Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

lb merge gvs branch #8248

Closed
wants to merge 664 commits into from
Closed

lb merge gvs branch #8248

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
664 commits
Select commit Hold shift + click to select a range
6e6bb01
execute_with_retry() refactor and error handling improvements [VS-159…
rsasch Sep 29, 2021
6c927ae
Small updates to GvsExtractCallset from beta callset, new workflow fo…
rsasch Oct 7, 2021
1e913f7
add flag in prepare to print out sql instead of executing (#7501)
ahaessly Oct 13, 2021
10444d1
Workflow to re-scatter and then merge "problematic" intervals from Ex…
rsasch Oct 14, 2021
9cc6b4f
changed README to reflect comments from Lee [VS-210] (#7502)
rsasch Oct 15, 2021
24a9971
Export the VAT into GCS (#7472)
RoriCremer Oct 18, 2021
63c856a
addresses VS-219 (#7508)
kcibul Oct 18, 2021
0dd2be0
small fix to MergeVCFs (#7517)
rsasch Oct 22, 2021
a603dee
small fixes to GVS pipeline (#7522)
rsasch Oct 26, 2021
e6a9f77
make sure ExtractTask is run on all interval files
rsasch Oct 27, 2021
0e6ca4b
Revert "make sure ExtractTask is run on all interval files"
rsasch Oct 27, 2021
24f91cc
make sure ExtractTask is run on all interval files (#7527)
rsasch Oct 27, 2021
308b870
Remove Sites only step from the VAT creation WDL (#7510)
RoriCremer Oct 28, 2021
fb67e8e
fix bad argument processing for bool (#7529)
ahaessly Oct 29, 2021
08446bb
Support for TDR DRS URIs in Import (#7528)
kcibul Nov 2, 2021
a46cd64
Match format of filename output in GvsRescatterCallsetInterval (#7539)
rsasch Nov 3, 2021
f232412
Reference block storage and query support (#7498)
kcibul Nov 4, 2021
9408133
update docs (#7540)
ahaessly Nov 4, 2021
9c76117
Kc fix rr load bug (#7550)
kcibul Nov 8, 2021
860f438
Update .dockstore.yml (#7553)
kcibul Nov 8, 2021
fbbea88
Ah add reblocking wdl (#7544)
ahaessly Nov 8, 2021
a9f0d45
Scatter over all interval files, not just scatter count (#7551)
rsasch Nov 9, 2021
41ef596
fixed docker (#7558)
kcibul Nov 10, 2021
7d8e782
take advantage of fixed version of SplitIntervals (#7566)
rsasch Nov 16, 2021
d69b273
Document AoU-specific tieout [VS-233] (#7552)
rsasch Nov 16, 2021
0d7319c
bad param assignment in aou reblocking (#7572)
ahaessly Nov 18, 2021
bd432c1
Small fixes to ImportGenomes (non-write api version) (#7574)
rsasch Nov 20, 2021
7148df0
Ah change output of reblocking wdl to external path (#7575)
ahaessly Nov 23, 2021
44aee08
close BQ Readers (#7583)
kcibul Nov 25, 2021
ac1dc9c
Ah spike writeapi (#7530)
ahaessly Dec 8, 2021
2257e79
bump WDL jar (#7593)
kcibul Dec 8, 2021
ff251d6
read api bytes logging, upgrade bigquery client versions (#7601)
kcibul Dec 17, 2021
20e7e7e
bump (#7610)
kcibul Dec 17, 2021
07489bf
upgrade log4j to 2.17 (#7616)
kcibul Dec 20, 2021
7a57588
Add drop_state default of Forty to extract (#7619)
RoriCremer Dec 22, 2021
b9496ed
Kc fix type (#7620)
kcibul Dec 27, 2021
372a7f4
VAT cleanup and documentation (#7531)
RoriCremer Jan 5, 2022
6dd01dc
fix empty flush (#7627)
kcibul Jan 6, 2022
8a17ca2
presorted avro files, fix performance issue (#7635)
kcibul Jan 12, 2022
3aa74a5
WIP extract for ranges (#7640)
kcibul Jan 19, 2022
aa2d114
VS-268 import more samples at once (#7629)
RoriCremer Jan 24, 2022
0ca6abb
clustering vqsr tables by location (#7656)
kcibul Jan 31, 2022
b2b2a83
First Version of a weight-based splitter (#7643)
kcibul Feb 11, 2022
5e1fcb5
Update GvsExtractCallset.wdl
kcibul Feb 11, 2022
c733b4b
Quoting of table names (#7666)
kcibul Feb 14, 2022
6295133
docs for analysis of shard runtimes for balanced sharding (#7645)
kcibul Feb 14, 2022
b4c0d1a
Wire through GvsExtractCohortFromSampleNames with new prepare/extract…
