Vs 299 spike speed up integration tests#8706

Draft

koncheto-broad wants to merge 901 commits intomasterfrom VS-299-spike-speed-up-integration-tests

+1,393,711-41

This pull request is big! We're only showing the most recent 250 commits

Commits on Feb 16, 2023

Document VCF generation [VS-795] (#8202 )
rsasch
authored

Commits on Feb 22, 2023

Commits on Feb 27, 2023

Hello Azure SQL Database from Cromwell on Azure [VS-812] (#8220 )
mcovarr
authored

Commits on Feb 28, 2023

Remove what appear to be accidentally added files [VS-834] (#8225 )
mcovarr
authored

Commits on Mar 1, 2023

VS-815: Add Support for YNG to VQSR Lite (#8206 )
gbggrant
authored

Commits on Mar 3, 2023

Commits on Mar 8, 2023

Track avro export costs [VS-769] (#8236 )
rsasch
authored

Commits on Mar 13, 2023

Add note that we deleted a VDS! (#8214 )
RoriCremer
authored

Commits on Mar 14, 2023

Commits on Mar 21, 2023

Add a test exclusion for gvs scripts (#8250 )
lbergelson
authored

Commits on Mar 24, 2023

Intro to Cosmos Spike [VS-845] (#8254 )
mcovarr
authored

Commits on Mar 27, 2023

Commits on Mar 28, 2023

Rename tieout WDL input to not match name of output [VS-860] (#8265 )
mcovarr
authored

Commits on Mar 29, 2023

VS-849 - Use the annotation 'AS_MQ' for indels. (#8261 )
gbggrant
authored

Commits on Mar 30, 2023

Tidy up ExtractCohortTest so it can be run in IntelliJ cleanly [VS-860] (#8274 )
mcovarr
authored

Commits on Apr 5, 2023

VS-838. Remove the unneeded SCORE field from the filter_set_info_vqsr table (#8278 )
gbggrant
authored

Commits on Apr 10, 2023

VS-775 vat validation shards (#8175 )
RoriCremer
authored

Commits on Apr 12, 2023

VS-883 - Add tests for extract cohort lite (#8284 )
gbggrant
authored

Commits on Apr 14, 2023

Fix broken gsutil in Variants Docker image [VS-888] (#8289 )
mcovarr
authored

Commits on Apr 16, 2023

Adding the uber_monitor.py script (#8268 )
gbggrant
authored

Commits on Apr 18, 2023

Commits on Apr 21, 2023

VS-776. Update to latest version of VQSR Lite. (#8269 )
gbggrant
authored

Commits on Apr 24, 2023

Azure SQL Database Ingest [VS-879] (#8293 )
mcovarr
authored

Commits on Apr 26, 2023

VS-895. Add VQSR lite support to 'extract cohort by sample names' (#8298 )
gbggrant
authored

Commits on May 1, 2023

Move monitoring script to public bucket [VS-908] (#8303 )
mcovarr
authored

Commits on May 2, 2023

remove GvsAoUReblockGVCF.wdl and references to it (#8300 )
mmorgantaylor
authored

Commits on May 5, 2023

Add python script to our repo (#8282 )
RoriCremer
authored

Commits on May 10, 2023

Commits on May 11, 2023

VS-917. Update override jar in GvsJointCalling wdl to fix support issue. (#8312 )
gbggrant
authored

Commits on May 12, 2023

Fix potential bug in VCF Integration test (#8316 )
gbggrant
authored

Commits on May 17, 2023

Commits on May 18, 2023

No empty alts if you please [VS-918] (#8326 )
mcovarr
authored

Commits on May 22, 2023

Process Sample gVCF headers during Ingest [VS-836] (#8321 )
rsasch
authored

Commits on May 23, 2023

Commits on May 25, 2023

VS-924 - Have pipeline automatically differentiate between VQSR Lite and Classic (#8336 )
gbggrant
authored

