// Import generic module functions include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] options = initOptions(params.options) process GATK4_SPLITNCIGARREADS { 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), meta:meta, publish_by_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) tuple path(fasta), path(fai), path(dict) output: tuple val(meta), path('*.split_cigar.bam'), emit: bam path '*.version.txt' , emit: version script: def software = getSoftwareName(task.process) def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" """ gatk SplitNCigarReads \\ -R $fasta \\ -I $bam \\ -O ${prefix}.split_cigar.bam \\ $options.args gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt """ }