yml Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
53 lines
1.7 KiB
Text
53 lines
1.7 KiB
Text
process PICARD_ADDORREPLACEREADGROUPS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.26.9--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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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def ID = task.ext.id ?: "id"
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def LIBRARY= task.ext.library ?: "library"
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def PLATFORM= task.ext.platform ?: "illumina"
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def BARCODE= task.ext.barcode ?: "barcode"
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def SAMPLE= task.ext.sample ?: "sample"
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def INDEX= task.ext.index ?: "index"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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picard \\
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AddOrReplaceReadGroups \\
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-Xmx${avail_mem}g \\
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--INPUT ${bam} \\
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--OUTPUT ${prefix}.bam \\
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-ID ${ID} \\
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-LB ${LIBRARY} \\
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-PL ${PLATFORM} \\
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-PU ${BARCODE} \\
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-SM ${SAMPLE} \\
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-CREATE_INDEX true
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(picard AddOrReplaceReadGroups --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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