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54 lines
2.1 KiB
Text
54 lines
2.1 KiB
Text
process MUSCLE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/muscle:3.8.1551--h7d875b9_6' :
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'quay.io/biocontainers/muscle:3.8.1551--h7d875b9_6' }"
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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 "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 fasta_out = args.contains('-fasta') ? "-fastaout ${prefix}_muscle_msa.afa" : ''
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def clw_out = args.contains('-clw') ? "-clwout ${prefix}_muscle_msa.clw" : ''
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def msf_out = args.contains('-msf') ? "-msfout ${prefix}_muscle_msa.msf" : ''
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def phys_out = args.contains('-phys') ? "-physout ${prefix}_muscle_msa.phys" : ''
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def phyi_out = args.contains('-phyi') ? "-phyiout ${prefix}_muscle_msa.phyi" : ''
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def html_out = args.contains('-html') ? "-htmlout ${prefix}_muscle_msa.html" : ''
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def tree_out = args.contains('-maketree') ? "-out ${prefix}_muscle_msa.tree" : ''
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"""
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muscle \\
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$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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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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muscle: \$(muscle -version | sed 's/^MUSCLE v//; s/by.*\$//')
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END_VERSIONS
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"""
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}
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