nf-core_modules/modules/cat/cat/main.nf
Ramprasad Neethiraj eeda4136c0
Update cat module (#1469)
* fix cat stub

* add test

* commit suggestions

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-03-31 13:42:44 +02:00

62 lines
2 KiB
Text

process CAT_CAT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
'quay.io/biocontainers/pigz:2.3.4' }"
input:
tuple val(meta), path(files_in)
output:
tuple val(meta), path("${prefix}"), emit: file_out
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def file_list = files_in.collect { it.toString() }
// | input | output | command1 | command2 |
// |-----------|------------|----------|----------|
// | gzipped | gzipped | cat | |
// | ungzipped | ungzipped | cat | |
// | gzipped | ungzipped | zcat | |
// | ungzipped | gzipped | cat | pigz |
// Use input file ending as default
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
out_zip = prefix.endsWith('.gz')
in_zip = file_list[0].endsWith('.gz')
command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
"""
$command1 \\
$args \\
${file_list.join(' ')} \\
$command2 \\
> ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
stub:
def file_list = files_in.collect { it.toString() }
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
"""
touch $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}