adding 10x wrapper function #1364

ekiernan · 2024-08-28T19:30:47Z

This PR adds a new docker to the ATAC workflow with SnapATAC2 v2.7.0. It modifies the existing CreateFragmentFile script to use the new SnapATAC2 10 wrapper function that produces library-level metrics, a fragment file, and an h5ad metric file in one function. We added the new library level metrics as a CSV output of the workflow, as well as an out of the Multiome and Paired-tag workflows.

github-actions · 2024-08-28T19:47:45Z

Remember to squash merge!

github-actions · 2024-08-28T19:47:54Z

🔍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
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 · 2024-08-28T21:47:54Z

🔍Version Validation Results:

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

github-actions · 2024-08-28T21:48:27Z

Remember to squash merge!

github-actions · 2024-08-28T21:48:42Z

🔍Version Validation Results:

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

github-actions · 2024-08-28T21:48:50Z

🔍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
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 · 2024-08-29T12:27:55Z

Remember to squash merge!

github-actions · 2024-08-29T12:28:06Z

🔍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
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 · 2024-08-29T12:28:07Z

🔍Version Validation Results:

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

github-actions · 2024-08-29T13:24:36Z

Remember to squash merge!

github-actions · 2024-08-29T13:24:46Z

🔍Version Validation Results:

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

github-actions · 2024-08-29T13:24:47Z

🔍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
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 · 2024-08-29T13:25:07Z

Remember to squash merge!

github-actions · 2024-08-29T13:25:20Z

🔍Version Validation Results:

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

github-actions · 2024-08-29T13:25:23Z

🔍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
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 · 2024-08-29T13:49:05Z

Remember to squash merge!

github-actions · 2024-08-29T13:49:15Z

🔍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
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 · 2024-08-29T13:49:17Z

🔍Version Validation Results:

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

github-actions · 2024-08-29T13:53:53Z

Remember to squash merge!

github-actions · 2024-08-29T13:54:03Z

🔍Version Validation Results:

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

github-actions · 2024-08-29T13:54:05Z

🔍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
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 · 2024-08-29T16:47:22Z

🔍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 · 2024-08-29T16:55:51Z

🔍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 · 2024-08-29T16:57:07Z

🔍Version Validation Results:

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

…dinstitute/warp into lk-PD-2738-Snapatac2metrics

github-actions · 2024-08-29T16:58:40Z

Remember to squash merge!

github-actions · 2024-08-29T16:58:49Z

🔍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 · 2024-08-29T16:58:50Z

🔍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.

pipelines/skylab/atac/atac.wdl

github-actions · 2024-08-29T18:07:11Z

Remember to squash merge!

github-actions · 2024-08-29T18:07:21Z

🔍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 · 2024-08-29T18:07:23Z

🔍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

looks good to me!

ekiernan · 2024-09-03T12:11:37Z

Multiome Scientific: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/83618/

Paired-tag scientific: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/83619/

aawdeh

LGTM

github-actions · 2024-09-06T12:37:26Z

Remember to squash merge!

github-actions · 2024-09-06T12:37:38Z

🔍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 · 2024-09-06T12:37:40Z

🔍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 · 2024-09-06T12:59:15Z

🔍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.

…dinstitute/warp into lk-PD-2738-Snapatac2metrics

github-actions · 2024-09-06T13:01:13Z

Remember to squash merge!

github-actions · 2024-09-06T13:01:23Z

🔍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 · 2024-09-06T13:01:23Z

🔍Changelog Validation Results:

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

ekiernan added 2 commits August 28, 2024 15:30

adding 10x wrapper function

bb5d9c2

fixing nhash_id variable

6340aca

added h5ad output

ae011cc

adding h5ad argument to second command

9e91e40

removing temp metrics

f553620

ekiernan added 2 commits August 29, 2024 09:41

Update atac.wdl

9f62353

removing header in ATAC and starting documentation for metrics

2e597da

added metric definitions to the library overview

1941d99

updating Multiome documentation and outputs with new ATAC metrics

0523b89

Updated pipeline_versions.txt with all pipeline version information

45bf059

ekiernan added 2 commits August 29, 2024 12:58

Update README.md

63f5b19

Merge branch 'lk-PD-2738-Snapatac2metrics' of https://github.com/broa…

8364196

…dinstitute/warp into lk-PD-2738-Snapatac2metrics

aawdeh reviewed Aug 29, 2024

View reviewed changes

pipelines/skylab/atac/atac.wdl Outdated Show resolved Hide resolved

fixed docker version

0eb8920

nikellepetrillo approved these changes Aug 30, 2024

View reviewed changes

aawdeh approved these changes Sep 3, 2024

View reviewed changes

updating memory on CreateFragment to 64 GB

aad3ddc

Updated pipeline_versions.txt with all pipeline version information

d8aa1b2

ekiernan added 2 commits September 6, 2024 09:00

Update atac.changelog.md

1d67da7

Merge branch 'lk-PD-2738-Snapatac2metrics' of https://github.com/broa…

2551d39

…dinstitute/warp into lk-PD-2738-Snapatac2metrics

ekiernan merged commit 7a03227 into develop Sep 6, 2024
12 checks passed

ekiernan deleted the lk-PD-2738-Snapatac2metrics branch September 6, 2024 17:30

adding 10x wrapper function #1364

adding 10x wrapper function #1364

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ekiernan commented Aug 28, 2024 •

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