include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] options = initOptions(params.options) process FGBIO_CALLMOLECULARCONSENSUSREADS { 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::fgbio=1.3.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0" } else { container "quay.io/biocontainers/fgbio:1.3.0--0" } input: tuple val(meta), path(bam) 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}" """ fgbio \\ CallMolecularConsensusReads \\ -i $bam \\ $options.args \\ -o ${prefix}.bam fgbio --version | sed -e "s/fgbio v//g" > ${software}.version.txt """ }