// Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] options = initOptions(params.options) process GATK4_FASTQTOSAM { 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=4.2.0.0" : 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(reads) 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 read_files = meta.single_end ? "-F1 $reads" : "-F1 ${reads[0]} -F2 ${reads[1]}" """ gatk FastqToSam \\ $read_files \\ -O ${prefix}.bam \\ -SM $prefix \\ $options.args gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt """ }