Update Beta User WDL to use bulk ingest [VS-982] #8379
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(Couldn't find ExtractCohortToVcf in ExtractTask method in GvsExtractCallset.wdl
Go with the official docker tag
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8379 +/- ##
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Coverage ? 76.504%
Complexity ? 21795
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Files ? 1392
Lines ? 83134
Branches ? 13184
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Hits ? 63601
Misses ? 14369
Partials ? 5164 |
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Github actions tests reported job failures from actions build 5404926238
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Github actions tests reported job failures from actions build 5405169587
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Github actions tests reported job failures from actions build 5405222155
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Github actions tests reported job failures from actions build 5405579628
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Github actions tests reported job failures from actions build 5405771210
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rsasch
changed the title
| @@ -243,13 +243,13 @@ def get_column_values(columnSamples, numSamples, user_defined_vcf, user_defined_ | |||
| # Check the contents of the columns: the duck algorithm. If its contents LOOK like vcfs and indexes, go from there | |||
| for col in path_ends_in_vcf_gz: | |||
| # ...and has an analogue that looks like an index file? | |||
| index_column = f"{column}_index" | |||
| index_column = f"{col}_index" | |||
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uh what was this doing before these changes?
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Heads up my one-FOFN-to-rule-them-all PR ended up turning into a PR that does (or at least tries to) do all the bulk ingest things. Happy to discuss in mobbing |
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closing in favor of #8404 (and possible other future PRs) |
latest run of Beta User WDL with bulk ingest and no data table column names provided: https://app.terra.bio/#workspaces/gvs-dev/RSA%20-%20GVS%20Quickstart%20V2%20/job_history/79337ea3-593f-4896-b056-9f47bfd7c7c7