process CSVTK_CONCAT { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0' : 'quay.io/biocontainers/csvtk:0.23.0--h9ee0642_0' }" input: tuple val(meta), path(csv) val in_format val out_format output: tuple val(meta), path("${prefix}.${out_extension}"), emit: csv path "versions.yml" , emit: versions script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def delimiter = in_format == "tsv" ? "\t" : (in_format == "csv" ? "," : in_format) def out_delimiter = out_format == "tsv" ? "\t" : (out_format == "csv" ? "," : out_format) out_extension = out_format == "tsv" ? 'tsv' : 'csv' """ csvtk \\ concat \\ $args \\ --num-cpus $task.cpus \\ --delimiter "${delimiter}" \\ --out-delimiter "${out_delimiter}" \\ --out-file ${prefix}.${out_extension} \\ $csv cat <<-END_VERSIONS > versions.yml "${task.process}": csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" )) END_VERSIONS """ }