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3f14b1fabe
* add shovill module * removed deprecated shovill module * fix line ending in functions.nf * fix yaml indentation * reduce spades memory usage * update md5sums * remove non reproducible md5sum * Update test.yml Remove last non-reproducible md5sum. * purely cosmetic order change * proper process label, improve output readability Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
47 lines
1.7 KiB
Text
47 lines
1.7 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 SHOVILL {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::shovill=1.1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/shovill:1.1.0--0"
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} else {
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container "quay.io/biocontainers/shovill:1.1.0--0"
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}
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("contigs.fa") , emit: contigs
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tuple val(meta), path("shovill.corrections") , emit: corrections
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tuple val(meta), path("shovill.log") , emit: log
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tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
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tuple val(meta), path("contigs.{fastg,gfa,LastGraph}") , optional:true, 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 memory = task.memory.toGiga()
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"""
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shovill \\
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--R1 ${reads[0]} \\
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--R2 ${reads[1]} \\
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$options.args \\
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--cpus $task.cpus \\
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--ram $memory \\
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--outdir ./ \\
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--force
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echo \$(shovill --version 2>&1) | sed 's/^.*shovill //' > ${software}.version.txt
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"""
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}
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