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60 lines
2.2 KiB
Text
60 lines
2.2 KiB
Text
process RTGTOOLS_VCFEVAL {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0':
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'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(query_vcf), path(query_vcf_tbi)
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tuple path(truth_vcf), path(truth_vcf_tbi)
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path(truth_regions)
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path(evaluation_regions)
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path(sdf)
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output:
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tuple val(meta), path("**results/{done,progress,*.log}") , emit: logs
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tuple val(meta), path("**tp.vcf.gz"), path("**tp.vcf.gz.tbi") , emit: tp
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tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn
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tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp
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tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline
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tuple val(meta), path("**.tsv.gz") , emit: roc
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tuple val(meta), path("**results/summary.txt") , emit: summary
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tuple val(meta), path("**results/phasing.txt") , emit: phasing
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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 ?: "${meta.id}"
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def bed_regions = truth_regions ? "--bed-regions=$truth_regions" : ""
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def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
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def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
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def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
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def avail_mem = task.memory.toGiga() + "G"
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"""
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$truth_index
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$query_index
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rtg RTG_MEM=$avail_mem vcfeval \\
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$args \\
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--baseline=$truth_vcf \\
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$bed_regions \\
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$eval_regions \\
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--calls=$query_vcf \\
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--output=${prefix}_results \\
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--template=$sdf \\
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--threads=$task.cpus \\
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
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END_VERSIONS
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"""
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}
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