mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
a74e8436cc
* create transdecoder/longorf module * module transdecoder * main.nf * transdecoder/longorf ready to PR * review comments update * transdecoder_longorf reviewed main.nf * removed predict * test.yml updated * pytest run Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
37 lines
1.2 KiB
Text
37 lines
1.2 KiB
Text
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
|
|
"""
|
|
}
|