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62 lines
2.1 KiB
Text
62 lines
2.1 KiB
Text
process GATK4_VARIANTRECALIBRATOR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(vcf) , path(tbi)
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path fasta
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path fai
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path dict
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val allelespecific
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tuple path(resvcfs), path(restbis), val(reslabels)
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val annotation
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val mode
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val create_rscript
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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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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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refCommand = fasta ? "-R ${fasta} " : ''
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alleleSpecificCommand = allelespecific ? '-AS' : ''
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resourceCommand = '--resource:' + reslabels.join( ' --resource:')
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annotationCommand = '-an ' + annotation.join( ' -an ')
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modeCommand = mode ? "--mode ${mode} " : 'SNP'
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rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : ''
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK VariantRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\
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${refCommand} \\
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-V ${vcf} \\
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${alleleSpecificCommand} \\
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${resourceCommand} \\
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${annotationCommand} \\
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${modeCommand} \\
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-O ${prefix}.recal \\
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--tranches-file ${prefix}.tranches \\
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${rscriptCommand}\\
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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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