rsasch Feb 14, 2022
1c960a7
Update GvsExtractCallset.wdl (#7678)
kcibul Feb 16, 2022
3bca3a3
cherry pick lb_lfs_force change (#7683)
rsasch Feb 17, 2022
1b53369
Tweak ingest messaging and failure mode [VS-267] (#7680)
rsasch Feb 18, 2022
d2ebecb
Additional tweaks for GvsExtractCohortFromSampleNames [VS-283] (#7698)
rsasch Feb 25, 2022
3aa3c3b
VS-280 Create a VAT intermediary (#7657)
RoriCremer Feb 25, 2022
dab3253
There something about split intervals [VS-306] (#7694)
RoriCremer Mar 2, 2022
13003ff
VS 284 Add prepare step to Quick Start (#7685)
RoriCremer Mar 2, 2022
38fa733
VS-222 dont hard code the dataset name! (#7704)
RoriCremer Mar 9, 2022
cc81b76
fixed bug; added tests (#7717)
kcibul Mar 11, 2022
db6b15f
Clean up optional and inconsistently named inputs [VS-294] [VS-218] (…
rsasch Mar 21, 2022
3b4c5ba
VS-263 notes on ingest and beyond (#7618)
RoriCremer Mar 23, 2022
f4973c7
Add task to ExtractCallset that verifies filter_set_name exists in GV…
rsasch Mar 23, 2022
91cef1c
Clean up input json files to reflect changes inputs [VS-337] (#7733)
rsasch Mar 24, 2022
55b9ead
used constants; implemented non-AS transformation (#7718)
kcibul Mar 24, 2022
47ec80d
Pass dataset name to gatk ExtractFeatures (#7735)
RoriCremer Mar 29, 2022
141023f
Add withdrawn and is_control columns [VS-70] [VS-213] (#7736)
rsasch Mar 30, 2022
b62026a
Allow interval lists that require the SA to see (#7743)
RoriCremer Mar 31, 2022
d07a944
allow for gatk to be overridden, update with known good jar (#7758)
kcibul Apr 6, 2022
e99e842
VS-361 Add GvsWithdrawSamples wdl (#7765)
gbggrant Apr 7, 2022
1f490f0
Extract Performance Improvements (#7686)
kcibul Apr 7, 2022
6bf03de
Don't put withdrawn sample data in alt_allele table [VS-369] (#7762)
rsasch Apr 8, 2022
f49e122
remove PET code (#7768)
kcibul Apr 11, 2022
fd960a4
Adding AD for scale testing VS 225 add AD (#7713)
RoriCremer Apr 12, 2022
1fecbf9
Deterministic Sample ID assignments [VS-371] (#7770)
mcovarr Apr 13, 2022
8a4f8df
remove R scripts from filtering (#7781)
RoriCremer Apr 14, 2022
463c8a1
Remove an old "temp table" dataset (#7780)
RoriCremer Apr 14, 2022
43a1480
Clean up LocalizeFile [VS-314] (#7771)
mcovarr Apr 14, 2022
7a15427
Remove pet code from CreateVariantIngestFiles and friends [VS-375] (#…
mcovarr Apr 15, 2022
1387d47
317 remove excess header values in VCF extract (#7786)
RoriCremer Apr 15, 2022
3c500f7
correct auth in split intervals (#7790)
RoriCremer Apr 19, 2022
3ff95df
Add code to (optionally) zero pad the vcf filename. (#7783)
gbggrant Apr 19, 2022
940777c
LoadData `maxRetries` parameterized, default increased [VS-383] (#7791)
mcovarr Apr 20, 2022
8d08a6e
Update to latest version of ah_var_store gatk override jar (#7793)
gbggrant Apr 20, 2022
8f429ad
GvsUnified WDL to wrap the 6 core GVS WDLs [VS-382] (#7789)
mcovarr Apr 21, 2022
f09b162
Pinned typing_extensions python package to 4.1.1 to fix conda environ…
samuelklee Apr 21, 2022
614a0f7
WeightedSplitInterval fixes [VS-384] [VS-332] (#7795)
mcovarr Apr 25, 2022
0593639
Replace Travis with GithubActions (#7754)
jamesemery Apr 21, 2022
dfc239d
Docker build only lfs pulls main/src/resources/large (#7727)
lbergelson Mar 17, 2022
6ac511b
Clean up gatk jars -- looks like we are not passing them properly in …
RoriCremer Apr 25, 2022
2381a09
Fix typo that broke git lfs pull (#7806)
mcovarr Apr 25, 2022
ba7a26c
Document AoU SOP (up to the VAT) [VS-63] (#7807)
rsasch Apr 26, 2022
75b5115
Incident VS 365 clinvar classification fix (#7769)
RoriCremer Apr 27, 2022
d51a4e5
VS-390. Add precision and sensitivity wdl (#7813)
gbggrant Apr 29, 2022
04aec08
Quickstart based integration test [VS-357] (#7812)
