mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
Split the output to different channels
This commit is contained in:
Nicolas Vannieuwkerke
parent
6008619603
commit
3a064b0a99
3 changed files with 105 additions and 39 deletions
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@ -15,8 +15,12 @@ process RTGTOOLS_VCFEVAL {
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path(sdf)
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output:
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tuple val(meta), path("${task.ext.prefix ?: meta.id}/*") , emit: results
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path "versions.yml" , emit: versions
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tuple val(meta), path("done"), path("progress"), path("*.log") , emit: logs
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tuple val(meta), path("*{tp,fn,fp,baseline}.vcf.gz.tbi"), path("*{tp,fn,fp,baseline}.vcf.gz") , emit: vcf
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tuple val(meta), path("*.tsv.gz") , emit: roc
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tuple val(meta), path("summary.txt") , emit: summary
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tuple val(meta), path("phasing.txt") , emit: phasing
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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@ -43,6 +47,8 @@ process RTGTOOLS_VCFEVAL {
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--template=$sdf \\
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--threads=$task.cpus \\
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mv ${prefix}/* .
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
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@ -58,10 +58,70 @@ output:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- results:
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- done:
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type: file
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description: A folder containing all results of the evaluation
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pattern: "*"
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description: A file containing the message on succesful completion
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pattern: "done"
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- progress:
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type: file
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description: A file containing the simplified logging of the process
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pattern: "progress"
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- vcfeval_log:
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type: file
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description: A file containing the extended logging of the process
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pattern: "*.log"
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- false_negatives_vcf:
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type: file
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description: A VCF file containing the false negative variants
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pattern: "fn.vcf.gz"
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- false_negatives_index:
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type: file
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description: The index file for the false negatives' VCF file
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pattern: "fn.vcf.gz.tbi"
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- false_positive_vcf:
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type: file
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description: A VCF file containing the false positive variants
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pattern: "fp.vcf.gz"
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- false_positives_index:
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type: file
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description: The index file for the false positives' VCF file
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pattern: "fp.vcf.gz.tbi"
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- true_positive_vcf:
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type: file
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description: A VCF file containing the true positive variants
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pattern: "tp.vcf.gz"
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- true_positives_index:
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type: file
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description: The index file for the true positives' VCF file
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pattern: "tp.vcf.gz.tbi"
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- true_positive_baseline_vcf:
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type: file
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description: A VCF file containing the true positive baseline variants
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pattern: "tp-baseline.vcf.gz"
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- true_positives_baseline_index:
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type: file
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description: The index file for the baseline true positives' VCF file
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pattern: "tp-baseline.vcf.gz.tbi"
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- non_snp_roc:
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type: file
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description: A TSV file containing the ROC data for the non-SNP variants
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pattern: "non_snp_roc.tsv.gz"
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- snp_roc:
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type: file
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description: A TSV file containing the ROC data for the SNP variants
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pattern: "snp_roc.tsv.gz"
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- weighted_roc:
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type: file
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description: A TSV file containing the weighted ROC data
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pattern: "weighted_roc.tsv.gz"
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- summary:
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type: file
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description: A TXT file containing the summary of the evaluation
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pattern: "summary.txt"
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- phasing:
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type: file
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description: A TXT file containing the data on the phasing
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pattern: "phasing.txt"
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authors:
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- "@nvnieuwk"
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@ -4,36 +4,36 @@
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- rtgtools
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- rtgtools/vcfeval
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files:
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- path: output/rtgtools/test/done
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- path: output/rtgtools/test/fn.vcf.gz
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- path: output/rtgtools/done
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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/progress
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- path: output/rtgtools/snp_roc.tsv.gz
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md5sum: ff2ece544adfcefaa06da054876a9ae3
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- path: output/rtgtools/test/summary.txt
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- path: output/rtgtools/summary.txt
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md5sum: f4c8df93c8bdab603036bbc27b4a28c3
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- path: output/rtgtools/test/tp-baseline.vcf.gz
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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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/vcfeval.log
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- path: output/rtgtools/versions.yml
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- path: output/rtgtools/weighted_roc.tsv.gz
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md5sum: 5209f1bdeb03704714ae92b183d08e0f
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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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@ -41,33 +41,33 @@
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- rtgtools
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- rtgtools/vcfeval
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files:
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- path: output/rtgtools/test/done
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- path: output/rtgtools/test/fn.vcf.gz
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- path: output/rtgtools/done
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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/progress
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- path: output/rtgtools/snp_roc.tsv.gz
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md5sum: 6006656c4a534935c7873398287bc110
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- path: output/rtgtools/test/summary.txt
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- path: output/rtgtools/summary.txt
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md5sum: f33feb32f84958fb931063044fba369b
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- path: output/rtgtools/test/tp-baseline.vcf.gz
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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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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- path: output/rtgtools/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/vcfeval.log
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- path: output/rtgtools/versions.yml
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- path: output/rtgtools/weighted_roc.tsv.gz
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md5sum: 0ba825084bd6b94accdf54fff23ea18c
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