TSPS-715 Add LowPassImputationQC wdl by mmorgantaylor · Pull Request #1801 · broadinstitute/warp

mmorgantaylor · 2026-03-20T18:55:47Z

Description

Here we add the InputQC wdl for the low pass imputation (Glimpse2) wdl, along with tests. Each failure mode has a test case.

Note: since this is a new wdl and a new set of tests, we expect the tests on this PR to fail, since there is no truth data yet. Once this PR is approved and merged, we will run the tests to generate truth data.

Crams that pass QC:

{ "qc_messages": "", "passes_qc": "true" }

Manifest that passes QC:

{ "qc_messages": "", "passes_qc": "true" }

No data provided:

{ "qc_messages": "No input data provided. Please provide either CRAM files or a CRAM manifest.", "passes_qc": "false" }

Both cram arrays and cram manifest provided:

{ "qc_messages": "Multiple input data types provided. Please provide only CRAM files (with corresponding CRAM index files and sample IDs) or a CRAM manifest.", "passes_qc": "false" }

Cram arrays provided, no crais:

{ "qc_messages": "CRAM indices and sample IDs are required when CRAM files are provided. Please provide both CRAM index files and a corresponding list of sample IDs.", "passes_qc": "false" }

Cram arrays provided, no sample ids:

{ "qc_messages": "CRAM indices and sample IDs are required when CRAM files are provided. Please provide both CRAM index files and a corresponding list of sample IDs.", "passes_qc": "false" }

Cram arrays provided, mismatched lengths:

{ "qc_messages": "Found different numbers of CRAMs (2), CRAIs (2), and sample IDs (1).", "passes_qc": "false" }

Cram arrays provided, duplicate sample_ids and duplicate cram_paths:

{ "qc_messages": "Duplicate sample IDs found: sample0, sample1\nDuplicate CRAM paths found: gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram, gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram", "passes_qc": "false" }

Cram arrays provided, duplicate cram paths:

{ "qc_messages": "Duplicate CRAM paths found: gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram", "passes_qc": "false" }

Cram arrays provided, file size too large:

{ "qc_messages": "The following CRAM files exceed the maximum allowed file size of 10GB: gs://pd-test-storage-public/CramToUnmappedBams/input/scientific/G94982.NA12878.WGS/NA12878.cram (19GB)", "passes_qc": "false" }

Manifest provided, duplicate sample_ids (basically just tests that a manifest gets properly converted to arrays):

{ "qc_messages": "Duplicate sample IDs found: sample0", "passes_qc": "false" }

Give your PR a concise yet descriptive title.
Please explain the changes you made here.
Explain the motivation for making this change. What existing problem does the pull request solve?
Mention any issues fixed, addressed, or otherwise related to this pull request, including issue numbers or hard links for issues in other repos.
You can delete these instructions once you have written your PR description.

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 · 2026-03-20T18:55:55Z

Remember to squash merge!

github-actions · 2026-03-20T18:56:06Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Glimpse2LowPassImputation.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2026-03-20T18:56:07Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
Glimpse2LowPassImputation.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

.github/workflows/test_low_pass_imputation_qc.yml

github-actions · 2026-03-20T19:15:05Z

Remember to squash merge!

github-actions · 2026-03-20T19:15:16Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
Glimpse2LowPassImputation.wdl has not had its version updated
Glimpse2LowPassImputation.wdl and Glimpse2LowPassImputation.changelog.md do not have matching versions
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2026-03-20T19:15:17Z

🔍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 · 2026-03-20T19:16:02Z

Remember to squash merge!

github-actions · 2026-03-20T19:16:14Z

🔍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 · 2026-03-20T19:16:15Z

🔍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 · 2026-03-20T19:26:08Z

Remember to squash merge!

github-actions · 2026-03-20T19:26:21Z

🔍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 · 2026-03-20T19:26:25Z

🔍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 · 2026-03-24T17:26:34Z

Remember to squash merge!

github-actions · 2026-03-24T17:26:45Z

🔍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 · 2026-03-24T17:26:55Z

🔍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 · 2026-04-01T18:22:11Z

Remember to squash merge!

github-actions · 2026-04-01T18:22:22Z

🔍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 · 2026-04-01T18:22:24Z

🔍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 · 2026-04-01T18:24:39Z

Remember to squash merge!

github-actions · 2026-04-01T18:24:51Z

🔍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 · 2026-04-01T18:24:51Z

🔍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 · 2026-04-01T18:37:49Z

Remember to squash merge!

github-actions · 2026-04-01T18:38:02Z

🔍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 · 2026-04-01T18:38:02Z

🔍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 · 2026-04-01T18:51:21Z

Remember to squash merge!

github-actions · 2026-04-01T18:51:32Z

🔍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 · 2026-04-01T18:51:35Z

🔍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 · 2026-04-01T18:55:44Z

Remember to squash merge!

github-actions · 2026-04-01T18:55:57Z

🔍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 · 2026-04-08T16:22:11Z

🔍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 · 2026-04-08T16:51:28Z

Remember to squash merge!

github-actions · 2026-04-08T16:51:39Z

🔍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 · 2026-04-08T16:51:40Z

🔍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 · 2026-04-08T17:09:03Z

Remember to squash merge!

github-actions · 2026-04-08T17:09:12Z

🔍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 · 2026-04-08T17:09:15Z

🔍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 · 2026-04-08T17:47:56Z

Remember to squash merge!

github-actions · 2026-04-08T17:48:06Z

🔍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 · 2026-04-08T17:48:06Z

🔍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 · 2026-04-08T18:23:44Z

Remember to squash merge!

github-actions · 2026-04-08T18:23:48Z

🔍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 · 2026-04-08T18:23:58Z

🔍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 · 2026-04-08T18:57:53Z

Remember to squash merge!

github-actions · 2026-04-08T18:58:05Z

🔍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 · 2026-04-08T18:58:08Z

🔍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 · 2026-04-08T19:50:34Z

Remember to squash merge!

github-actions · 2026-04-08T19:50:44Z

🔍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 · 2026-04-08T19:50:44Z

🔍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 · 2026-04-08T20:03:15Z

Remember to squash merge!

github-actions · 2026-04-08T20:03:24Z

🔍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 · 2026-04-08T20:03:39Z

🔍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-advanced-security bot found potential problems Mar 20, 2026

View reviewed changes

.github/workflows/test_low_pass_imputation_qc.yml Fixed Show fixed Hide fixed

handle no size found

4564468

try to handle billing project

f2fa906

explicitly set user_project on calls

180851f

this should work tm

4e9703a

try bot's suggestion

1384fb3

mmorgantaylor added 2 commits April 8, 2026 15:37

add better file not found errors

e0ac639

update test inputs to real bucket

07bbeec

add back missing ref dict oops

c34e672

Conversation

mmorgantaylor commented Mar 20, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Description

Checklist

Uh oh!

github-actions bot commented Mar 20, 2026

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Version Validation Results:

Uh oh!

Uh oh!

github-actions bot commented Mar 20, 2026

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Mar 20, 2026

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Mar 20, 2026

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Mar 20, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Mar 24, 2026

Uh oh!

github-actions bot commented Mar 24, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Mar 24, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Version Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

🔍Changelog Validation Results:

Uh oh!

github-actions bot commented Apr 1, 2026

mmorgantaylor commented Mar 20, 2026 •

edited

Loading