// Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] options = initOptions(params.options) process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0" } else { container "quay.io/biocontainers/gatk4:4.2.0.0--0" } input: tuple val(meta), path(bam), path(bai), path(bqsr_table) path fasta path fastaidx path dict path intervals output: tuple val(meta), path("*.bam"), emit: bam path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def interval = intervals ? "-L ${intervals}" : "" """ gatk ApplyBQSR \\ -R $fasta \\ -I $bam \\ --bqsr-recal-file $bqsr_table \\ $interval \\ -O ${prefix}.bam \\ $options.args echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//' > ${software}.version.txt """ }