Commits on May 26, 2023

Update to the latest import_gvs() code (#8330 )
RoriCremer
authored

Commits on May 30, 2023

VS-943. Fix bug in summarize_monitoring_logs script (#8345 )
gbggrant
authored

Commits on May 31, 2023

VS-910 Handling ploidy issues in GVS (#8334 )
koncheto-broad
authored

Commits on Jun 1, 2023

updating beta to use the latest code changes (#8349 )
koncheto-broad
authored

Commits on Jun 2, 2023

Commits on Jun 5, 2023

GVS BigQuery Traversal Artifact [VS-927] (#8344 )
mcovarr
authored

Commits on Jun 8, 2023

Docker build script --branch and --release options [VS-935] (#8354 )
mcovarr
authored

Commits on Jun 13, 2023

Commits on Jun 14, 2023

Commits on Jun 15, 2023

Add ability to run S&P workflow on arbitrary multiple chromosomes [VS-941] (#8365 )
rsasch
authored

Commits on Jun 21, 2023

Remove unused parameter. (#8370 )
gbggrant
authored

Commits on Jun 22, 2023

Commits on Jun 23, 2023

updated GvsJointVariantCalling.wdl with latest override_gatk (#8376 )
rsasch
authored

Commits on Jun 25, 2023

Bulk Ingest with sample sets (#8325 )
RoriCremer
authored

Commits on Jun 28, 2023

Commits on Jun 29, 2023

VS-1000 - Migrate VQSR Classic Code to own WDL (#8393 )
gbggrant
authored

Commits on Jun 30, 2023

Commits on Jul 5, 2023

VS-1001 update dockers for google storage library update (#8401 )
gbggrant
authored

Commits on Jul 6, 2023

VS-950 - Developer Documentation for running Exomes through GVS (#8398 )
gbggrant
authored

Commits on Jul 11, 2023

Update documentation to point to newly released BGE exome calling list. (#8407 )
gbggrant
authored

Commits on Jul 14, 2023

VS-1007 - Use default names for VQSR-Lite generated code. (#8412 )
gbggrant
authored

Commits on Jul 20, 2023

VS-1009 Add SCORE to VQSR Lite VCF (#8423 )
gbggrant
authored

Commits on Jul 25, 2023

Copy/paste cleanup magic for Github Action CI (#8437 )
mcovarr
authored

Commits on Aug 3, 2023

pin hail version in the integration test (#8424 )
RoriCremer
authored

Commits on Aug 11, 2023

Kd GVS bulk ingest docs (#8397 )

committed
Bulk ingest: single FOFN + Quickstart + Beta [VS-962] [VS-984] [VS-982] (#8404 )
mcovarr
committed
Update logic around missing sample data in TDM [VS-997] (#8422 )

rsasch
authored and
mcovarr
committed
dockstore

Rebecca Asch
authored and
mcovarr
committed
more dockstore

Rebecca Asch
authored and
mcovarr
committed
Fix AssignIds pipefail with head [VS-1011] (#8441 )
mcovarr
committed
VS-991. Wire interval list from Joint Calling through to other workflows #8426 (#8429 )

gbggrant
authored and
mcovarr
committed
All sample inputs as files instead of strings [VS-1019] (#8444 )

rsasch
authored and
mcovarr
committed
VS-1004. Increasing max auto batch size to 25K to allow for larger beta sets. (#8446 )

gbggrant
authored and
mcovarr
committed
Update P + S WDL to get around input limits [VS-970] (#8449 )
mcovarr
committed
Update override jar in bulk ingest staging (#8451 )

gbggrant
authored and
mcovarr
committed
VS-931 Exome integration test on bulk ingest staging (#8448 )

gbggrant
authored and
mcovarr
committed
VS-1004 Changes to make benchmarking VQSR Classic possible. (#8452 )

gbggrant
authored and
mcovarr
committed
Stop mysterious sample drops in curation, improve performance [VS-1027] (#8454 )
mcovarr
committed
Centralize and standardize Docker image versioning [VS-965] (#8457 )
mcovarr
committed
Centralized Docker fixups (#8469 )
mcovarr
committed
Update GVS docs with VETS information (#8466 )

kbergin
authored and
mcovarr
committed

Commits on Aug 12, 2023

update Dockers
mcovarr
committed

Commits on Aug 15, 2023

Fix copy/paste errors with Docker image variable names (#8474 )
mcovarr
authored

Commits on Aug 16, 2023

Bump up some disk sizes for P&S (#8480 )
mcovarr
authored

Commits on Aug 21, 2023

Commits on Aug 28, 2023

Initial updates to bulk ingest docs with 25k run (#8475 )
kbergin
authored

Commits on Aug 29, 2023

Commits on Aug 30, 2023

Commits on Sep 7, 2023

Add support for ingest from requester pays bucket [VS-1038] (#8514 )
rsasch
authored