mcovarr May 3, 2022
d77ebf5
365 vat python testing additions (#7756)
RoriCremer May 3, 2022
02cbbf1
VS 396 clinvar grabs too many values (#7823)
RoriCremer May 4, 2022
43f3192
Added a test to validate WDLs in the scripts directory. (#7826) (#7829)
gbggrant May 5, 2022
c1c8154
VAT Performance / Reliability Improvements (#7828)
kcibul May 5, 2022
9363f15
VAT naming conventions [VS-410] (#7827)
mcovarr May 5, 2022
9f1148f
Rc remove ad from vat (#7832)
RoriCremer May 5, 2022
4e7b1f8
bugfix, we were trying to grep a binary file (#7837)
kcibul May 6, 2022
bfa671b
Cleanup scripts/variantstore [VS-414] (#7834)
mcovarr May 12, 2022
900651f
Merge VAT TSV files into single bgzipped file [VS-304] (#7848)
rsasch May 13, 2022
17a5e5e
Handle fully and partially loaded samples [VS-262] [VS-258] (#7843)
mcovarr May 13, 2022
bfccaf6
Ingest Error Handling Fixes [VS-261] (#7841)
mcovarr May 13, 2022
f58e9b2
First cut at a python notebook to validate inputs. (#7845)
gbggrant May 16, 2022
1dc9776
Compute filter scatter [VS-392] (#7852)
rsasch May 18, 2022
7388851
remove withdrawn req (#7844)
RoriCremer May 18, 2022
6767947
Improve import error message [VS-437] (#7855)
mcovarr May 18, 2022
e7539d5
Fix Input Validation python notebook (#7853)
gbggrant May 23, 2022
6d6cb98
Add VAT Validation check that aa_change and exon_number are consisten…
gbggrant May 26, 2022
a4ac264
Ingest 10K [VS-344] (#7860)
mcovarr May 26, 2022
91c33df
X/Y chromosome reweighting for better extract shard runtime balance […
mcovarr May 26, 2022
4d30135
VET Ingest Validation / Allow Ingest of non-VQSR'ed data (#7870)
gbggrant Jun 2, 2022
f6fde4e
Fix AoU workflow bugs (#7874)
calbach Jun 3, 2022
00e7d57
Curate input arrays to skip already ingested sample data [VS-246] (#7…
rsasch Jun 3, 2022
e4c4bfc
KM upload GVS product sheet (#7883)
kayleemathews Jun 7, 2022
b48282e
Default extract scatter width [VS-415] (#7878)
mcovarr Jun 8, 2022
db90162
Volatile tasks review [VS-447] (#7880)
mcovarr Jun 8, 2022
7dca9fb
Update Quickstart Integration for X/Y scaling changes [VS-464] (#7881)
mcovarr Jun 9, 2022
d0f00d8
clean up dockstore
RoriCremer Jun 10, 2022
0be4453
Rc vs 63 vat sop documentation (#7879)
RoriCremer Jun 10, 2022
727c1da
Fix up FQ and race condition issues with volatile tasks work [VS-478]…
mcovarr Jun 10, 2022
8e84f0a
Use gvs-internal project in integration test (#7901)
rsasch Jun 14, 2022
89a7d5d
Add cost observability BQ table [VS-441] (#7891)
mcovarr Jun 15, 2022
00f07e9
Add preliminary labels to queries [VS-381] (#7902)
rsasch Jun 17, 2022
8cd0f5f
Workflow compute costs [VS-472] (#7905)
mcovarr Jun 22, 2022
8781b56
Fix bug and update images (#7912)
rsasch Jun 22, 2022
13b5660
VS 483 Beta user wdl (#7894)
RoriCremer Jun 28, 2022
586f3f7
Core storage model cost [VS-473] (#7913)
mcovarr Jun 28, 2022
32a6106
Update Quickstart & Integration to use re-blocked v2 gVCFs [VS-491] (…
rsasch Jun 29, 2022
9f857df
KM GVS documentation (#7903)
kayleemathews Jun 29, 2022
d9cd014
Track BigQuery costs of GVS python VS-480 (#7915)
rsasch Jun 29, 2022
a75a399
Read cost observability table [VS-475] (#7923)
mcovarr Jul 5, 2022
874d615
Fix Race Condition, Add Support for Extract by Array of Sample Names …
kcibul Jul 6, 2022
3e60f0d
Rightsize import batches [VS-486] (#7925)
mcovarr Jul 6, 2022
4b2cf4b
[AoU DRC] Support uppercase site_ids for reblocking (#7929)
mmorgantaylor Jul 7, 2022
faf3347
Populate cost metadata for GATK tasks. (#7919)
gbggrant Jul 8, 2022
0f9780a
remove accidentally added input (#7931)
mcovarr Jul 8, 2022
201df7f
VS_492 - Beta User Jar release (#7934)
gbggrant Jul 11, 2022
c00e54b
Cost WDL should throw on FISS API errors [VS-518] (#7942)
mcovarr Jul 14, 2022
