// Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] def options = initOptions(params.options) process GATK4_SAMTOFASTQ { tag "$meta.id" label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0' } else { container 'quay.io/biocontainers/gatk4:4.1.9.0--py39_0' } input: tuple val(meta), path(bam) output: tuple val(meta), path('*.fastq.gz') , emit: fastq path '*.version.txt' , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz" """ gatk SamToFastq \\ I=$bam \\ $output \\ $options.args gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt """ }