lb merge gvs branch#8248

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lbergelson wants to merge 664 commits intomasterfrom lb_merge_gvs_branch

+79,043-205

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Commits on Sep 29, 2021

execute_with_retry() refactor and error handling improvements [VS-159] (#7480 )
rsasch
authored

Commits on Oct 7, 2021

Small updates to GvsExtractCallset from beta callset, new workflow for re-scattered shards (#7493 )
rsasch
authored

Commits on Oct 13, 2021

add flag in prepare to print out sql instead of executing (#7501 )
ahaessly
authored

Commits on Oct 14, 2021

Workflow to re-scatter and then merge "problematic" intervals from ExtractCallset [VS-209] (#7495 )
rsasch
authored

Commits on Oct 15, 2021

changed README to reflect comments from Lee [VS-210] (#7502 )
rsasch
authored

Commits on Oct 18, 2021

Commits on Oct 22, 2021

small fix to MergeVCFs (#7517 )
rsasch
authored

Commits on Oct 26, 2021

small fixes to GVS pipeline (#7522 )
rsasch
authored

Commits on Oct 27, 2021

Commits on Oct 28, 2021

Remove Sites only step from the VAT creation WDL (#7510 )
RoriCremer
authored

Commits on Oct 29, 2021

fix bad argument processing for bool (#7529 )
ahaessly
authored

Commits on Nov 2, 2021

Support for TDR DRS URIs in Import (#7528 )
kcibul
authored

Commits on Nov 3, 2021

Match format of filename output in GvsRescatterCallsetInterval (#7539 )
rsasch
authored

Commits on Nov 4, 2021

Commits on Nov 8, 2021

Commits on Nov 9, 2021

Scatter over all interval files, not just scatter count (#7551 )
rsasch
authored

Commits on Nov 10, 2021

fixed docker (#7558 )
kcibul
authored

Commits on Nov 16, 2021

Commits on Nov 18, 2021

bad param assignment in aou reblocking (#7572 )
ahaessly
authored

Commits on Nov 20, 2021

Small fixes to ImportGenomes (non-write api version) (#7574 )
rsasch
authored

Commits on Nov 23, 2021

Ah change output of reblocking wdl to external path (#7575 )
ahaessly
authored

Commits on Nov 25, 2021

close BQ Readers (#7583 )
kcibul
authored

Commits on Dec 8, 2021

Commits on Dec 17, 2021

Commits on Dec 20, 2021

upgrade log4j to 2.17 (#7616 )
kcibul
authored

Commits on Dec 22, 2021

Add drop_state default of Forty to extract (#7619 )
RoriCremer
authored

Commits on Dec 27, 2021

Kc fix type (#7620 )
kcibul
authored

Commits on Jan 5, 2022

VAT cleanup and documentation (#7531 )
RoriCremer
authored

Commits on Jan 6, 2022

fix empty flush (#7627 )
kcibul
authored

Commits on Jan 12, 2022

presorted avro files, fix performance issue (#7635 )
kcibul
authored

Commits on Jan 19, 2022

WIP extract for ranges (#7640 )
kcibul
authored

Commits on Jan 24, 2022

VS-268 import more samples at once (#7629 )
RoriCremer
authored

Commits on Jan 31, 2022

clustering vqsr tables by location (#7656 )
kcibul
authored

Commits on Feb 11, 2022

Commits on Feb 16, 2022

Update GvsExtractCallset.wdl (#7678 )
kcibul
authored

Commits on Feb 17, 2022

cherry pick lb_lfs_force change (#7683 )
rsasch
authored

Commits on Feb 18, 2022

Tweak ingest messaging and failure mode [VS-267] (#7680 )
rsasch
authored

Commits on Feb 25, 2022

Commits on Mar 2, 2022

Commits on Mar 9, 2022

VS-222 dont hard code the dataset name! (#7704 )
RoriCremer
authored

Commits on Mar 11, 2022

fixed bug; added tests (#7717 )
kcibul
authored

Commits on Mar 21, 2022

Clean up optional and inconsistently named inputs [VS-294] [VS-218] (#7715 )
rsasch
authored

Commits on Mar 23, 2022

Commits on Mar 24, 2022

Commits on Mar 29, 2022

Pass dataset name to gatk ExtractFeatures (#7735 )
RoriCremer
authored

Commits on Mar 30, 2022

Add withdrawn and is_control columns [VS-70] [VS-213] (#7736 )
rsasch
authored

Commits on Mar 31, 2022

Allow interval lists that require the SA to see (#7743 )
RoriCremer
authored

Commits on Apr 6, 2022

allow for gatk to be overridden, update with known good jar (#7758 )

kcibul
and
rsasch
authored

Commits on Apr 7, 2022

Commits on Apr 8, 2022

Don't put withdrawn sample data in alt_allele table [VS-369] (#7762 )
rsasch
authored