63108be
Fix bad check for missing workflow name [VS-520] (#7943)
mcovarr Jul 14, 2022
de4479a
Remove usage of service account from GvsValidateVAT.wdl (#7937)
gbggrant Jul 15, 2022
210a6ae
refactoring for testablity (#7946)
kcibul Jul 18, 2022
28ed209
More import retries [VS-532] (#7953)
mcovarr Jul 21, 2022
2d1e304
A few last doc changes (#7927)
RoriCremer Jul 25, 2022
8dd4541
WDL to extract a single callset cost (BQ only, not Terra) (#7940)
RoriCremer Aug 1, 2022
fc2b7a8
Temporarily swap in Corretto for Temurin as we can't download Temurin…
mcovarr Aug 1, 2022
0f7e2fd
GL-548 - Update CreateVat code to handle samples that do not contain …
gbggrant Aug 2, 2022
3e62331
Restore Temurin 11 [VS-570] (#7972)
mcovarr Aug 3, 2022
de42a7a
Add table size check to quickstart integration test [VS-501] (#7970)
rsasch Aug 3, 2022
798d4e8
Consolidate various docs for AoU callset generation into one to rule …
rsasch Aug 3, 2022
361ce37
VS-567. Removing usage of ServiceAccount from CreateVat related WDLs …
gbggrant Aug 10, 2022
42a9382
WDL to extract Avro files for Hail import [VS-579] (#7981)
mcovarr Aug 10, 2022
0130bb8
Removed usage of service account from WDLs (#7985)
gbggrant Aug 16, 2022
bed8af2
Document steps for GVS cleanup for base use case [VS-586] (#7989)
rsasch Aug 17, 2022
0d80de6
Change backticks to single quotes in several error messages - causing…
gbggrant Aug 18, 2022
315303b
VS-598 - Minor update to AoU Documentation. (#7994)
gbggrant Aug 18, 2022
187fe60
Allow for incremental addition of data to alt_allele [VS-52] (#7993)
rsasch Aug 22, 2022
aff1c48
Minor AoU Documentation Update (#7999)
gbggrant Aug 23, 2022
092cb76
Batch population of alt_allele table from vet_ tables [VS-265] (#7998)
rsasch Aug 24, 2022
0ff86b1
Change drop_state to NONE for Ingest/Extract [VS-607] (#8000)
rsasch Aug 24, 2022
0d914c5
python -> python3 (#8001)
rsasch Aug 24, 2022
d3f63e5
Generate Hail import/export script [VS-605] (#8002)
mcovarr Aug 26, 2022
08b62a8
clearer error when values are missing (#7939)
RoriCremer Aug 30, 2022
a1a8e57
Ah [VS-565] output intervals and sample list (#8010)
koncheto-broad Sep 6, 2022
76c969d
make CreateAltAlleleTable task volatile (#8011)
rsasch Sep 7, 2022
51387f1
Restore withdrawn [VS-581] (#8006)
mcovarr Sep 7, 2022
ff05126
Km gvs add storage cost and cleanup doc (#8012)
kayleemathews Sep 7, 2022
91c9c9c
Updating documentation to reflect the changed outputs [VS-565] (#8014)
koncheto-broad Sep 8, 2022
08c1ad7
File of callset samples -> samples marked as 'withdrawn' in GVS [VS-4…
rsasch Sep 8, 2022
d52f05d
fix quota guidelines for CPUs (#8016)
rsasch Sep 9, 2022
f427624
Add in ability to tweak sample-every-Nth-variant parameter for SNP mo…
rsasch Sep 16, 2022
53cf8a7
add initial notebook copy pasta (#8008)
RoriCremer Sep 16, 2022
0ef7433
add sample_table_timestamp to GetNumSamplesLoaded (#8022)
rsasch Sep 19, 2022
ae56b88
Batched Avro export [VS-630] (#8020)
mcovarr Sep 20, 2022
6b9f171
Updating references to old GATK for VS-620 (#8023)
koncheto-broad Sep 21, 2022
f8914cf
VS-517 Use standard version of GetBQTableLastModifiedDatetime in Gv…
koncheto-broad Sep 21, 2022
55668c3
Fix bug in GvsWithdrawSamples.wdl (#8026)
gbggrant Sep 21, 2022
95849f5
Ah 617 exposing the drop_state parameter to the GvsJointVariantCallin…
koncheto-broad Sep 23, 2022
3b74d0a
Expose maximum-training-variants VQSR parameter [VS-634] (#8029)
rsasch Sep 27, 2022
953f68c
Callset statistics [VS-560] (#8018)
mcovarr Sep 27, 2022
9994658
Check for withdrawn before exporting to AVRO files [VS-646] (#8039)
rsasch Sep 28, 2022
0735df7
Small updates to GVS Integration WDL [VS-618] (#8042)
rsasch Sep 29, 2022
c7df760
