Made changes for SnapATAC2 v2.6.0 #1273

ekiernan · 2024-04-25T17:09:43Z

Description

Updated the SnapATAC2 docker to include SnapATAC v2.6.0
Updated Multiome, ATAC, and PairedTag to be compatible with changes in SnapATAC2 v2.6.0

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 · 2024-04-25T17:09:58Z

Remember to squash merge!

github-actions · 2024-04-25T17:10:11Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-04-25T17:32:49Z

Remember to squash merge!

github-actions · 2024-04-25T17:33:01Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-04-25T19:04:18Z

Remember to squash merge!

github-actions · 2024-04-25T19:04:29Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-04-29T13:58:15Z

Remember to squash merge!

github-actions · 2024-04-29T13:58:26Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-05-03T17:51:56Z

Remember to squash merge!

github-actions · 2024-05-03T17:52:04Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-05-03T18:06:02Z

Remember to squash merge!

github-actions · 2024-05-03T18:06:15Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-05-06T20:52:51Z

Remember to squash merge!

github-actions · 2024-05-06T20:53:01Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-05-09T17:12:05Z

Remember to squash merge!

github-actions · 2024-05-09T17:12:15Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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 · 2024-05-10T17:53:49Z

Remember to squash merge!

github-actions · 2024-05-10T17:53:58Z

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not had its version updated
SlideSeq.wdl has not been changed and needs updating
Optimus.wdl has not been changed and needs updating
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

ekiernan · 2024-05-13T13:23:41Z

retest this please

github-actions · 2024-05-13T13:57:17Z

Remember to squash merge!

github-actions · 2024-05-20T19:34:55Z

🔍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 · 2024-05-20T19:52:07Z

Remember to squash merge!

github-actions · 2024-05-20T19:52:17Z

🔍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
atac.changelog.md has not been changed and needs to be updated
SlideSeq.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 · 2024-05-20T19:52:22Z

🔍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 · 2024-05-21T00:41:11Z

Remember to squash merge!

github-actions · 2024-05-21T00:41:19Z

🔍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 · 2024-05-21T00:41:20Z

🔍Version Validation Results:

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

github-actions · 2024-05-21T00:43:46Z

Remember to squash merge!

github-actions · 2024-05-21T00:43:58Z

🔍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 · 2024-05-21T00:44:00Z

🔍Changelog Validation Results:

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

ekiernan · 2024-05-21T13:09:24Z

Fragment file differences in paired-tag data are the result of sorting - when we sort the files, the md5sums match. For example, the BI015 sample: 54b66cf8c81392595a15c9480612a33d sorted.test.tsv
54b66cf8c81392595a15c9480612a33d sorted.truth.tsv

pipelines/skylab/paired_tag/PairedTag.changelog.md

Co-authored-by: Nikelle Petrillo <[email protected]>

github-actions · 2024-05-21T15:44:34Z

Remember to squash merge!

github-actions · 2024-05-21T15:44:43Z

🔍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 · 2024-05-21T15:44:44Z

🔍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.

…ute/warp into lk-PD-2608-snapatac2

github-actions · 2024-05-22T13:44:35Z

Remember to squash merge!

github-actions · 2024-05-22T13:44:51Z

🔍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 · 2024-05-22T13:44:55Z

🔍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.

ekiernan · 2024-05-23T12:18:35Z

retest this please

Made changes for SnapATAC2 v2.6.0

801c59f

updated min tsse parameter

b69f57b

updated docker to include one with bgzip

7f31bf6

calculate snap metrics earlier

2416c9a

adding tsse metrics back into ATAC workflow

ff85447

took out annotations gtf from parsebarcodes call

259784c

added anndata to atac

d50aebc

update snapatac2 dockers to v2.6.2

df1729a

Merge branch 'develop' into lk-PD-2608-snapatac2

64a59f5

added more threads

f48ef54

added annotations gtf back into atac preindex

7a84034

updated changelogs for snapatac2

e9c8e00

updated slideseq version

b55654d

nikellepetrillo reviewed May 21, 2024

View reviewed changes

pipelines/skylab/paired_tag/PairedTag.changelog.md Outdated Show resolved Hide resolved

nikellepetrillo approved these changes May 21, 2024

View reviewed changes

Update pipelines/skylab/paired_tag/PairedTag.changelog.md

088f95f

Co-authored-by: Nikelle Petrillo <[email protected]>

ekiernan added 2 commits May 22, 2024 09:44

fixing multiome and optimus versions and changelogs

08af91f

Merge branch 'lk-PD-2608-snapatac2' of https://github.com/broadinstit…

09b681f

…ute/warp into lk-PD-2608-snapatac2

khajoue2 approved these changes May 22, 2024

View reviewed changes

kevinpalis approved these changes May 22, 2024

View reviewed changes

ekiernan merged commit a22865d into develop May 23, 2024
11 checks passed

ekiernan deleted the lk-PD-2608-snapatac2 branch May 23, 2024 13:08

Made changes for SnapATAC2 v2.6.0 #1273

Made changes for SnapATAC2 v2.6.0 #1273

Conversation

ekiernan commented Apr 25, 2024

Description

Checklist

github-actions bot commented Apr 25, 2024

github-actions bot commented Apr 25, 2024

Validation Results:

github-actions bot commented Apr 25, 2024

github-actions bot commented Apr 25, 2024

Validation Results:

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Validation Results:

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Validation Results:

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Validation Results:

ekiernan commented May 13, 2024

github-actions bot commented May 13, 2024

github-actions bot commented May 20, 2024

🔍Version Validation Results:

github-actions bot commented May 20, 2024

github-actions bot commented May 20, 2024

🔍Changelog Validation Results:

github-actions bot commented May 20, 2024

🔍Version Validation Results:

github-actions bot commented May 21, 2024

github-actions bot commented May 21, 2024

🔍Changelog Validation Results:

github-actions bot commented May 21, 2024

🔍Version Validation Results:

github-actions bot commented May 21, 2024

github-actions bot commented May 21, 2024

🔍Version Validation Results:

github-actions bot commented May 21, 2024

🔍Changelog Validation Results:

ekiernan commented May 21, 2024

github-actions bot commented May 21, 2024

github-actions bot commented May 21, 2024

🔍Changelog Validation Results:

github-actions bot commented May 21, 2024

🔍Version Validation Results:

github-actions bot commented May 22, 2024

github-actions bot commented May 22, 2024

🔍Changelog Validation Results:

github-actions bot commented May 22, 2024

🔍Version Validation Results:

ekiernan commented May 23, 2024