process GATK4_VARIANTRECALIBRATOR { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" input: tuple val(meta), path(vcf) , path(tbi) path fasta path fai path dict val allelespecific tuple path(resvcfs), path(restbis), val(reslabels) val annotation val mode val create_rscript output: tuple val(meta), path("*.recal") , emit: recal tuple val(meta), path("*.idx") , emit: idx tuple val(meta), path("*.tranches"), emit: tranches tuple val(meta), path("*plots.R") , emit: plots, optional:true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" refCommand = fasta ? "-R ${fasta} " : '' alleleSpecificCommand = allelespecific ? '-AS' : '' resourceCommand = '--resource:' + reslabels.join( ' --resource:') annotationCommand = '-an ' + annotation.join( ' -an ') modeCommand = mode ? "--mode ${mode} " : 'SNP' rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : '' def avail_mem = 3 if (!task.memory) { log.info '[GATK VariantRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { avail_mem = task.memory.giga } """ gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\ ${refCommand} \\ -V ${vcf} \\ ${alleleSpecificCommand} \\ ${resourceCommand} \\ ${annotationCommand} \\ ${modeCommand} \\ -O ${prefix}.recal \\ --tranches-file ${prefix}.tranches \\ ${rscriptCommand}\\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ }