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55 lines
1.6 KiB
Text
55 lines
1.6 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(truth_vcf), path(truth_vcf_tbi), path(query_vcf), path(query_vcf_tbi), path(bed)
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path(sdf)
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output:
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tuple val(meta), path("*.txt"), emit: results
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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 ?: "${meta.id}"
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def regions = bed ? "--bed-regions=$bed" : ""
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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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sdf_basename = sdf.getBaseName().replace(".tar","")
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tar_decomp = ""
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if((sdf =~ /.tar.gz\b/).find() == true) {
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tar_decomp = "tar -xzf $sdf"
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}
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"""
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$tar_decomp
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$truth_index
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$query_index
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rtg vcfeval \\
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$args \\
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--baseline=$truth_vcf \\
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$regions \\
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--calls=$query_vcf \\
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--output=$prefix \\
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--template=$sdf_basename \\
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--threads=$task.cpus \\
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> ${prefix}_results.txt
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cat <<-END_VERSIONS > versions.yml
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"${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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