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74 lines
3.2 KiB
Text
74 lines
3.2 KiB
Text
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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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options = initOptions(params.options)
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process ARTIC_MINION {
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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::artic=1.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0"
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} else {
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container "quay.io/biocontainers/artic:1.2.1--py_0"
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}
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input:
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tuple val(meta), path(fastq)
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path fast5_dir
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path sequencing_summary
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path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
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path ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
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path medaka_model
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val scheme
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val scheme_version
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output:
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tuple val(meta), path("${prefix}.*") , emit: results
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tuple val(meta), path("${prefix}.sorted.bam") , emit: bam
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tuple val(meta), path("${prefix}.sorted.bam.bai") , emit: bai
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tuple val(meta), path("${prefix}.trimmed.rg.sorted.bam") , emit: bam_trimmed
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tuple val(meta), path("${prefix}.trimmed.rg.sorted.bam.bai") , emit: bai_trimmed
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tuple val(meta), path("${prefix}.primertrimmed.rg.sorted.bam") , emit: bam_primertrimmed
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tuple val(meta), path("${prefix}.primertrimmed.rg.sorted.bam.bai"), emit: bai_primertrimmed
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tuple val(meta), path("${prefix}.consensus.fasta") , emit: fasta
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tuple val(meta), path("${prefix}.pass.vcf.gz") , emit: vcf
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tuple val(meta), path("${prefix}.pass.vcf.gz.tbi") , emit: tbi
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tuple val(meta), path("*.json"), optional:true , emit: json
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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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prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def version = scheme_version.toString().toLowerCase().replaceAll('v','')
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def fast5 = params.fast5_dir ? "--fast5-directory $fast5_dir" : ""
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def summary = params.sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
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def model = ""
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if (options.args.tokenize().contains('--medaka')) {
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fast5 = ""
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summary = ""
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model = file(params.artic_minion_medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $params.artic_minion_medaka_model"
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}
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"""
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artic \\
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minion \\
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$options.args \\
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--threads $task.cpus \\
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--read-file $fastq \\
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--scheme-directory ./primer-schemes \\
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--scheme-version $version \\
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$model \\
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$fast5 \\
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$summary \\
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$scheme \\
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$prefix
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echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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