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60 lines
2.6 KiB
Text
60 lines
2.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process MUSCLE {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6"
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} else {
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container "quay.io/biocontainers/muscle:3.8.1551--h7d875b9_6"
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}
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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("*.afa") , optional: true, emit: aligned_fasta
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tuple val(meta), path("*.phyi"), optional: true, emit: phyi
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tuple val(meta), path("*.phys"), optional: true, emit: phys
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tuple val(meta), path("*.clw") , optional: true, emit: clustalw
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tuple val(meta), path("*.html"), optional: true, emit: html
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tuple val(meta), path("*.msf") , optional: true, emit: msf
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tuple val(meta), path("*.tree"), optional: true, emit: tree
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path "*.log" , emit: log
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def fasta_out = options.args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : ''
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def clw_out = options.args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : ''
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def msf_out = options.args.contains('-msf') ? "-msfout ${prefix}_muscle_msa.msf" : ''
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def phys_out = options.args.contains('-phys') ? "-physout ${prefix}_muscle_msa.phys" : ''
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def phyi_out = options.args.contains('-phyi') ? "-phyiout ${prefix}_muscle_msa.phyi" : ''
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def html_out = options.args.contains('-html') ? "-htmlout ${prefix}_muscle_msa.html" : ''
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def tree_out = options.args.contains('-maketree') ? "-out ${prefix}_muscle_msa.tree" : ''
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"""
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muscle \\
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$options.args \\
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-in $fasta \\
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$fasta_out \\
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$clw_out \\
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$msf_out \\
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$phys_out \\
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$phyi_out \\
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$html_out \\
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$tree_out \\
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-loga muscle_msa.log
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muscle -version | sed 's/^MUSCLE v//; s/by.*\$//' > ${software}.version.txt
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"""
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}
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