Commits on Apr 11, 2022

remove PET code (#7768 )
kcibul
authored

Commits on Apr 12, 2022

Adding AD for scale testing VS 225 add AD (#7713 )
RoriCremer
authored

Commits on Apr 13, 2022

Deterministic Sample ID assignments [VS-371] (#7770 )
mcovarr
authored

Commits on Apr 15, 2022

Commits on Apr 19, 2022

Commits on Apr 20, 2022

Commits on Apr 21, 2022

Commits on Apr 26, 2022

Document AoU SOP (up to the VAT) [VS-63] (#7807 )
rsasch
authored

Commits on Apr 27, 2022

Incident VS 365 clinvar classification fix (#7769 )
RoriCremer
authored

Commits on Apr 29, 2022

VS-390. Add precision and sensitivity wdl (#7813 )
gbggrant
authored

Commits on May 3, 2022

Commits on May 4, 2022

VS 396 clinvar grabs too many values (#7823 )

RoriCremer
and
mcovarr
authored

Commits on May 6, 2022

bugfix, we were trying to grep a binary file (#7837 )
kcibul
authored

Commits on May 12, 2022

Cleanup scripts/variantstore [VS-414] (#7834 )
mcovarr
authored

Commits on May 16, 2022

First cut at a python notebook to validate inputs. (#7845 )
gbggrant
authored

Commits on May 23, 2022

Fix Input Validation python notebook (#7853 )
gbggrant
authored

Commits on Jun 2, 2022

VET Ingest Validation / Allow Ingest of non-VQSR'ed data (#7870 )
gbggrant
authored

Commits on Jun 3, 2022

Commits on Jun 7, 2022

KM upload GVS product sheet (#7883 )
kayleemathews
authored

Commits on Jun 8, 2022

Commits on Jun 9, 2022

Update Quickstart Integration for X/Y scaling changes [VS-464] (#7881 )
mcovarr
authored

Commits on Jun 10, 2022

Commits on Jun 14, 2022

Use gvs-internal project in integration test (#7901 )
rsasch
authored

Commits on Jun 15, 2022

Add cost observability BQ table [VS-441] (#7891 )
mcovarr
authored

Commits on Jun 17, 2022

Add preliminary labels to queries [VS-381] (#7902 )
rsasch
authored

Commits on Jun 22, 2022

Commits on Jun 28, 2022

Commits on Jun 29, 2022

Commits on Jul 5, 2022

Read cost observability table [VS-475] (#7923 )
mcovarr
authored

Commits on Jul 6, 2022

Commits on Jul 7, 2022

[AoU DRC] Support uppercase site_ids for reblocking (#7929 )
mmorgantaylor
authored

Commits on Jul 8, 2022

Commits on Jul 11, 2022

VS_492 - Beta User Jar release (#7934 )
gbggrant
authored

Commits on Jul 14, 2022

Commits on Jul 15, 2022

Remove usage of service account from GvsValidateVAT.wdl (#7937 )
gbggrant
authored

Commits on Jul 18, 2022

refactoring for testablity (#7946 )
kcibul
authored

Commits on Jul 21, 2022

More import retries [VS-532] (#7953 )
mcovarr
authored

Commits on Jul 25, 2022

A few last doc changes (#7927 )

RoriCremer
and
kayleemathews
authored

Commits on Aug 1, 2022

Commits on Aug 2, 2022

GL-548 - Update CreateVat code to handle samples that do not contain all population groups. (#7965 )
gbggrant
authored

Commits on Aug 10, 2022

Commits on Aug 16, 2022

Removed usage of service account from WDLs (#7985 )
gbggrant
authored

Commits on Aug 17, 2022

Document steps for GVS cleanup for base use case [VS-586] (#7989 )
rsasch
authored

Commits on Aug 18, 2022

Commits on Aug 22, 2022

Allow for incremental addition of data to alt_allele [VS-52] (#7993 )
rsasch
authored

Commits on Aug 23, 2022

Minor AoU Documentation Update (#7999 )
gbggrant
authored

Commits on Aug 26, 2022

Generate Hail import/export script [VS-605] (#8002 )
mcovarr
authored

Commits on Aug 30, 2022

clearer error when values are missing (#7939 )
RoriCremer
authored

Commits on Sep 6, 2022

Ah [VS-565] output intervals and sample list (#8010 )
koncheto-broad
authored

Commits on Sep 8, 2022

Commits on Sep 9, 2022

fix quota guidelines for CPUs (#8016 )
rsasch
authored

Commits on Sep 16, 2022

Commits on Sep 19, 2022

add sample_table_timestamp to GetNumSamplesLoaded (#8022 )
rsasch
authored

Commits on Sep 20, 2022

Batched Avro export [VS-630] (#8020 )
mcovarr
authored

Commits on Sep 23, 2022

Ah 617 exposing the drop_state parameter to the GvsJointVariantCalling wdl used for beta (and internal customer) (#8032 )
koncheto-broad
authored

