nf-core_modules/modules/csvtk/concat/main.nf
2022-02-04 09:53:32 +01:00

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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
when:
task.ext.when == null || task.ext.when
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
"""
}