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63 lines
2.0 KiB
Plaintext
63 lines
2.0 KiB
Plaintext
process PICARD_FILTERSAMREADS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
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'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(readlist)
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val filter
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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 ?: "${meta.id}"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Picard FilterSamReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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if ( filter == 'includeAligned' || filter == 'excludeAligned' ) {
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"""
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picard \\
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FilterSamReads \\
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-Xmx${avail_mem}g \\
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--INPUT $bam \\
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--OUTPUT ${prefix}.bam \\
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--FILTER $filter \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(picard FilterSamReads --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
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END_VERSIONS
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"""
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} else if ( filter == 'includeReadList' || filter == 'excludeReadList' ) {
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"""
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picard \\
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FilterSamReads \\
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-Xmx${avail_mem}g \\
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--INPUT $bam \\
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--OUTPUT ${prefix}.bam \\
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--FILTER $filter \\
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--READ_LIST_FILE $readlist \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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picard: \$(picard FilterSamReads --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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}
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