Rework Hail script generation [VS-616] (#8034)
mcovarr Sep 30, 2022
2ae759b
Alpine based Variant Store Docker image [VS-648] (#8044)
mcovarr Oct 6, 2022
b088a5c
update warp version (#7906)
RoriCremer Oct 6, 2022
01b2880
Fail Avro extract and callset stats on bad filter name [VS-655] (#8046)
mcovarr Oct 7, 2022
5f1f998
Vs 629 failure to retrieve job information during ingest (#8047)
koncheto-broad Oct 11, 2022
b338cc9
Restore accidentally removed bcftools [VS-661] (#8051)
mcovarr Oct 13, 2022
c263ce3
Allowing our pipeline to function with a sample size of one (#8055)
koncheto-broad Oct 17, 2022
2a8c210
Vs 665 re create vcf for cd 68 po 52339 with ad padding fixed (#8057)
koncheto-broad Oct 17, 2022
bde383b
VS-665 and VS-620 updating code to use latest docker images containin…
koncheto-broad Oct 18, 2022
1c5c486
updating the beta workflow to use the latest jar, representing the ve…
koncheto-broad Oct 18, 2022
f2dcc68
VS-637 Address a couple of issues in SampleLoadStatus handling in GVS…
gbggrant Oct 19, 2022
4c8abaa
Revert Alpinizing of apt dependent task [VS-688] (#8065)
mcovarr Oct 20, 2022
116db44
Fix missing vat schema JSONs [VS-699] (#8072)
mcovarr Oct 25, 2022
11bf415
Fix integration expectations for fixed AD [VS-689] (#8066)
mcovarr Oct 26, 2022
e6d736b
VS-698 Remove unnecessary columns from Call set statistics (#8073)
gbggrant Oct 26, 2022
31e8cb7
Fix Dockerfile nits that break 20.10.21 (#8078)
mcovarr Oct 31, 2022
18fa298
Nirvana 3.18.1 Docker images support [VS-661] (#8082)
mcovarr Nov 1, 2022
7dd6ede
Add option to not prepare __REF_DATA or __SAMPLES tables to Prepare […
rsasch Nov 7, 2022
d1907a8
"build-base" Docker image for faster variantstore image builds [VS-71…
mcovarr Nov 8, 2022
aa97a09
GVS / Hail VDS integration test [VS-639] (#8086)
mcovarr Nov 10, 2022
dfe7b7e
Remove AI/AN from VDS docs [VS-726] (#8096)
mcovarr Nov 17, 2022
08048f1
Add flag for cost_observability table writing to support sub-cohort u…
rsasch Nov 21, 2022
335a1b1
Document STS delivery process for VDS [VS-727] (#8101)
mcovarr Nov 22, 2022
f52992c
delete obsolete callset_QC directory and its contents [VS-318] (#8108)
mcovarr Nov 30, 2022
e29a3d8
doc link typo and add check for control samples in AVRO export (#8110)
rsasch Nov 30, 2022
1412b4e
Add defaults for scatter_count in GvsExtractCohortFromSampleNames [VS…
rsasch Nov 30, 2022
5b94b27
Escape table names properly in ValidateVat WDL (#8116)
gbggrant Dec 1, 2022
a69661b
Vs 741 fix indefinite freeze in split intervals task when using exome…
koncheto-broad Dec 1, 2022
290fd23
VAT Readme updates (#8090)
RoriCremer Dec 5, 2022
080d66a
WDL and python scripts to use the VDS in the VAT (#8077)
RoriCremer Dec 15, 2022
10a737c
VS-757 - Use JASIX to make sub-jsons of annotated output of Nirvana (…
gbggrant Dec 22, 2022
ea3408b
add note about permissions for P&S workflow to work (#8135)
rsasch Jan 3, 2023
20409d9
VS-759 (and VS-760) (#8137)
gbggrant Jan 5, 2023
6f2e75a
VS-765. Scatter the RemoveDuplicates task. (#8144)
gbggrant Jan 9, 2023
8705cb5
update delivery docs based on latest VDS delivery run [VS-770] (#8150)
rsasch Jan 9, 2023
700dacd
Add monitoring to index vcf (#8151)
gbggrant Jan 10, 2023
498a4a6
Make some noise when VDS validation succeeds (#8155)
mcovarr Jan 11, 2023
fedb320
Handle empty genes annotation file. (#8153)
gbggrant Jan 12, 2023
8a7b95d
Add escapes for otherwise problematic dataset / table names. (#8162)
mcovarr Jan 13, 2023
c15e5fc
New WDL to create VAT tsvs from previously generated BigQuery table. …
gbggrant Jan 20, 2023
9cf8021
Treat withdrawn samples in sub-cohort prepare correctly [VS-772] (#8156)
rsasch Jan 23, 2023
50f4af6
Remove unused VAT Creation WDL (#8172)
