// Import generic module functions include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' params.options = [:] options = initOptions(params.options) process CNVKIT { 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::cnvkit=0.9.9' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0" } else { container "quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0" } input: tuple val(meta), path(tumourbam), path(normalbam) path fasta path targetfile output: tuple val(meta), path("*.bed"), emit: bed tuple val(meta), path("*.cnn"), emit: cnn tuple val(meta), path("*.cnr"), emit: cnr tuple val(meta), path("*.cns"), emit: cns path "versions.yml" , emit: versions script: """ cnvkit.py \\ batch \\ $tumourbam \\ --normal $normalbam\\ --fasta $fasta \\ --targets $targetfile \\ $options.args cat <<-END_VERSIONS > versions.yml ${getProcessName(task.process)}: ${getSoftwareName(task.process)}: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ }