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043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
48 lines
1.5 KiB
Text
48 lines
1.5 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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options = initOptions(params.options)
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process GATK4_APPLYBQSR {
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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::gatk4=4.2.0.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/gatk4:4.2.0.0--0"
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} else {
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container "quay.io/biocontainers/gatk4:4.2.0.0--0"
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}
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input:
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tuple val(meta), path(bam), path(bai), path(bqsr_table)
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path fasta
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path fastaidx
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path dict
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path intervalsBed
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output:
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tuple val(meta), path("*.bam"), emit: bam
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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 intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
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"""
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gatk ApplyBQSR \\
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-R $fasta \\
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-I $bam \\
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--bqsr-recal-file $bqsr_table \\
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$intervalsCommand \\
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-O ${prefix}.bam \\
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$options.args
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gatk --version | grep Picard | sed "s/Picard Version: //g" > ${software}.version.txt
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"""
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}
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