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67 lines
2.1 KiB
Text
67 lines
2.1 KiB
Text
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process GATK4_PRINTSVEVIDENCE {
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tag "${meta.id}"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(evidence), path(evidence_index)
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path bed
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path fasta
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path fasta_fai
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path dict
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output:
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tuple val(meta), path("*.txt.gz") , emit: printed_evidence
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tuple val(meta), path("*.txt.gz.tbi") , emit: printed_evidence_index
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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 intervals = bed ? "--intervals ${bed}" : ""
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def reference = fasta ? "--reference ${fasta}" : ""
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def file_name = evidence.getFileName()
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def file_type = file_name =~ ".sr.txt" ? "sr" :
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file_name =~ ".pe.txt" ? "pe" :
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file_name =~ ".baf.txt" ? "baf" :
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file_name =~ ".rd.txt" ? "rd" :
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false
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if(!file_type){
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error("The input file name should contain one of the following: '.sr.txt', '.pe.txt', '.baf.txt', '.rd.txt'")
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}
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK PRINTSVEVIDENCE] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" PrintSVEvidence \\
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--evidence-file ${evidence} \\
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--sequence-dictionary ${dict} \\
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${intervals} \\
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${reference} \\
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--output ${prefix}.${file_type}.txt.gz \\
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--tmp-dir . \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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