gbggrant Jan 24, 2023
31c3a02
Gg consistently use dataset name as input parameter (#8173)
gbggrant Jan 25, 2023
e706dc0
AoU cleanup docs, round 1 [VS-671] (#8104)
mcovarr Jan 30, 2023
053594d
VDS docs remove samples and correct GT [VS-807] (#8178)
mcovarr Jan 31, 2023
cdb74b7
[VS-693] Add support for VQSR Lite to GvsCreateFilterSet (#8157)
koncheto-broad Feb 2, 2023
2e90d46
VAT Documentation Update Round 1 [VS-531]
RoriCremer Feb 2, 2023
39070f0
VS-530 VDS creation documentation for AoU (#8169)
RoriCremer Feb 3, 2023
d07e773
Update beta docs to tell people not to use free credits (#8184)
rsasch Feb 3, 2023
0c48d6d
VS-816 Keeping ingestion under quota (#8193)
koncheto-broad Feb 9, 2023
69ad63b
CromwellOnAzure + Azure SQL DB + AAD first steps doc [VS-805] (#8191)
mcovarr Feb 9, 2023
4797463
Edit and re-format VDS -> VAT doc [VS-821] (#8187)
rsasch Feb 13, 2023
d1a6df3
VS-820 Incorporate code to stay under Google quotas for new accounts …
koncheto-broad Feb 14, 2023
5b34ade
Update docs for Nirvana reference disk [VS-531] [VS-796] (#8170)
mcovarr Feb 15, 2023
ac04b54
VS-694 - Extract Callset for VQSR Lite (#8182)
gbggrant Feb 15, 2023
7b4091a
Updating docker image (#8210)
koncheto-broad Feb 16, 2023
4a1c203
Document VCF generation [VS-795] (#8202)
rsasch Feb 16, 2023
1ce13b3
Variants GATK Docker image building docs + script [VS-827] (#8207)
mcovarr Feb 22, 2023
fdbaa14
Update GATK jar used in GvsJointVariantCalling WDL (#8216)
rsasch Feb 22, 2023
0014005
Hello Azure SQL Database from Cromwell on Azure [VS-812] (#8220)
mcovarr Feb 27, 2023
6f747d0
Remove what appear to be accidentally added files [VS-834] (#8225)
mcovarr Feb 28, 2023
6d41adf
VS-815: Add Support for YNG to VQSR Lite (#8206)
gbggrant Mar 1, 2023
3a7f6e2
Disentangle non-GVS code from GVS code [VS-834] (#8229)
mcovarr Mar 3, 2023
5645e88
VS-695. Updates to run Precision and Sensitivity on VQSR Lite (#8230)
gbggrant Mar 3, 2023
781bb14
Track avro export costs [VS-769] (#8236)
rsasch Mar 8, 2023
b09d909
Add note that we deleted a VDS! (#8214)
RoriCremer Mar 13, 2023
3e5a756
Vs 822 Add documentation for the work that we did on the latest itera…
RoriCremer Mar 14, 2023
291bfd0
Rc vs 822 gq0 documentation (#8240)
RoriCremer Mar 14, 2023
8bb0d6d
merge GVS branch
lbergelson Mar 17, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
277 changes: 238 additions & 39 deletions .dockstore.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,105 +6,304 @@ workflows:
testParameterFiles:
- /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
filters:
branches:
branches:
- master
- name: cnv_germline_case_workflow
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
testParameterFiles:
- /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
- /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
filters:
branches:
- master
branches:
- master
- name: cnv_germline_cohort_workflow
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
testParameterFiles:
- /scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
- /scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
filters:
branches:
- master
branches:
- master
- name: cnv_somatic_pair_workflow
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
testParameterFiles:
- /scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json
testParameterFiles:
- /scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json
filters:
branches:
- master
branches:
- master
- name: cnv_somatic_panel_workflow
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
testParameterFiles:
- /scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json
- /scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json
filters:
branches:
