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378fa5fbb4
* initial version of gamma module * remove trailing whitespace * prettier fix * hardcode version number * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/gamma/meta.yml Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * update meta and prettier * add whitespaces * add fasta output and tests Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
41 lines
1.2 KiB
Text
41 lines
1.2 KiB
Text
def VERSION = '2.1' // Version information not provided by tool on CLI
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process GAMMA {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
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'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(fasta)
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path(db)
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output:
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tuple val(meta), path("*.gamma") , emit: gamma
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tuple val(meta), path("*.psl") , emit: psl
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tuple val(meta), path("*.gff") , optional:true , emit: gff
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tuple val(meta), path("*.fasta"), optional:true , emit: fasta
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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GAMMA.py \\
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$args \\
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$fasta \\
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$db \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gamma: $VERSION
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END_VERSIONS
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"""
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}
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