Vs 1619 #9196
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Vs 1619 #9196
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Pull Request Overview
This PR extends the filter‐set creation tools to support fully custom references by accepting a contig-mapping file and, in WDL workflows, a custom truth resources file.
- Adds
--contig-mapping-fileargument and logic in Java tools to set a custom contig map when--ref-version CUSTOMis used - Updates WDL (
GvsUtils.wdlandGvsCreateFilterSet.wdl) to pass--contig-mapping-fileand allow acustom_training_resourcesoverride - Registers the new branch in
.dockstore.yml
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| CreateSiteFilteringFiles.java | Added contigMappingFile argument and conditional custom contig map loading |
| CreateFilteringFiles.java | Same additions for indel/SNP filter builder |
| scripts/variantstore/wdl/GvsUtils.wdl | Introduced optional custom_contig_mapping and made --ref-version dynamic |
| scripts/variantstore/wdl/GvsCreateFilterSet.wdl | Added custom_reference, custom_contig_mapping, custom_training_resources; wired flags |
| .dockstore.yml | Added new branch VS-1619 to workflows |
Comments suppressed due to low confidence (1)
scripts/variantstore/wdl/GvsCreateFilterSet.wdl:352
- You added
custom_referenceas an input but the GATK call still uses the originalreferencevariable. Replace-R "~{reference}"with a reference that falls back tocustom_reference(e.g., useeffective_reference) so the task actually uses the custom fasta when supplied.
-R "~{reference}"
mcovarr
reviewed
Jun 10, 2025
mcovarr
approved these changes
Jun 10, 2025
gbggrant
approved these changes
Jun 10, 2025
| @@ -16,6 +16,11 @@ workflow GvsCreateFilterSet { | |||
| String reference_name = "hg38" | |||
| String? interval_list | |||
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| # for supporting non-hg38 references | |||
| File? custom_reference | |||
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In practice, you could put the new reference information into the Reference struct and then use the corresponding reference_name (e.g. kitty) to look it up in GvsUtils.py - But might be too early for that yet?
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Modifying the create filter set code to accept custom references AND a custom truth file. Completes successfully, but we don't have truth data to test it against because it's using custom training data.
Successful completion: https://app.terra.bio/#workspaces/gvs-dev/GVS%20Tiny%20Quickstart%20for%20Felis%20catus%20adoribus/submission_history/0b40a0ae-494f-4f79-871f-46a776a2376e
Successful integration run: https://app.terra.bio/#workspaces/gvs-dev/GVS%20Integration%20ahatcher/submission_history/c3567b95-8594-43fe-8507-98db01734a5e