- master
branches:
- master
- name: cnv_joint_call_exomes
subclass: WDL
primaryDescriptorPath: /scripts/cnv_wdl/germline/joint_call_exome_cnvs.wdl
filters:
branches:
- master
branches:
- master
- name: cram2filtered
subclass: WDL
primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2filtered.wdl
testParameterFiles:
- /scripts/cnn_variant_wdl/jsons/cram2filtered.json
- /scripts/cnn_variant_wdl/jsons/cram2filtered.json
filters:
branches:
- master
branches:
- master
- name: cram2model
subclass: WDL
primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2model.wdl
testParameterFiles:
- /scripts/cnn_variant_wdl/jsons/cram2model.json
- /scripts/cnn_variant_wdl/jsons/cram2model.json
filters:
branches:
- master
branches:
- master
- name: Funcotator
subclass: WDL
primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl
testParameterFiles:
- /scripts/funcotator_wdl/funcotator.json
- /scripts/funcotator_wdl/funcotator.json
filters:
branches:
- master
branches:
- master
- name: GvsAssignIds
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsAssignIds.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsAssignIds.example.inputs.json
filters:
branches:
- master
- ah_var_store
- name: GvsAoUReblockGvcf
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsAoUReblockGvcf.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsBenchmarkExtractTask
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsBenchmarkExtractTask.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsRescatterCallsetInterval
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsRescatterCallsetInterval.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsCreateFilterSet
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateFilterSet.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsCreateFilterSet.example.inputs.json
filters:
branches:
- master
- ah_var_store
- gg_VS-695_RunPandSForVQSR_Lite
- name: GvsPopulateAltAllele
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsPopulateAltAllele.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsCreateTables
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateTables.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsCreateTables.example.inputs.json
filters:
branches:
- master
- ah_var_store
- name: GvsExtractCallset
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCallset.wdl
filters:
branches:
- master
- ah_var_store
- gg_VS-695_RunPandSForVQSR_Lite
- name: GvsImportGenomes
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsImportGenomes.wdl
filters:
branches:
- master
- ah_var_store
- VS-816
- name: GvsPrepareRangesCallset
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
testParameterFiles:
- /scripts/variantstore/wdl/GvsPrepareRangesCallset.example.inputs.json
filters:
branches:
- master
- ah_var_store
- name: GvsCreateVATfromVDS
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCreateVATfromVDS.wdl
filters:
branches:
- master
- ah_var_store
- mc_nirvana_reference_disk
- name: GvsCreateVATFilesFromBigQuery
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/variant_annotations_table/GvsCreateVATFilesFromBigQuery.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsValidateVat
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl
testParameterFiles:
- /scripts/variantstore/variant_annotations_table/GvsValidateVat.example.inputs.json
filters:
branches:
- master
- ah_var_store
- name: GvsExtractCohortFromSampleNames
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractCohortFromSampleNames.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsWithdrawSamples
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsWithdrawSamples.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsUnified
