318 Sites only filtered vcf then annotate wdl #7305
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RoriCremer
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* private branch * added partial SA support * switch to ssd * update docker * attempt to improve performance and call caching * wip * full SA support * wrong task * added SA to json parsing
rsasch
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Jul 13, 2021
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It looks like there are a lot of comments/TODOs in GvsSitesOnlyVCF that are either outdated or should be documented in separate tickets.
Note: don't forget to remove your inclusion of your branch (rc-318-sites-only-filtered-vcf-then-annotate-wdl) in .dockstore.yml before merging.
RoriCremer
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Jul 13, 2021
rsasch
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Jul 13, 2021
| } | ||
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| task ExtractACANAF { |
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doesn't look like this task is ever called?
| call PrepAnnotationJson { | ||
| input: | ||
| annotation_json = AnnotateShardedVCF.annotation_json, | ||
| output_name = "${i}.json.gz", |
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nit: maybe something like output_file_suffix for clarity?
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| File nirvana_schema_json_file | ||
| File vat_vt_schema_json_file | ||
| File vat_genes_schema_json_file |
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Not sure why these are inputs; aren't these files part of this PR to the repo? Is the nirvana schema likely to change?
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This was referenced Mar 17, 2023
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