nf-core_modules/modules/csvtk/concat/main.nf

51 lines
1.8 KiB
Text
Raw Normal View History

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process CSVTK_CONCAT {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::csvtk=0.23.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/csvtk:0.23.0--h9ee0642_0"
} else {
container "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:
prefix = options.suffix ? "${meta.id}${options.suffix}" : "${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 \\
$options.args \\
--num-cpus $task.cpus \\
--delimiter "${delimiter}" \\
--out-delimiter "${out_delimiter}" \\
--out-file ${prefix}.${out_extension} \\
$csv
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
END_VERSIONS
"""
}