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43 lines
1.3 KiB
Text
43 lines
1.3 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 LOFREQ_CALL {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::lofreq=2.1.5" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4"
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} else {
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container "quay.io/biocontainers/lofreq:2.1.5--py38h588ecb2_4"
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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("*.vcf.gz"), emit: vcf
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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}" : "${meta.id}"
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"""
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lofreq \\
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call \\
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$options.args \\
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-f $fasta \\
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-o ${prefix}.vcf.gz \\
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$bam
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echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//' > ${software}.version.txt
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"""
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}
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