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42 lines
1.5 KiB
Text
42 lines
1.5 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 RASUSA {
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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::rasusa=0.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/rasusa:0.3.0--h779adbc_1"
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} else {
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container "quay.io/biocontainers/rasusa:0.3.0--h779adbc_1"
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}
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input:
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tuple val(meta), path(reads), val(genome_size)
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val depth_cutoff
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output:
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tuple val(meta), path('*.fastq.gz'), emit: reads
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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 output = meta.single_end ? "--output ${prefix}.fastq.gz" : "--output ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz"
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"""
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rasusa \\
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$options.args \\
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--coverage $depth_cutoff \\
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--genome-size $genome_size \\
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--input $reads \\
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$output
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echo \$(rasusa --version 2>&1) | sed -e "s/rasusa //g" > ${software}.version.txt
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"""
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}
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