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57 lines
2.1 KiB
Text
57 lines
2.1 KiB
Text
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process GATK4_COLLECTSVEVIDENCE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
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container "${ 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(input), path(input_index), path(allele_count_vcf), path(allele_count_vcf_tbi)
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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("*.sr.txt.gz") , emit: split_read_evidence
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tuple val(meta), path("*.sr.txt.gz.tbi"), emit: split_read_evidence_index
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tuple val(meta), path("*.pe.txt.gz") , emit: paired_end_evidence
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tuple val(meta), path("*.pe.txt.gz.tbi"), emit: paired_end_evidence_index
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tuple val(meta), path("*.ld.txt.gz") , emit: allele_counts, optional:true
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tuple val(meta), path("*.ld.txt.gz.tbi"), emit: allele_counts_index, optional:true
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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 allele_vcf = allele_count_vcf ? "--allele-count-file ${prefix}.ld.txt.gz --allele-count-vcf ${allele_count_vcf}" : ""
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def reference = fasta ? "--reference ${fasta}" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK COLLECTSVEVIDENCE] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" CollectSVEvidence \\
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${args} \\
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--input ${input} \\
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--sr-file ${prefix}.sr.txt.gz \\
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--pe-file ${prefix}.pe.txt.gz \\
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${allele_vcf} \\
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${reference} \\
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--tmp-dir . \\
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cat <<-END_VERSIONS > versions.yml
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"${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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