nf-core_modules/modules/transdecoder/longorf/main.nf

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process TRANSDECODER_LONGORF {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::transdecoder=5.5.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4' :
'quay.io/comp-bio-aging/transdecoder' }"
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("${meta.id}/*.pep") , emit: pep
tuple val(meta), path("${meta.id}/*.gff3"), emit: gff3
tuple val(meta), path("${meta.id}/*.cds") , emit: cds
tuple val(meta), path("${meta.id}/*.dat") , emit: dat
path("${meta.id}/") , emit: folder
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
TransDecoder.LongOrfs \\
$args \\
-O $prefix \\
-t \\
$fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
transdecoder: \$(echo \$(TransDecoder.LongOrfs --version) | sed -e "s/TransDecoder.LongOrfs //g")
END_VERSIONS
"""
}