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49 lines
1.5 KiB
Text
49 lines
1.5 KiB
Text
process GATK4_APPLYBQSR_SPARK {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1 conda-forge::openjdk=8.0.312" : null)
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container 'broadinstitute/gatk:4.2.6.1'
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input:
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tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
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path fasta
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path fai
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path dict
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output:
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tuple val(meta), path("*.bam") , emit: bam, optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def interval_command = intervals ? "--intervals $intervals" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK ApplyBQSRSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" ApplyBQSRSpark \\
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--input $input \\
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--output ${prefix}.${input.getExtension()} \\
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--reference $fasta \\
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--bqsr-recal-file $bqsr_table \\
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$interval_command \\
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--spark-master local[${task.cpus}] \\
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--tmp-dir . \\
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$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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