nf-core_modules/modules/mcroni/main.nf
2022-06-27 10:35:41 +02:00

43 lines
1.4 KiB
Text

process MCRONI {
tag "$meta.id"
label 'process_low'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0':
'quay.io/biocontainers/mcroni:1.0.4--pyh5e36f6f_0' }"
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("*.tsv") , emit: tsv
tuple val(meta), path("*.fa"), optional: true, emit: fa
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
def fasta_name = fasta.getName().replace(".gz", "")
def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
if [ "$is_compressed" == "true" ]; then
gzip -c -d $fasta > $fasta_name
fi
mcroni \\
$args \\
--output $prefix \\
--fasta $fasta_name
cat <<-END_VERSIONS > versions.yml
"${task.process}":
mcroni: $VERSION
END_VERSIONS
"""
}