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https://github.com/MillironX/nf-core_modules.git
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Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)
This commit is contained in:
Nicolas Vannieuwkerke
parent
bd7e1414a4
commit
c69d5cc23e
4 changed files with 87 additions and 20 deletions
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@ -11,19 +11,21 @@ process RTGTOOLS_VCFEVAL {
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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("*.txt"), emit: results
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path "versions.yml" , emit: versions
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tuple val(meta), path("${task.ext.prefix ?: meta.id}/*") , emit: results
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ""
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def prefix = task.ext.prefix ?: "${meta.id}"
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def regions = truth_regions ? "--bed-regions=$truth_regions" : ""
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def bed_regions = truth_regions ? "--bed-regions=$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 $query_vcf"
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@ -34,12 +36,12 @@ process RTGTOOLS_VCFEVAL {
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rtg vcfeval \\
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$args \\
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--baseline=$truth_vcf \\
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$regions \\
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$bed_regions \\
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$eval_regions \\
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--calls=$query_vcf \\
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--output=$prefix \\
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--template=$sdf \\
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--threads=$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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@ -37,7 +37,11 @@ input:
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pattern: "*.tbi"
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- truth_regions:
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type: file
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description: The BED file containing the truth regions
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description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)
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pattern: "*.bed"
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- evaluation_regions:
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type: file
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description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)
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pattern: "*.bed"
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- sdf:
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type: file
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@ -56,8 +60,8 @@ output:
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pattern: "versions.yml"
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- results:
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type: file
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description: A text file containing the results of the benchmark
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pattern: "*.txt"
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description: A folder containing all results of the evaluation
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pattern: "*"
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authors:
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- "@nvnieuwk"
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@ -18,7 +18,9 @@ workflow test_rtgtools_vcfeval {
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
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]
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bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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compressed_sdf = [
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[],
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@ -32,10 +34,10 @@ workflow test_rtgtools_vcfeval {
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})
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RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
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RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
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}
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workflow test_rtgtools_vcfeval_no_index {
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workflow test_rtgtools_vcfeval_no_optional_inputs {
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input = [
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[ id:'test' ], // meta map
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@ -48,7 +50,9 @@ workflow test_rtgtools_vcfeval_no_index {
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[]
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]
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bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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truth_regions = []
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evaluation_regions = []
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compressed_sdf = [
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[],
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@ -61,5 +65,5 @@ workflow test_rtgtools_vcfeval_no_index {
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[folder]
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})
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RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
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RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
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}
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@ -4,16 +4,73 @@
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- rtgtools
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- rtgtools/vcfeval
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files:
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- path: output/rtgtools/test_results.txt
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md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
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- path: output/rtgtools/test/done
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md5sum: 8b5623b26ee9b8722816afbec270bff0
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- path: output/rtgtools/test/fn.vcf.gz
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md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
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- path: output/rtgtools/test/fn.vcf.gz.tbi
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md5sum: 092a7a3162e7cff25d273525751eb284
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- path: output/rtgtools/test/fp.vcf.gz
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md5sum: 1417bb8ac7a0e202df660291a74de0db
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- path: output/rtgtools/test/fp.vcf.gz.tbi
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md5sum: 092a7a3162e7cff25d273525751eb284
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- path: output/rtgtools/test/non_snp_roc.tsv.gz
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md5sum: 8fd51a1e5084d15d43880cb1e31a0180
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- path: output/rtgtools/test/phasing.txt
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md5sum: 133677dbd8be657439ea2b03fdfb8795
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- path: output/rtgtools/test/progress
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- path: output/rtgtools/test/snp_roc.tsv.gz
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md5sum: ff2ece544adfcefaa06da054876a9ae3
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- path: output/rtgtools/test/summary.txt
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md5sum: f4c8df93c8bdab603036bbc27b4a28c3
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- path: output/rtgtools/test/tp-baseline.vcf.gz
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md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
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- path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
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md5sum: 092a7a3162e7cff25d273525751eb284
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- path: output/rtgtools/test/tp.vcf.gz
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md5sum: 1417bb8ac7a0e202df660291a74de0db
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- path: output/rtgtools/test/tp.vcf.gz.tbi
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md5sum: 092a7a3162e7cff25d273525751eb284
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- path: output/rtgtools/test/vcfeval.log
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- path: output/rtgtools/test/weighted_roc.tsv.gz
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md5sum: 5209f1bdeb03704714ae92b183d08e0f
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- path: output/rtgtools/versions.yml
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- name: rtgtools vcfeval test_rtgtools_vcfeval_no_index
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command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_index -c tests/config/nextflow.config
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- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
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command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
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tags:
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- rtgtools
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- rtgtools/vcfeval
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files:
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- path: output/rtgtools/test_results.txt
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md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
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- path: output/rtgtools/test/done
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md5sum: 8b5623b26ee9b8722816afbec270bff0
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- path: output/rtgtools/test/fn.vcf.gz
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md5sum: e51420e4be520ae309a2384830bf4c15
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- path: output/rtgtools/test/fn.vcf.gz.tbi
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md5sum: 092a7a3162e7cff25d273525751eb284
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- path: output/rtgtools/test/fp.vcf.gz
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md5sum: 7d818cf526983de6cbb5cf517c44a8f7
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- path: output/rtgtools/test/fp.vcf.gz.tbi
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md5sum: 092a7a3162e7cff25d273525751eb284
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- path: output/rtgtools/test/non_snp_roc.tsv.gz
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md5sum: a535fb80081b43b19788347152b6b8b4
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- path: output/rtgtools/test/phasing.txt
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md5sum: 133677dbd8be657439ea2b03fdfb8795
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- path: output/rtgtools/test/progress
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- path: output/rtgtools/test/snp_roc.tsv.gz
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md5sum: 6006656c4a534935c7873398287bc110
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- path: output/rtgtools/test/summary.txt
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md5sum: f33feb32f84958fb931063044fba369b
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- path: output/rtgtools/test/tp-baseline.vcf.gz
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md5sum: ed68ea567a26d3b864ada79e9253bc97
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- path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
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md5sum: 3518deff814eed340b0f5386294b5879
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- path: output/rtgtools/test/tp.vcf.gz
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md5sum: 92fd51021d101c99da066324655d24c9
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- path: output/rtgtools/test/tp.vcf.gz.tbi
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md5sum: 169063c1f570f0055059f3cb3518a8b4
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- path: output/rtgtools/test/vcfeval.log
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- path: output/rtgtools/test/weighted_roc.tsv.gz
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md5sum: 0ba825084bd6b94accdf54fff23ea18c
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- path: output/rtgtools/versions.yml
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