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feat: add version of benchmark as key in presets and include in report #80

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Merged
merged 14 commits into from
Jun 20, 2024
Merged

feat: add version of benchmark as key in presets and include in report #80

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8536343
feat: add version flag to genomes
famosab Jun 19, 2024
e4cba4f
feat: add bm version to name
famosab Jun 19, 2024
ff2b251
feat: add bm version as label
famosab Jun 19, 2024
8671388
fix: snakefmt
famosab Jun 19, 2024
bc85f45
fix: remov version from title
famosab Jun 19, 2024
b374803
feat: function to get version
famosab Jun 19, 2024
6338e75
fix: remove version from label and add as param
famosab Jun 19, 2024
4552e21
fix: add version to title (can also be changed to description)
famosab Jun 19, 2024
92cc0f9
fix: snakefmt
famosab Jun 19, 2024
cafa1e6
fix: include genome version in description
famosab Jun 19, 2024
c1e58fb
fix: get genome name for precision and recall
famosab Jun 19, 2024
065b177
fix: f strings
famosab Jun 19, 2024
f74dfc3
fix: change text for bm version
famosab Jun 20, 2024
2ee70e7
fix: snakefmt
famosab Jun 20, 2024
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2 changes: 1 addition & 1 deletion workflow/resources/datavzrd/precision-recall-config.yte.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ views:
- "#6baed6"
vaf:
plot:
heatmap:
heatmap:
scale: linear
custom-content:
function(value, row) {
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4 changes: 4 additions & 0 deletions workflow/resources/presets.yaml
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Expand Up @@ -50,6 +50,7 @@ benchmarks:

genomes:
na12878:
version: 4.2.1
truth:
grch37: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh37/HG001_GRCh37_1_22_v4.2.1_benchmark.vcf.gz
grch38: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
Expand All @@ -58,6 +59,7 @@ genomes:
grch38: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed

chm-eval:
version: 0.5
archive: https://github.com/lh3/CHM-eval/releases/download/v0.5/CHM-evalkit-20180222.tar
truth:
grch38: full.38.vcf.gz
Expand All @@ -67,6 +69,7 @@ genomes:
grch37: full.37m.bed.gz

seqc2-somatic:
version: 1.2
truth:
grch38:
snvs: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sSNV_in_HC_regions_v1.2.vcf.gz
Expand All @@ -76,6 +79,7 @@ genomes:
somatic: true

na12878-somatic:
version: 4.2.1
truth:
grch38: https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
confidence-regions:
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6 changes: 5 additions & 1 deletion workflow/rules/eval.smk
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Expand Up @@ -273,7 +273,11 @@ rule report_precision_recall:
directory("results/report/precision-recall/{benchmark}/{vartype}"),
htmlindex="index.html",
category="precision/recall",
labels={"benchmark": "{benchmark}", "vartype": "{vartype}"},
labels={
"benchmark": "{benchmark}",
"version": "{version}",
"vartype": "{vartype}",
},
),
log:
"logs/datavzrd/precision-recall/{benchmark}/{vartype}.log",
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