process CNVKIT_BATCH { tag "$meta.id" label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0' : 'quay.io/biocontainers/cnvkit:0.9.9--pyhdfd78af_0' }" input: tuple val(meta), path(tumor), path(normal) path fasta path targets path reference output: tuple val(meta), path("*.bed"), emit: bed tuple val(meta), path("*.cnn"), emit: cnn, optional: true tuple val(meta), path("*.cnr"), emit: cnr, optional: true tuple val(meta), path("*.cns"), emit: cns, optional: true path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' def normal_args = normal ? "--normal $normal" : "" def fasta_args = fasta ? "--fasta $fasta" : "" def reference_args = reference ? "--reference $reference" : "" def target_args = "" if (args.contains("--method wgs") || args.contains("-m wgs")) { target_args = targets ? "--targets $targets" : "" } else { target_args = "--targets $targets" } """ cnvkit.py \\ batch \\ $tumor \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ }