2021-02-17 17:19:47 +00:00
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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2021-03-15 12:16:43 +00:00
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options = initOptions(params.options)
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2021-02-17 17:19:47 +00:00
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def VERSION = '0.4.1'
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process SEQWISH_INDUCE {
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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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2021-04-09 16:23:56 +00:00
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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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2021-02-17 17:19:47 +00:00
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2021-07-28 08:10:44 +00:00
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conda (params.enable_conda ? 'bioconda::seqwish=0.7.1' : null)
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2021-02-17 17:19:47 +00:00
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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2021-07-28 08:10:44 +00:00
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container "https://depot.galaxyproject.org/singularity/seqwish:0.7.1--h2e03b76_0"
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2021-02-17 17:19:47 +00:00
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} else {
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2021-07-28 08:10:44 +00:00
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container "quay.io/biocontainers/seqwish:0.7.1--h2e03b76_0"
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2021-02-17 17:19:47 +00:00
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}
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input:
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tuple val(meta), path(paf), path(fasta)
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output:
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tuple val(meta), path("*.gfa"), emit: gfa
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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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"""
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seqwish \\
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--threads $task.cpus \\
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--paf-alns=$paf \\
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--seqs=$fasta \\
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--gfa=${prefix}.gfa \\
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$options.args
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echo $VERSION > ${software}.version.txt
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"""
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}
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