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https://github.com/MillironX/nf-core_modules.git
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74b569b66a
* Created epang module from template * Module seems to be working * Namechange to epang_place * Move model to meta map * Fix linting problems * Prettier * Forgot --threads! * Moved module to epang * Move reference file params * Directory output * Make all args optional * Added inputs for three other types of file arguments * Update modules/epang/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Add directory to output doc, reorder the other * Make model specification less hardcoded Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
56 lines
2 KiB
Text
56 lines
2 KiB
Text
process EPANG {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1':
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'quay.io/biocontainers/epa-ng:0.3.8--h9a82719_1' }"
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input:
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tuple val(meta), path(queryaln)
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path referencealn
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path referencetree
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path bfastfile
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path splitfile
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path binaryfile
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output:
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tuple val(meta), path("./."), emit: epang , optional: true
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path "*.epa_result.jplace" , emit: jplace , optional: true
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path "*.epa_info.log" , emit: log
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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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def queryarg = queryaln ? "--query $queryaln" : ""
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def refalnarg = referencealn ? "--ref-msa $referencealn" : ""
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def reftreearg = referencetree ? "--tree $referencetree" : ""
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def bfastarg = bfastfile ? "--bfast $bfastfile" : ""
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def splitarg = splitfile ? "--split $splitfile" : ""
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def binaryarg = binaryfile ? "--binary $binaryfile" : ""
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if ( binaryfile && ( referencealn || referencetree ) ) error "[EPANG] Cannot supply both binary and reference MSA or reference tree. Check input"
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"""
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epa-ng \\
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$args \\
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--threads $task.cpus \\
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$queryarg \\
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$refalnarg \\
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$reftreearg \\
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$bfastarg \\
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$splitarg \\
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$binaryarg
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[ -e epa_result.jplace ] && mv epa_result.jplace ${prefix}.epa_result.jplace
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[ -e epa_info.log ] && mv epa_info.log ${prefix}.epa_info.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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epang: \$(echo \$(epa-ng --version 2>&1) | sed 's/^EPA-ng v//')
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END_VERSIONS
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"""
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}
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