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aa97b1be3e
* create transdecoder/longorf module * module transdecoder * main.nf * transdecoder/longorf ready to PR * review comments update * transdecoder/predict module create * test transdecoder/predict module * fix pytest * pytest passed * removed whitespace * Update meta.yml * Update meta.yml Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
37 lines
1.2 KiB
Text
37 lines
1.2 KiB
Text
process TRANSDECODER_PREDICT {
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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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path(fold)
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output:
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tuple val(meta), path("*.transdecoder.pep") , emit: pep
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tuple val(meta), path("*.transdecoder.gff3") , emit: gff3
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tuple val(meta), path("*.transdecoder.cds") , emit: cds
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tuple val(meta), path("*.transdecoder.bed") , emit: bed
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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 ?: "${meta.id}"
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"""
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TransDecoder.Predict \\
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$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.Predict --version) | sed -e "s/TransDecoder.Predict //g")
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END_VERSIONS
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"""
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}
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