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3b600af50e
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0 * update md5checksum * commit all files * actually checksum was good, but I suspect something fishy with the tests
42 lines
1.5 KiB
Text
42 lines
1.5 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 GATK4_SAMTOFASTQ {
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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::gatk4=4.2.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0"
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}
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path('*.fastq.gz'), emit: fastq
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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}" : "${meta.id}"
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def output = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
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"""
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gatk SamToFastq \\
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I=$bam \\
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$output \\
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$options.args
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
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END_VERSIONS
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"""
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}
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