Update output names for ReblockGVCF #1443

jessicaway · 2024-12-03T17:42:09Z

Description

Change requested by the variants team

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.

Did you add inputs, outputs, or tasks to a workflow?
Did you modify, delete or move: file paths, file names, input names, output names, or task names?
If you made a changelog update, did you update the pipeline version number?

github-actions · 2024-12-03T17:42:22Z

Remember to squash merge!

github-actions · 2024-12-03T17:42:32Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
UltimaGenomicsWholeGenomeGermline.changelog.md has not been changed and needs to be updated
BroadInternalUltimaGenomics.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-12-03T17:42:36Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
UltimaGenomicsWholeGenomeGermline.wdl has not had its version updated
BroadInternalUltimaGenomics.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

koncheto-broad · 2024-12-03T18:30:01Z

pipelines/broad/dna_seq/germline/single_sample/ugwgs/UltimaGenomicsWholeGenomeGermline.wdl

@@ -202,8 +202,8 @@ workflow UltimaGenomicsWholeGenomeGermline {

  # Outputs that will be retained when execution is complete
  output {
-    File output_gvcf = ReblockGVCF.output_vcf
-    File output_gvcf_index = ReblockGVCF.output_vcf_index
+    File output_gvcf = ReblockGVCF.reblocked_gvcf


Do we need to change the outputs here to? I don't think we (GVS) ever direct consume the output of this WDL, so it's likely that maintaining its output naming scheme was deliberate. But I just wanted to verify that here

This change is necessary since the output of the reblock workflow is being referenced. I left the output name for this workflow the same, but needed to update the reference to the output of ReblockGVCF

yup, totally makes sense why this change was needed. As I don't know the users of this particular wdl, I mostly wanted to ensure that it wasn't something any end users would be running before sending the data into GVS (in which case we'd want to update its outputs as well). It sounds as though this is not expected behavior though, and this one has only been touched because it consumes ReblockGVCF for other reasons. Thanks!

It's a good question. I'm not sure whether we expect the outputs of this workflow to be used in joint calling.
@rickymagner would you be able to comment on whether we expect the outputs of UltimaGenomicsWholeGenomeGermline to be used for joint calling in GVS?

Hm I don't know if GVS has been used on Ultima samples before. Does anyone from the Variants team know if that's an existing/planned application for GVS?

Thanks @rickymagner!
Sounds like this isn't currently a known issue @koncheto-broad, let me know if this becomes an issue in the future and we can change it here too.

Thanks for clarifying, y'all! I think we pretty exclusively use Illumina samples at this point, so the Ultima pipeline is unlikely to affect us. And if we discover that it does, we can always just reach out then!

…e_reblock

github-actions · 2024-12-03T21:52:32Z

Remember to squash merge!

github-actions · 2024-12-03T21:52:43Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2024-12-03T21:52:46Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

…e_reblock

github-actions · 2024-12-05T15:11:50Z

Remember to squash merge!

github-actions · 2024-12-05T15:12:03Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2024-12-05T15:12:04Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

koncheto-broad

LGTM

github-actions · 2024-12-05T17:58:14Z

Remember to squash merge!

github-actions · 2024-12-05T17:58:24Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2024-12-05T17:58:25Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

…e_reblock

github-actions · 2024-12-05T18:14:00Z

Remember to squash merge!

github-actions · 2024-12-05T18:14:09Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2024-12-05T18:14:09Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2024-12-05T18:20:56Z

Remember to squash merge!

github-actions · 2024-12-05T18:21:05Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2024-12-05T18:21:06Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

Update output names for ReblockGVCF

71d8002

Updated pipeline_versions.txt with all pipeline version information

2e62ede

koncheto-broad reviewed Dec 3, 2024

View reviewed changes

jessicaway added 2 commits December 3, 2024 14:51

Update versions and changelogs

a8b7bfe

Merge remote-tracking branch 'origin/jw_update_reblock' into jw_updat…

1abe40b

…e_reblock

Updated pipeline_versions.txt with all pipeline version information

e84d265

jessicaway added 2 commits December 5, 2024 08:10

update changelogs

00955ad

Merge remote-tracking branch 'origin/jw_update_reblock' into jw_updat…

bfb58cf

…e_reblock

Updated pipeline_versions.txt with all pipeline version information

f4e3b62

koncheto-broad approved these changes Dec 5, 2024

View reviewed changes

nikellepetrillo approved these changes Dec 5, 2024

View reviewed changes

Merge branch 'develop' into jw_update_reblock

46168f4

jessicaway added 2 commits December 5, 2024 11:13

the most minor major change

5badc4c

Merge remote-tracking branch 'origin/jw_update_reblock' into jw_updat…

ed5064d

…e_reblock

Updated pipeline_versions.txt with all pipeline version information

b9f8211

update version again

f53ba80

Updated pipeline_versions.txt with all pipeline version information

a8dba53

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Update output names for ReblockGVCF #1443

Update output names for ReblockGVCF #1443

jessicaway commented Dec 3, 2024 •

edited

Loading

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 3, 2024

koncheto-broad Dec 3, 2024

jessicaway Dec 3, 2024

koncheto-broad Dec 3, 2024

jessicaway Dec 3, 2024

rickymagner Dec 3, 2024

jessicaway Dec 4, 2024

koncheto-broad Dec 5, 2024

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

koncheto-broad left a comment

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

Update output names for ReblockGVCF #1443

Are you sure you want to change the base?

Update output names for ReblockGVCF #1443

Conversation

jessicaway commented Dec 3, 2024 • edited Loading

Description

Checklist

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 3, 2024

🔍Changelog Validation Results:

github-actions bot commented Dec 3, 2024

🔍Version Validation Results:

koncheto-broad Dec 3, 2024

Choose a reason for hiding this comment

jessicaway Dec 3, 2024

Choose a reason for hiding this comment

koncheto-broad Dec 3, 2024

Choose a reason for hiding this comment

jessicaway Dec 3, 2024

Choose a reason for hiding this comment

rickymagner Dec 3, 2024

Choose a reason for hiding this comment

jessicaway Dec 4, 2024

Choose a reason for hiding this comment

koncheto-broad Dec 5, 2024

Choose a reason for hiding this comment

github-actions bot commented Dec 3, 2024

github-actions bot commented Dec 3, 2024

🔍Version Validation Results:

github-actions bot commented Dec 3, 2024

🔍Changelog Validation Results:

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

🔍Changelog Validation Results:

github-actions bot commented Dec 5, 2024

🔍Version Validation Results:

koncheto-broad left a comment

Choose a reason for hiding this comment

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

🔍Version Validation Results:

github-actions bot commented Dec 5, 2024

🔍Changelog Validation Results:

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

🔍Version Validation Results:

github-actions bot commented Dec 5, 2024

🔍Changelog Validation Results:

github-actions bot commented Dec 5, 2024

github-actions bot commented Dec 5, 2024

🔍Version Validation Results:

github-actions bot commented Dec 5, 2024

🔍Changelog Validation Results:

jessicaway commented Dec 3, 2024 •

edited

Loading