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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
52 lines
1.8 KiB
Text
52 lines
1.8 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 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), meta:meta, publish_by_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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path gff
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output:
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tuple val(meta), path("*.tsv") , emit: tsv
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tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
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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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def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
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def features = params.gff ? "-g $gff" : ""
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"""
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samtools mpileup \\
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$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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$features \\
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-r $fasta \\
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-p $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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