Create README.md for QTL analysis by ekiernan · Pull Request #1729 · broadinstitute/warp

ekiernan · 2025-11-20T20:36:07Z

Adding a first draft readme for RNA qtl analysis for AoU v9

github-actions · 2025-11-20T20:36:17Z

Remember to squash merge!

github-actions · 2025-11-20T20:36:29Z

🔍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 · 2025-11-20T20:37:19Z

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

nikellepetrillo

looks good!

khajoue2

lgtm

github-actions · 2026-01-09T20:30:05Z

Remember to squash merge!

github-actions · 2026-01-09T20:30:16Z

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2026-01-09T20:30:17Z

🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
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 · 2026-01-09T20:35:37Z

Remember to squash merge!

github-actions · 2026-01-09T20:35:47Z

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2026-01-09T20:35:47Z

🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
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 · 2026-01-13T20:20:34Z

Remember to squash merge!

github-actions · 2026-01-13T20:20:48Z

🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
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All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-01-13T20:20:49Z

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2026-01-13T20:22:01Z

Remember to squash merge!

github-actions · 2026-01-13T20:22:11Z

🔍Changelog Validation Results:

basename: missing operand
Try 'basename --help' for more information.
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2026-01-13T20:22:12Z

🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
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All WDLs and changelog files appear to be valid for this release.

github-actions · 2026-01-29T19:20:55Z

Remember to squash merge!

github-actions · 2026-01-29T19:21:07Z

🔍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 · 2026-01-29T19:21:09Z

🔍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 · 2026-01-29T19:22:00Z

Remember to squash merge!

github-actions · 2026-01-29T19:22:10Z

🔍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 · 2026-01-29T19:22:25Z

🔍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.

Copilot

Pull request overview

This PR adds comprehensive documentation for the All of Us RNA-seq QTL analysis pipeline and enhances error handling across multiple WDL workflows by adding bash strict mode (set -euo pipefail).

Changes:

Created a detailed README documenting the end-to-end eQTL and sQTL analysis workflow
Added set -euo pipefail to command blocks in multiple WDL tasks for improved error handling
Incremented pipeline versions and updated changelogs to reflect these improvements

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
all_of_us/rna_seq/README.md	New comprehensive documentation covering the complete QTL analysis pipeline workflow
all_of_us/rna_seq/susieR_workflow.wdl	Added bash strict mode to susieR task
all_of_us/rna_seq/susieR_workflow.changelog.md	Version bump to aou_9.0.1 with changelog entry
all_of_us/rna_seq/aggregate_rsem_results.wdl	Added bash strict mode and version bump to aou_9.0.1
all_of_us/rna_seq/aggregate_rsem_results.changelog.md	Added changelog entry for version aou_9.0.1
all_of_us/rna_seq/CalculatePhenotypeGroups.wdl	Added bash strict mode to PrepareSpliceData task
all_of_us/rna_seq/CalculatePhenotypeGroups.changelog.md	Added changelog entry for version aou_9.0.1
all_of_us/rna_seq/AggregateSusieWorkflow.wdl	Added bash strict mode to two tasks and version bump to aou_9.0.2
all_of_us/rna_seq/AggregateSusieWorkflow.changelog.md	Added changelog entry for version aou_9.0.2

Copilot · 2026-01-29T19:23:04Z

+# aou_9.0.1
+2026-01-29 (Date of Last Commit)
+
+* Added set euo pipefail to tasks


Missing hyphen in bash option. Should be 'set -euo pipefail' to correctly describe the bash command.

Suggested change

* Added set euo pipefail to tasks

* Added `set -euo pipefail` to tasks

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

github-actions · 2026-01-29T19:29:36Z

Remember to squash merge!

github-actions · 2026-01-29T19:29:48Z

🔍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 · 2026-01-29T19:29:49Z

🔍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 · 2026-01-30T00:22:35Z

Remember to squash merge!

github-actions · 2026-01-30T00:22:46Z

🔍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 · 2026-01-30T00:22:51Z

🔍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 · 2026-01-30T16:53:37Z

Remember to squash merge!

github-actions · 2026-01-30T16:53:48Z

🔍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 · 2026-01-30T16:53:50Z

🔍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.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

github-actions · 2026-01-30T16:55:05Z

Remember to squash merge!

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

github-actions · 2026-01-30T16:55:15Z

Remember to squash merge!

github-actions · 2026-01-30T16:55:16Z

🔍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 · 2026-01-30T16:55:16Z

🔍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 · 2026-01-30T16:55:26Z

🔍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 · 2026-01-30T16:55:26Z

🔍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.

Create README.md

b6f5e31

nikellepetrillo approved these changes Nov 21, 2025

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khajoue2 approved these changes Nov 21, 2025

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Merge branch 'develop' into lk_aou_add_rna_documentation

6ad5cda

adding link to prepareVCF

4e55654

updates with links

638f739

fix toc

82838c8

added pipefails to rna pipelines

9051667

Merge branch 'develop' into lk_aou_add_rna_documentation

63a9c15

ekiernan requested a review from Copilot January 29, 2026 19:22

Copilot AI reviewed Jan 29, 2026

View reviewed changes

Update all_of_us/rna_seq/README.md

cc0eedd

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update CalculatePhenotypeGroups.changelog.md

bb6a49c

Merge branch 'develop' into lk_aou_add_rna_documentation

5d874d1

Update all_of_us/rna_seq/README.md

8ebda2b

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update all_of_us/rna_seq/README.md

6430a7b

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

ekiernan merged commit 59e915a into develop Jan 30, 2026
10 checks passed

ekiernan deleted the lk_aou_add_rna_documentation branch January 30, 2026 17:03

	* Added set euo pipefail to tasks
	* Added `set -euo pipefail` to tasks

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Pull request overview

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