2022-05-17 17:09:46 +00:00
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process GATK4_CNNSCOREVARIANTS {
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tag "$meta.id"
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label 'process_low'
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2022-05-18 12:26:21 +00:00
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//Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811
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if (params.enable_conda) {
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exit 1, "Conda environments cannot be used for GATK4/CNNScoreVariants at the moment. Please use docker or singularity containers."
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}
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2022-05-17 21:06:52 +00:00
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container 'broadinstitute/gatk:4.2.6.1' //Biocontainers is missing a package
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2022-05-17 17:09:46 +00:00
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input:
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tuple val(meta), path(vcf), path(aligned_input), 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 architecture
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path weights
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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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 aligned_input = aligned_input ? "--input $aligned_input" : ""
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def interval_command = intervals ? "--intervals $intervals" : ""
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def architecture = architecture ? "--architecture $architecture" : ""
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def weights = weights ? "--weights $weights" : ""
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def avail_mem = 3
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if (!task.memory) {
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log.info '[GATK CnnScoreVariants] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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gatk --java-options "-Xmx${avail_mem}g" CNNScoreVariants \\
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--variant $vcf \\
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--output ${prefix}.vcf.gz \\
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--reference $fasta \\
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$interval_command \\
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$aligned_input \\
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$architecture \\
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$weights \\
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--tmp-dir . \\
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$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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