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48 lines
1.8 KiB
Text
48 lines
1.8 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process CLONALFRAMEML {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::clonalframeml=1.12" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/clonalframeml:1.12--h7d875b9_1"
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} else {
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container "quay.io/biocontainers/clonalframeml:1.12--h7d875b9_1"
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}
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input:
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tuple val(meta), path(newick), path(msa)
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output:
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tuple val(meta), path("*.emsim.txt") , emit: emsim, optional: true
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tuple val(meta), path("*.em.txt") , emit: em
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tuple val(meta), path("*.importation_status.txt") , emit: status
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tuple val(meta), path("*.labelled_tree.newick") , emit: newick
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tuple val(meta), path("*.ML_sequence.fasta") , emit: fasta
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tuple val(meta), path("*.position_cross_reference.txt"), emit: pos_ref
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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ClonalFrameML \\
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$newick \\
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<(gzip -cdf $msa) \\
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$prefix \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo \$(ClonalFrameML -version 2>&1) | sed 's/^.*ClonalFrameML v//' )
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END_VERSIONS
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"""
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}
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