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

Update Beta User WDL to use bulk ingest [VS-982] #8379

Closed
wants to merge 36 commits into from
Closed

Update Beta User WDL to use bulk ingest [VS-982] #8379

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
36 commits
Select commit Hold shift + click to select a range
473be67
starting to rearrange workflows and tasks
rsasch Jun 20, 2023
1896ec1
remove GvsPrepareBulkImport.wdl
rsasch Jun 20, 2023
9063bb5
removed GvsCreateTables.wdl
rsasch Jun 20, 2023
a8c916f
undoing file reorg
rsasch Jun 21, 2023
afc8090
bypass GvsUnified but add BulkIngest
rsasch Jun 21, 2023
0a99841
take out terra data table inputs
rsasch Jun 21, 2023
693eded
Update to latest docker.
gbggrant Jun 21, 2023
d5c68db
Merge remote-tracking branch 'origin/ah_var_store' into gg_VS-987_Out…
gbggrant Jun 21, 2023
27e8ba2
more cleanup
rsasch Jun 21, 2023
298c41e
Fix a bug where there were NO variants in a range.
gbggrant Jun 21, 2023
1191feb
only guess vcf and vcf_index column names if nothing passed
rsasch Jun 21, 2023
b486ed0
Remove other change in order to expedite this fix.
gbggrant Jun 21, 2023
2870af5
removed unnecessary line returns
rsasch Jun 21, 2023
0ca5275
Merge branch 'gg_VS-987_OutOfDateDocker' into rsa_vs_982
rsasch Jun 21, 2023
63a0bea
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 22, 2023
b6dd21c
update jar
rsasch Jun 22, 2023
86f95b3
use beta workflow for integration tests
rsasch Jun 22, 2023
9a4105b
wire up integration tests to use GvsJointVariantCalling.wdl instead o…
rsasch Jun 22, 2023
6188ec8
more integration wiring
rsasch Jun 22, 2023
71fd767
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 22, 2023
223558d
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 23, 2023
479703e
wire through vqsr option and hopefully make more consistent
rsasch Jun 23, 2023
08346b3
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 26, 2023
58a2f43
cleanup after merge, wire through filter_set_name
rsasch Jun 26, 2023
42e7e0b
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 26, 2023
ae1ba40
more cleanup
rsasch Jun 26, 2023
0056e33
even more cleanup
rsasch Jun 26, 2023
0496053
cleanup with womtool working
rsasch Jun 26, 2023
c210782
undo integration test changes
rsasch Jun 28, 2023
53f3b17
finish backing out of integration test changes
rsasch Jun 28, 2023
a99aac2
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 28, 2023
252606a
cleanup before PR review
rsasch Jun 28, 2023
d96880b
PR feedback
rsasch Jun 28, 2023
d1409bc
make sure to incorporate latest version of bulk ingest tasks
rsasch Jun 28, 2023
f6771a4
Merge branch 'ah_var_store' into rsa_vs_982
rsasch Jun 28, 2023
763bce9
python fix and docker update
rsasch Jun 28, 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
19 changes: 5 additions & 14 deletions .dockstore.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -118,18 +118,14 @@ workflows:
branches:
- master
- ah_var_store
- name: GvsPrepareBulkImport
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsPrepareBulkImport.wdl
filters:
branches:
- ah_var_store
- name: GvsBulkIngestGenomes
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsBulkIngestGenomes.wdl
filters:
branches:
- master
rsasch marked this conversation as resolved.
Show resolved Hide resolved
- ah_var_store
- rsa_vs_982
- name: GvsPrepareRangesCallset
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsPrepareRangesCallset.wdl
Expand Down Expand Up @@ -176,13 +172,6 @@ workflows:
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
Expand All @@ -191,7 +180,6 @@ workflows:
- master
- ah_var_store
- rsa_vs_982
- rsa_jar_fix_230722
- name: GvsJointVariantCallsetCost
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsJointVariantCallsetCost.wdl
Expand All @@ -213,20 +201,23 @@ workflows:
branches:
- master
- ah_var_store
- rsa_vs_982
- name: GvsQuickstartHailIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartHailIntegration.wdl
filters:
branches:
- master
- ah_var_store
- rsa_vs_982
- name: GvsQuickstartIntegration
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsQuickstartIntegration.wdl
filters:
branches:
- master
- ah_var_store
- rsa_vs_982
- name: GvsIngestTieout
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsIngestTieout.wdl
Expand Down
Loading
Loading