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsUnified.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsJointVariantCalling
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCalling.wdl
filters:
branches:
- master
- ah_var_store
- rsa_vs_831
- name: GvsJointVariantCallsetCost
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCallsetCost.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsCalculatePrecisionAndSensitivity
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCalculatePrecisionAndSensitivity.wdl
filters:
branches:
- master
- ah_var_store
- gg_VS-695_RunPandSForVQSR_Lite
- name: GvsQuickstartVcfIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartVcfIntegration.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsQuickstartHailIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsQuickstartIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
filters:
branches:
- master
- ah_var_store
- vs_834_disentangle
- name: GvsIngestTieout
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsCallsetCost
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCallsetCost.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsExtractAvroFilesForHail
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
filters:
branches:
- master
- ah_var_store
- name: GvsCallsetStatistics
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsCallsetStatistics.wdl
filters:
branches:
- master
- ah_var_store
- name: MitochondriaPipeline
subclass: WDL
primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
testParameterFiles:
- /scripts/mitochondria_m2_wdl/ExampleInputsMitochondriaPipeline.json
- /scripts/mitochondria_m2_wdl/ExampleInputsMitochondriaPipeline.json
filters:
branches:
- master
branches:
- master
- name: mutect2
subclass: WDL
primaryDescriptorPath: /scripts/mutect2_wdl/mutect2.wdl
testParameterFiles:
- /scripts/m2_cromwell_tests/mutect2.inputs.json
- /scripts/m2_cromwell_tests/mutect2.inputs.json
filters:
branches:
- master
branches:
- master
- name: mutect2_pon
subclass: WDL
primaryDescriptorPath: /scripts/mutect2_wdl/mutect2_pon.wdl
filters:
branches:
- master
branches:
- master
- name: run_happy
subclass: WDL
primaryDescriptorPath: /scripts/cnn_variant_wdl/run_happy.wdl
testParameterFiles:
- /scripts/cnn_variant_wdl/jsons/run_happy.json
- /scripts/cnn_variant_wdl/jsons/run_happy.json
filters:
branches:
- master
branches:
- master
- name: pathseq_pipeline
subclass: WDL
primaryDescriptorPath: /scripts/pathseq/wdl/pathseq_pipeline.wdl
testParameterFiles:
- /scripts/pathseq/wdl/pathseq_pipeline_template.json
- /scripts/pathseq/wdl/pathseq_pipeline_template.json
filters:
branches:
- master
branches:
- master
3 changes: 1 addition & 2 deletions .gitattributes
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,7 @@ src/test/resources/large/funcotator/funcotator_dataSources/dna_repair_genes/hg38
src/test/resources/large/funcotator/funcotator_dataSources/familial/hg38 -filter=lfs -diff=lfs -merge=lfs -text
src/test/resources/large/funcotator/funcotator_dataSources/hgnc/hg38 -filter=lfs -diff=lfs -merge=lfs -text
src/test/resources/large/funcotator/funcotator_dataSources/simple_uniprot/hg38 -filter=lfs -diff=lfs -merge=lfs -text

#Otherwise, track everything in large
src/test/resources/large/** filter=lfs diff=lfs merge=lfs -text
src/main/resources/large/** filter=lfs diff=lfs merge=lfs -text

*.psd filter=lfs diff=lfs merge=lfs -text
1 change: 1 addition & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ out/
gatkcondaenv.yml
gatkcondaenv.intel.yml
gatkPythonPackageArchive.zip
testfiles/

#Please don't commit me
client_secret.json
Expand Down
Loading