Commits on Sep 18, 2023

VS-1047 remove --location=US in bq command calls (#8519 )
gbggrant
authored

Commits on Sep 19, 2023

Make a VDS (how to / how do we even) for VS-1026 (#8513 )
RoriCremer
authored

Commits on Sep 22, 2023

Vs-327 (#8507 )
koncheto-broad
authored

Commits on Sep 26, 2023

VS-974 - Better error on GvsCreateFilterSet.PopulateFilterSetInfo (#8530 )
gbggrant
authored

Commits on Sep 27, 2023

Hail Dataproc from WDL, cluster tracking [VS-1013] [VS-1021] (#8525 )
mcovarr
authored

Commits on Sep 28, 2023

VS-1056 support import of PS (#8531 )
gbggrant
authored

Commits on Sep 29, 2023

Commits on Oct 2, 2023

Commits on Oct 4, 2023

Merge master, fixups for changes in JointVariantCalling.wdl [VS-1065]
mcovarr
committed

Commits on Oct 11, 2023

Release docs fixup [VS-1088] (#8548 )
mcovarr
authored

Commits on Oct 12, 2023

Commits on Oct 16, 2023

Commits on Oct 18, 2023

Commits on Oct 23, 2023

Bitpacking fixup [VS-1104] (#8559 )
mcovarr
authored

Commits on Oct 24, 2023

Commits on Oct 26, 2023

Commits on Nov 3, 2023

Commits on Nov 6, 2023

More memory for PopulateFilterSetInfo (#8575 )
gbggrant
authored

Commits on Nov 8, 2023

Phasing and GT removal in VDS [VS-1060] [VS-1122] [VS-1123] (#8553 )
mcovarr
authored

Commits on Nov 16, 2023

Plumb through disk and memory overrides for ExtractTask [VS-1124] (#8582 )
rsasch
authored

Commits on Nov 20, 2023

Compressed reference smarts [VS-1138] (#8586 )
mcovarr
authored

Commits on Nov 21, 2023

Commits on Dec 1, 2023

Add parameter to give tables created by prepare step a two week TTL [VS-597] (#8595 )
rsasch
authored

Commits on Dec 5, 2023

VS-1159 - Enhance GVSWithdrawSamples (#8599 )
gbggrant
authored

Commits on Dec 7, 2023

VS 678 - adding optional interval list to the subcohort extract workflow (#8601 )
koncheto-broad
authored

Commits on Dec 15, 2023

Echo Scale Test VDS Updates [VS-1095] [VS-1112] (#8602 )
mcovarr
authored

Commits on Dec 18, 2023

Adjust ingest/extract scatter calculations for exomes [VS-1146] (#8615 )
rsasch
authored

Commits on Jan 4, 2024

Commits on Jan 8, 2024

Updates to CHANGELOG.md in preparation for release 0.5.1 (#8641 )
gbggrant
authored

Commits on Jan 9, 2024

Commits on Jan 16, 2024

Address ExtractTask OOMs [VS-1127] (#8648 )
mcovarr
authored

Commits on Jan 17, 2024

Commits on Jan 29, 2024

Fix population typo [VS-1155] (#8665 )
rsasch
authored

Commits on Jan 30, 2024

Commits on Jan 31, 2024

Add CheckForNullColumns to and fixed ClinvarSignificance in VAT validation [VS-1156] (#8669 )
rsasch
authored

Commits on Feb 2, 2024

Minor changes for updated VAT reference testing [VS-1054] (#8670 )
mcovarr
authored

Commits on Feb 6, 2024

VS-1206 (#8679 )
koncheto-broad
authored

Commits on Feb 12, 2024

Commits on Feb 14, 2024

Commits on Feb 16, 2024

Commits on Feb 21, 2024

Commits on Feb 28, 2024

Commits on Feb 29, 2024