Commits on Sep 27, 2022

Commits on Sep 28, 2022

Check for withdrawn before exporting to AVRO files [VS-646] (#8039 )
rsasch
authored

Commits on Sep 29, 2022

Small updates to GVS Integration WDL [VS-618] (#8042 )
rsasch
authored

Commits on Sep 30, 2022

Rework Hail script generation [VS-616] (#8034 )
mcovarr
authored

Commits on Oct 6, 2022

Commits on Oct 7, 2022

Fail Avro extract and callset stats on bad filter name [VS-655] (#8046 )
mcovarr
authored

Commits on Oct 11, 2022

Vs 629 failure to retrieve job information during ingest (#8047 )
koncheto-broad
authored

Commits on Oct 13, 2022

Restore accidentally removed bcftools [VS-661] (#8051 )
mcovarr
authored

Commits on Oct 17, 2022

Commits on Oct 18, 2022

Commits on Oct 19, 2022

VS-637 Address a couple of issues in SampleLoadStatus handling in GVSImportGenomes. (#8052 )
gbggrant
authored

Commits on Oct 20, 2022

Revert Alpinizing of apt dependent task [VS-688] (#8065 )
mcovarr
authored

Commits on Oct 25, 2022

Fix missing vat schema JSONs [VS-699] (#8072 )
mcovarr
authored

Commits on Oct 26, 2022

Commits on Oct 31, 2022

Fix Dockerfile nits that break 20.10.21 (#8078 )
mcovarr
authored

Commits on Nov 1, 2022

Nirvana 3.18.1 Docker images support [VS-661] (#8082 )
mcovarr
authored

Commits on Nov 7, 2022

Add option to not prepare __REF_DATA or __SAMPLES tables to Prepare [VS-697] (#8079 )
rsasch
authored

Commits on Nov 8, 2022

"build-base" Docker image for faster variantstore image builds [VS-712] (#8085 )
mcovarr
authored

Commits on Nov 10, 2022

GVS / Hail VDS integration test [VS-639] (#8086 )
mcovarr
authored

Commits on Nov 17, 2022

Remove AI/AN from VDS docs [VS-726] (#8096 )
mcovarr
authored

Commits on Nov 21, 2022

Add flag for cost_observability table writing to support sub-cohort use case [VS-521] (#8093 )
rsasch
authored

Commits on Nov 22, 2022

Document STS delivery process for VDS [VS-727] (#8101 )
mcovarr
authored

Commits on Dec 1, 2022

Commits on Dec 5, 2022

VAT Readme updates (#8090 )
RoriCremer
authored

Commits on Dec 15, 2022

WDL and python scripts to use the VDS in the VAT (#8077 )
RoriCremer
authored

Commits on Dec 22, 2022

VS-757 - Use JASIX to make sub-jsons of annotated output of Nirvana (#8133 )
gbggrant
authored

Commits on Jan 3, 2023

add note about permissions for P&S workflow to work (#8135 )
rsasch
authored

Commits on Jan 5, 2023

VS-759 (and VS-760) (#8137 )
gbggrant
authored

Commits on Jan 9, 2023

Commits on Jan 10, 2023

Add monitoring to index vcf (#8151 )
gbggrant
authored

Commits on Jan 11, 2023

Make some noise when VDS validation succeeds (#8155 )
mcovarr
authored

Commits on Jan 12, 2023

Handle empty genes annotation file. (#8153 )
gbggrant
authored

Commits on Jan 13, 2023

Add escapes for otherwise problematic dataset / table names. (#8162 )
mcovarr
authored

Commits on Jan 20, 2023

New WDL to create VAT tsvs from previously generated BigQuery table. (#8165 )
gbggrant
authored

Commits on Jan 23, 2023

Treat withdrawn samples in sub-cohort prepare correctly [VS-772] (#8156 )
rsasch
authored

Commits on Jan 24, 2023

Remove unused VAT Creation WDL (#8172 )
gbggrant
authored

Commits on Jan 25, 2023

Gg consistently use dataset name as input parameter (#8173 )
gbggrant
authored

Commits on Jan 30, 2023

AoU cleanup docs, round 1 [VS-671] (#8104 )
mcovarr
authored

Commits on Jan 31, 2023

VDS docs remove samples and correct GT [VS-807] (#8178 )
mcovarr
authored

Commits on Feb 2, 2023

Commits on Feb 3, 2023

Commits on Feb 9, 2023

Commits on Feb 13, 2023

Edit and re-format VDS -> VAT doc [VS-821] (#8187 )
rsasch
authored

Commits on Feb 14, 2023

VS-820 Incorporate code to stay under Google quotas for new accounts into beta workflow (#8200 )

koncheto-broad
and
mcovarr
authored

Commits on Feb 15, 2023

Commits on Feb 16, 2023

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 17, 2023

merge GVS branch
lbergelson
committed