Np loom to h5ad snss2 #1363

nikellepetrillo · 2024-08-26T19:43:47Z

Description

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 documentation team by tagging either @ekiernan or @kayleemathews 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 · 2024-08-26T19:44:01Z

Remember to squash merge!

github-actions · 2024-08-26T19:44:09Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
SmartSeq2SingleSample.wdl has not been changed and needs updating
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-26T19:44:12Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-27T16:33:13Z

Remember to squash merge!

github-actions · 2024-08-27T16:33:23Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-27T16:33:24Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
SmartSeq2SingleSample.wdl has not been changed and needs updating
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-27T17:17:15Z

Remember to squash merge!

github-actions · 2024-08-27T17:17:24Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-27T17:17:24Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
SmartSeq2SingleSample.wdl has not been changed and needs updating
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-27T18:29:41Z

Remember to squash merge!

github-actions · 2024-08-27T18:29:50Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-27T18:29:52Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
SmartSeq2SingleSample.wdl has not been changed and needs updating
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-30T15:23:56Z

Remember to squash merge!

github-actions · 2024-08-30T15:24:09Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-30T15:24:10Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
SmartSeq2SingleSample.wdl has not been changed and needs updating
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-08-30T15:33:25Z

Remember to squash merge!

github-actions · 2024-08-30T15:33:37Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
SmartSeq2SingleSample.wdl has not been changed and needs updating
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-09-06T15:24:34Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.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
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
Multiome.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 · 2024-09-06T15:26:12Z

Remember to squash merge!

github-actions · 2024-09-06T15:26:20Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
MultiSampleSmartSeq2.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
Optimus.wdl has not had its version updated
atac.wdl has not been changed and needs updating
SmartSeq2SingleSample.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2024-09-06T15:26:21Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.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
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
Multiome.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 · 2024-09-06T15:27:19Z

Remember to squash merge!

github-actions · 2024-09-06T15:27:30Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.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
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
Multiome.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 · 2024-09-06T15:27:33Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
MultiSampleSmartSeq2.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
Optimus.wdl has not had its version updated
atac.wdl has not been changed and needs updating
SmartSeq2SingleSample.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

ekiernan · 2024-09-10T13:45:29Z

tasks/skylab/LoomUtils.wdl

@@ -297,98 +298,7 @@ task SingleNucleusOptimusLoomOutput {
 }


-task SingleNucleusSmartSeq2LoomOutput {


@nikellepetrillo Should we leave the original task in place? We left the other Loom tasks in.

@ekiernan I think we can leave it so it is consistent with other pipelines. Maybe one day we can clean up all unused tasks.

ekiernan

Looks good! But I had a comment about whether we wanted to delete the old task. Thank you for all the work you did on this!

github-actions · 2024-09-11T15:32:12Z

Remember to squash merge!

github-actions · 2024-09-11T15:32:24Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
MultiSampleSmartSeq2.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
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
Multiome.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 · 2024-09-11T15:32:25Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not had its version updated
MultiSampleSmartSeq2.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
Optimus.wdl has not had its version updated
atac.wdl has not been changed and needs updating
SmartSeq2SingleSample.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

…oom-to-h5ad-snss2

github-actions · 2024-09-11T15:38:44Z

Remember to squash merge!

github-actions · 2024-09-11T15:38:55Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2.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
SmartSeq2SingleSample.changelog.md has not been changed and needs to be updated
Multiome.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 · 2024-09-11T15:39:00Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
Optimus.wdl has not had its version updated
atac.wdl has not been changed and needs updating
SmartSeq2SingleSample.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
SlideSeq.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

…oom-to-h5ad-snss2

github-actions · 2024-09-11T17:37:25Z

Remember to squash merge!

github-actions · 2024-09-11T17:37:37Z

🔍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 · 2024-09-11T17:37:39Z

🔍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.

