added nhash_id to multiome, optimus, paired-tag, and atac #1316

ekiernan · 2024-07-01T19:16:52Z

Description

Adding NHash ID as input to BICAN workflows

This PR add optional nhash_id to Optimus, ATAC, Multiome, and Paired-tag workflows. It outputs the nhash_id to the h5ads in the adata.uns section and the gene expression library-level metrics (first line). It also names the library metrics CSV using the nhash_id.

github-actions · 2024-07-01T19:17:03Z

Remember to squash merge!

github-actions · 2024-07-01T19:17:13Z

🔍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 · 2024-07-01T19:17:16Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-01T19:32:33Z

Remember to squash merge!

github-actions · 2024-07-01T19:32:43Z

🔍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 · 2024-07-01T19:32:44Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-03T16:41:41Z

Remember to squash merge!

github-actions · 2024-07-03T16:41:52Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-03T16:41:54Z

🔍Version Validation Results:

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

github-actions · 2024-07-03T16:52:49Z

Remember to squash merge!

github-actions · 2024-07-03T16:52:58Z

🔍Version Validation Results:

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

github-actions · 2024-07-03T16:53:00Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-08T16:15:51Z

Remember to squash merge!

github-actions · 2024-07-08T16:15:51Z

Remember to squash merge!

github-actions · 2024-07-08T16:16:00Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-08T16:16:00Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-08T16:16:02Z

🔍Version Validation Results:

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

github-actions · 2024-07-08T16:16:05Z

🔍Version Validation Results:

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

github-actions · 2024-07-08T16:48:59Z

Remember to squash merge!

github-actions · 2024-07-08T16:49:09Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-08T16:49:14Z

🔍Version Validation Results:

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

…e/warp into lk-PD-2690-NHashID

github-actions · 2024-07-08T17:32:03Z

Remember to squash merge!

github-actions · 2024-07-08T17:32:14Z

🔍Version Validation Results:

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

github-actions · 2024-07-08T17:32:15Z

🔍Changelog Validation Results:

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

github-actions · 2024-07-09T15:17:36Z

Remember to squash merge!

github-actions · 2024-07-09T15:17:46Z

🔍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 · 2024-07-09T15:17:47Z

🔍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 · 2024-07-09T16:03:09Z

Remember to squash merge!

github-actions · 2024-07-09T16:03:20Z

🔍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 · 2024-07-09T16:03:20Z

🔍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 · 2024-07-09T17:32:29Z

Remember to squash merge!

github-actions · 2024-07-09T17:32:40Z

🔍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 · 2024-07-09T17:32:42Z

🔍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.

kevinpalis

LGTM

ekiernan · 2024-07-10T15:29:57Z

retest this please

ekiernan · 2024-07-11T00:45:04Z

retest this please

added nhash_id to multiome, optimus, paired-tag, and atac

5014b44

changed to null input

ce7fb4f

Fix testing wdls for nhash_id

ce88b4e

Merge branch 'develop' into lk-PD-2690-NHashID

e96cfe1

ekiernan closed this Jul 8, 2024

ekiernan added 6 commits July 8, 2024 09:27

fixing nhash id errors

a0e6755

fixed nhash_id examples and verification wdls

3c4626d

made gex_nash_id optional in STARAlign mergestaroutputs task

3a7198e

fixing h5ad utils

8c64fd3

fixing nash id python variable in atac wdl

30e625a

fixed h5ad variable name in atac fragment file creation

7f2dcc0

ekiernan reopened this Jul 8, 2024

ekiernan added 2 commits July 8, 2024 13:31

fixed echo in STARAlign for nhash id

da79070

Merge branch 'lk-PD-2690-NHashID' of https://github.com/broadinstitut…

c171210

…e/warp into lk-PD-2690-NHashID

ekiernan closed this Jul 9, 2024

ekiernan added 2 commits July 9, 2024 09:45

passing nhash id through pipeline

e2f6b1a

updated changelogs

dbb93e5

ekiernan reopened this Jul 9, 2024

Merge branch 'develop' into lk-PD-2690-NHashID

4e12111

updated documentation for nhash_id

ced03c0

Merge branch 'develop' into lk-PD-2690-NHashID

25717aa

kevinpalis approved these changes Jul 9, 2024

View reviewed changes

khajoue2 approved these changes Jul 9, 2024

View reviewed changes

ekiernan merged commit e52f2c1 into develop Jul 11, 2024
12 checks passed

ekiernan deleted the lk-PD-2690-NHashID branch July 11, 2024 13:30

added nhash_id to multiome, optimus, paired-tag, and atac #1316

added nhash_id to multiome, optimus, paired-tag, and atac #1316

Conversation

ekiernan commented Jul 1, 2024 • edited Loading

Description

Adding NHash ID as input to BICAN workflows

github-actions bot commented Jul 1, 2024

github-actions bot commented Jul 1, 2024

🔍Version Validation Results:

github-actions bot commented Jul 1, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 1, 2024

github-actions bot commented Jul 1, 2024

🔍Version Validation Results:

github-actions bot commented Jul 1, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 3, 2024

github-actions bot commented Jul 3, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 3, 2024

🔍Version Validation Results:

github-actions bot commented Jul 3, 2024

github-actions bot commented Jul 3, 2024

🔍Version Validation Results:

github-actions bot commented Jul 3, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 8, 2024

github-actions bot commented Jul 8, 2024

github-actions bot commented Jul 8, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 8, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 8, 2024

🔍Version Validation Results:

github-actions bot commented Jul 8, 2024

🔍Version Validation Results:

github-actions bot commented Jul 8, 2024

github-actions bot commented Jul 8, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 8, 2024

🔍Version Validation Results:

github-actions bot commented Jul 8, 2024

github-actions bot commented Jul 8, 2024

🔍Version Validation Results:

github-actions bot commented Jul 8, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 9, 2024

github-actions bot commented Jul 9, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 9, 2024

🔍Version Validation Results:

github-actions bot commented Jul 9, 2024

github-actions bot commented Jul 9, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 9, 2024

🔍Version Validation Results:

github-actions bot commented Jul 9, 2024

github-actions bot commented Jul 9, 2024

🔍Changelog Validation Results:

github-actions bot commented Jul 9, 2024

🔍Version Validation Results:

kevinpalis left a comment

Choose a reason for hiding this comment

ekiernan commented Jul 10, 2024

ekiernan commented Jul 11, 2024

ekiernan commented Jul 1, 2024 •

edited

Loading