mirror of
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71 lines
3 KiB
Text
71 lines
3 KiB
Text
process ARTIC_MINION {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::artic=1.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/artic:1.2.1--py_0' :
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'quay.io/biocontainers/artic:1.2.1--py_0' }"
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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 "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def version = scheme_version.toString().toLowerCase().replaceAll('v','')
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def fast5 = fast5_dir ? "--fast5-directory $fast5_dir" : ""
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def summary = sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""
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def model = ""
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if (args.tokenize().contains('--medaka')) {
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fast5 = ""
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summary = ""
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model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
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}
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def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
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"""
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$hd5_plugin_path
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artic \\
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minion \\
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$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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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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artic: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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