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* add racon * add medaka module * add medaka module * add medaka module * add medaka module * add medaka module * add medaka module * Indentation * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update main.nf * Update main.nf * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
47 lines
1.5 KiB
Text
47 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 MEDAKA {
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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::medaka=1.4.4" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0"
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} else {
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container "quay.io/biocontainers/medaka:1.4.4--py38h130def0_0"
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}
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input:
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tuple val(meta), path(reads), path(assembly)
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output:
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tuple val(meta), path("*.fa.gz"), emit: 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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medaka_consensus \\
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-t $task.cpus \\
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$options.args \\
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-i $reads \\
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-d $assembly \\
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-o ./
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mv consensus.fasta ${prefix}.fa
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gzip -n ${prefix}.fa
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( medaka --version 2>&1 | sed 's/medaka //g' )
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END_VERSIONS
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"""
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}
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