Lk pd 2814 adding gtf h5ad #1470

ekiernan · 2025-01-08T20:25:28Z

This PR updates the warp-tools docker to 2.6.0, which includes updates to all h5ad generations scripts. The h5ad files now have a the path to the annotation gtf file in the unstructured metadata, enabling users to know exactly which GTF file (and therefore genomic features) is used for analysis.

github-actions · 2025-01-08T20:25:39Z

Remember to squash merge!

github-actions · 2025-01-08T20:25:49Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-08T20:25:50Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
atac.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-08T20:31:09Z

Remember to squash merge!

github-actions · 2025-01-08T20:31:21Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
atac.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-08T20:31:24Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-08T23:31:10Z

Remember to squash merge!

github-actions · 2025-01-08T23:31:19Z

🔍Changelog Validation Results:

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

github-actions · 2025-01-08T23:31:21Z

🔍Version Validation Results:

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

github-actions · 2025-01-09T19:19:12Z

Remember to squash merge!

github-actions · 2025-01-09T19:19:23Z

🔍Changelog Validation Results:

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

github-actions · 2025-01-09T19:19:32Z

🔍Version Validation Results:

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

github-actions · 2025-01-10T17:45:49Z

Remember to squash merge!

github-actions · 2025-01-10T17:45:57Z

🔍Version Validation Results:

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

github-actions · 2025-01-10T17:46:00Z

🔍Changelog Validation Results:

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

github-actions · 2025-01-10T20:23:52Z

Remember to squash merge!

github-actions · 2025-01-10T20:24:01Z

🔍Version Validation Results:

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

github-actions · 2025-01-10T20:24:03Z

🔍Changelog Validation Results:

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

github-actions · 2025-01-10T20:41:16Z

Remember to squash merge!

github-actions · 2025-01-10T20:41:27Z

🔍Version Validation Results:

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

github-actions · 2025-01-10T20:41:31Z

🔍Changelog Validation Results:

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

github-actions · 2025-01-10T21:01:03Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-11T01:02:10Z

Remember to squash merge!

github-actions · 2025-01-11T01:02:18Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
atac.wdl has not had its version updated
SlideSeq.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-11T01:02:18Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-13T14:54:19Z

Remember to squash merge!

github-actions · 2025-01-13T14:54:30Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-13T14:54:31Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
SlideSeq.wdl has not had its version updated
atac.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-13T15:33:08Z

Remember to squash merge!

github-actions · 2025-01-13T15:33:18Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
SlideSeq.wdl has not had its version updated
atac.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-13T15:33:22Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-13T20:04:10Z

Remember to squash merge!

github-actions · 2025-01-13T20:04:18Z

🔍Version Validation Results:

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

github-actions · 2025-01-13T20:04:24Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

…institute/warp into lk-PD-2814-adding-gtf-h5ad

github-actions · 2025-01-13T20:04:52Z

Remember to squash merge!

github-actions · 2025-01-13T20:05:01Z

🔍Version Validation Results:

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

github-actions · 2025-01-13T20:05:03Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
Multiome.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SlideSeq.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
atac.changelog.md has not been changed and needs to be updated
Optimus.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-01-13T20:11:15Z

Remember to squash merge!

github-actions · 2025-01-13T20:11:28Z

🔍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 · 2025-01-13T20:11:28Z

🔍Changelog Validation Results:

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

nikellepetrillo · 2025-01-14T14:25:19Z

pipelines/skylab/atac/atac.wdl

+    # Original path from args.annotation_file
+    gtf_path = "~{gtf_path}"  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+
+    # # Transform the path


should we delete this commented code?

nikellepetrillo

one small comment, otherwise looks good!!

ekiernan added 3 commits January 8, 2025 13:06

testing h5adutils with new docker

e2fef9f

added GTF file to adata_uns

12b99ac

changing name of warp_tools_docker variable so be version agnostic

87b73d5

Merge branch 'develop' into lk-PD-2814-adding-gtf-h5ad

8458661

removed quotes

2fec7b8

testing all wdls with new warp-tools docker

38d731c

Merge branch 'develop' into lk-PD-2814-adding-gtf-h5ad

ab17c78

updated h5ad with gs:// path for reference_gtf_file

13fbf2a

testing gtf path

7b5cae5

testing fix for wdl gtf_path syntax

422ad3b

added annotation file as string to h5ad utils task

29a37fc

Updated pipeline_versions.txt with all pipeline version information

ee6c5b7

updating gtf_path for remaining scripts

4e74a75

ekiernan and others added 2 commits January 13, 2025 15:01

updated warp-tools docker to versioned docker 2.6.0

e1ee332

Merge branch 'develop' into lk-PD-2814-adding-gtf-h5ad

f30b7cc

Merge branch 'lk-PD-2814-adding-gtf-h5ad' of https://github.com/broad…

f7cf151

…institute/warp into lk-PD-2814-adding-gtf-h5ad

changelog updates

9b6b190

Updated pipeline_versions.txt with all pipeline version information

343595e

nikellepetrillo reviewed Jan 14, 2025

View reviewed changes

nikellepetrillo approved these changes Jan 14, 2025

View reviewed changes

Lk pd 2814 adding gtf h5ad #1470

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Lk pd 2814 adding gtf h5ad #1470

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ekiernan commented Jan 8, 2025 • edited Loading

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🔍Changelog Validation Results:

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nikellepetrillo Jan 14, 2025

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ekiernan commented Jan 8, 2025 •

edited

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