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977d96ed0b
* add racon * add racon * add racon * add racon module * add racon module * edit racon module * edit racon module * edit racon module * edit racon module Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
// 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 RACON {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::racon=1.4.20" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1"
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} else {
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container "quay.io/biocontainers/racon:1.4.20--h9a82719_1"
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}
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input:
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tuple val(meta), path(reads), path(assembly), path(paf)
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output:
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tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
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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}" : "${meta.id}"
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"""
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racon -t "${task.cpus}" \\
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"${reads}" \\
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"${paf}" \\
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$options.args \\
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"${assembly}" > \\
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${prefix}_assembly_consensus.fasta
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gzip -n ${prefix}_assembly_consensus.fasta
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( racon --version 2>&1 | sed 's/^.*v//' )
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END_VERSIONS
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"""
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}
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