nikellepetrillo added 8 commits August 1, 2024 13:14

pin all latest docker version

2510aae

Merge remote-tracking branch 'origin/develop' into develop

87b4b46

Merge remote-tracking branch 'origin/develop' into develop

52b66aa

run with h5ad isntead o floom

8590e2e

run with h5ad isntead o floom

da11f5b

run with h5ad isntead o floom

53e914d

run with h5ad isntead o floom

8bc0bb2

new docker

852fa7e

merge h5ad files

8dcd844

new path

27d938e

redo h5ad merge

56fcdf5

add verify task

21b5840

add verify task

5ae5eb5

formatting again

065a534

formatting again

8848522

kevinpalis approved these changes Sep 10, 2024

View reviewed changes

ekiernan reviewed Sep 10, 2024

View reviewed changes

ekiernan approved these changes Sep 10, 2024

View reviewed changes

Merge branch 'develop' into np-loom-to-h5ad-snss2

19cddd6

nikellepetrillo added 2 commits September 11, 2024 11:38

changelogs and add SingleNucleusSmartSeq2LoomOutput back in

11364d9

Merge remote-tracking branch 'origin/np-loom-to-h5ad-snss2' into np-l…

26f0d9b

…oom-to-h5ad-snss2

Updated pipeline_versions.txt with all pipeline version information

f30f2c5

nikellepetrillo added 2 commits September 11, 2024 13:36

changelogs

e2a7217

Merge remote-tracking branch 'origin/np-loom-to-h5ad-snss2' into np-l…

dbcb249

…oom-to-h5ad-snss2

Updated pipeline_versions.txt with all pipeline version information

e122010

nikellepetrillo merged commit 07f8b2f into develop Sep 12, 2024
5 of 6 checks passed

nikellepetrillo deleted the np-loom-to-h5ad-snss2 branch September 12, 2024 12:09

		@@ -297,98 +298,7 @@ task SingleNucleusOptimusLoomOutput {
		}


		task SingleNucleusSmartSeq2LoomOutput {

Np loom to h5ad snss2 #1363

Np loom to h5ad snss2 #1363

Conversation

nikellepetrillo commented Aug 26, 2024

Description

Checklist

github-actions bot commented Aug 26, 2024

github-actions bot commented Aug 26, 2024

🔍Version Validation Results:

github-actions bot commented Aug 26, 2024

🔍Changelog Validation Results:

github-actions bot commented Aug 27, 2024

github-actions bot commented Aug 27, 2024

🔍Changelog Validation Results:

github-actions bot commented Aug 27, 2024

🔍Version Validation Results:

github-actions bot commented Aug 27, 2024

github-actions bot commented Aug 27, 2024

🔍Changelog Validation Results:

github-actions bot commented Aug 27, 2024

🔍Version Validation Results:

github-actions bot commented Aug 27, 2024

github-actions bot commented Aug 27, 2024

🔍Changelog Validation Results:

github-actions bot commented Aug 27, 2024

🔍Version Validation Results:

github-actions bot commented Aug 30, 2024

github-actions bot commented Aug 30, 2024

🔍Changelog Validation Results:

github-actions bot commented Aug 30, 2024

🔍Version Validation Results:

github-actions bot commented Aug 30, 2024

github-actions bot commented Aug 30, 2024

🔍Version Validation Results:

github-actions bot commented Sep 6, 2024

🔍Changelog Validation Results:

github-actions bot commented Sep 6, 2024

github-actions bot commented Sep 6, 2024

🔍Version Validation Results:

github-actions bot commented Sep 6, 2024

🔍Changelog Validation Results:

github-actions bot commented Sep 6, 2024

github-actions bot commented Sep 6, 2024

🔍Changelog Validation Results:

github-actions bot commented Sep 6, 2024

🔍Version Validation Results:

ekiernan Sep 10, 2024

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github-actions bot commented Sep 11, 2024

github-actions bot commented Sep 11, 2024

🔍Changelog Validation Results:

github-actions bot commented Sep 11, 2024

🔍Version Validation Results:

github-actions bot commented Sep 11, 2024

github-actions bot commented Sep 11, 2024

🔍Changelog Validation Results:

github-actions bot commented Sep 11, 2024

🔍Version Validation Results:

github-actions bot commented Sep 11, 2024

github-actions bot commented Sep 11, 2024

🔍Changelog Validation Results:

github-actions bot commented Sep 11, 2024

🔍Version Validation Results: