process CONTROLFREEC_FREEC2BED { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::control-freec=11.6" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1': 'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }" input: tuple val(meta), path(ratio) output: tuple val(meta), path("*.bed"), emit: bed path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ freec2bed.pl -f ${ratio} ${args} > ${prefix}.bed cat <<-END_VERSIONS > versions.yml "${task.process}": controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" ) END_VERSIONS """ stub: def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.bed cat <<-END_VERSIONS > versions.yml "${task.process}": controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" ) END_VERSIONS """ }