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