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edfe28a5e0
* update tests * update * update * make the manta inputs consistant for germline/somatic/tumoronly * match chromosomes to cram file (chr21) * undo genotypegvfs * undo genotypegvfs * update VariantRecalibrator * lint * add '--resource:' tag Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
56 lines
2 KiB
Text
56 lines
2 KiB
Text
process GATK4_VARIANTRECALIBRATOR {
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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(vcf), path(tbi) // input vcf and tbi of variants to recalibrate
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path resource_vcf // resource vcf
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path resource_tbi // resource tbi
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val labels // string (or list of strings) containing dedicated resource labels already formatted with '--resource:' tag
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path fasta
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path fai
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path dict
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output:
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tuple val(meta), path("*.recal") , emit: recal
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tuple val(meta), path("*.idx") , emit: idx
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tuple val(meta), path("*.tranches"), emit: tranches
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tuple val(meta), path("*plots.R") , emit: plots, 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 reference_command = fasta ? "--reference $fasta " : ''
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def labels_command = labels.join(' ')
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK VariantRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\
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--variant $vcf \\
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--output ${prefix}.recal \\
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--tranches-file ${prefix}.tranches \\
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$reference_command \\
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--tmp-dir . \\
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$labels_command \\
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$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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