process CNVPYTOR_CALLCNVS { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2': 'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }" input: tuple val(meta), path(pytor) output: tuple val(meta), path("*.tsv"), emit: cnvs path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '1000' def prefix = task.ext.prefix ?: "${meta.id}" """ cnvpytor \\ -root $pytor \\ -call $args > ${prefix}.tsv cat <<-END_VERSIONS > versions.yml "${task.process}": cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' )) END_VERSIONS """ }