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https://github.com/MillironX/nf-core_modules.git
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d16f1ea4d7
* add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
36 lines
1.1 KiB
Text
36 lines
1.1 KiB
Text
process PIRATE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' :
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'quay.io/biocontainers/pirate:1.0.4--hdfd78af_2' }"
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input:
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tuple val(meta), path(gff)
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output:
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tuple val(meta), path("results/*") , emit: results
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tuple val(meta), path("results/core_alignment.fasta"), optional: true, emit: aln
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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 ?: "${meta.id}"
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"""
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PIRATE \\
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$args \\
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--threads $task.cpus \\
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--input ./ \\
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--output results/
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
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END_VERSIONS
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"""
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}
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