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54 lines
1.6 KiB
Text
54 lines
1.6 KiB
Text
process GATK_INDELREALIGNER {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11':
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'quay.io/biocontainers/gatk:3.5--hdfd78af_11' }"
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input:
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tuple val(meta), path(bam), path(bai), path(intervals)
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path(fasta)
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path(fai)
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path(dict)
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path(known_vcf)
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output:
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tuple val(meta), path("*.bam"), path("*.bai"), emit: bam
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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 known = known_vcf ? "-known ${known_vcf}" : ""
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if ("$input" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK IndelRealigner] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk3 \\
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-Xmx${avail_mem}g \\
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-T IndelRealigner \\
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-R ${fasta} \\
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-I ${input} \\
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--targetIntervals ${intervals} \\
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${known} \\
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-o ${prefix}.bam \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gatk: \$(echo \$(gatk3 --version))
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END_VERSIONS
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"""
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}
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