process ICHORCNA_CREATEPON { label 'process_low' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : 'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }" input: path wigs path gc_wig path map_wig path centromere output: path "*.rds" , emit: rds path "*.txt" , emit: txt path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def centro = centromere ? "--centromere ${centromere}" : '' def prefix = task.ext.prefix ?: "PoN" def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ echo ${wigs} | tr " " "\\n" > wig_files.txt createPanelOfNormals.R \\ --filelist wig_files.txt \\ --gcWig ${gc_wig} \\ --mapWig ${map_wig} \\ ${centro} \\ ${args} \\ --outfile ${prefix} rm wig_files.txt cat <<-END_VERSIONS > versions.yml "${task.process}": ichorcna: $VERSION END_VERSIONS """ }