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48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
process GATK4_APPLYBQSR {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
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'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
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path fasta
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path fai
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path dict
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output:
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tuple val(meta), path("*.bam"), emit: bam, optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def interval = intervals ? "-L ${intervals}" : ""
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def file_type = input.getExtension()
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" ApplyBQSR \\
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-R $fasta \\
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-I $input \\
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--bqsr-recal-file $bqsr_table \\
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$interval \\
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--tmp-dir . \\
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-O ${prefix}.${file_type} \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk4: \$(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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