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49 lines
1.6 KiB
Text
49 lines
1.6 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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def options = initOptions(params.options)
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process IVAR_VARIANTS {
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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::ivar=1.3.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
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} else {
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container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
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}
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input:
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tuple val(meta), path(bam)
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path fasta
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output:
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tuple val(meta), path("*.tsv"), emit: variants
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tuple val(meta), path("*.mpileup"), emit: mpileup
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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 prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def save_mpileup = params.containsKey('save_mpileup') ? "tee ${prefix}.mpileup |" : ""
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def gff = params.containsKey('gff') ? "-g ${params.get('gff')}" : ""
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"""
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samtools mpileup \\
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$options.args2 \\
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--reference $fasta \\
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$bam | \\
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$save_mpileup \\
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ivar variants \\
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$options.args \\
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$gff \\
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-r $fasta \\
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-p $prefix
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ivar version | head -n1 2>&1 | sed 's/^.*iVar version //g' > ${software}.version.txt
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"""
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}
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