Staging -> master #1414
Merged
Staging -> master #1414
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* gatk docker update * gatk docker update * revert bqsr to gstk 4.3 * revert genotypeconcordance to gstk 4.3 * revert genotypeconcordance to gstk 4.3 * add megans commit * add megans commit * fix names of inputs for CompareVCFsVerbosely * fix names of inputs for CompareVCFsVerbosely * hook up index files * missed some test inputs * changelogs and versions * Updated pipeline_versions.txt with all pipeline version information * changelogs * Updated pipeline_versions.txt with all pipeline version information * changelogs * Updated pipeline_versions.txt with all pipeline version information --------- Co-authored-by: GitHub Action <[email protected]>
* Fix: Use CSI instead of TBI indexing in tabix command to support chromosomes larger than 512 Mbp. * Updated pipeline_versions.txt with all pipeline version information * Updated pipeline_versions.txt with all pipeline version information * updated changelogs * Updated pipeline_versions.txt with all pipeline version information * updated pairedtag version * Updated pipeline_versions.txt with all pipeline version information * CreateFragmentFile task now uses csi index format * Update pipelines/skylab/multiome/Multiome.changelog.md Co-authored-by: Elizabeth Kiernan <[email protected]> * Update pipelines/skylab/optimus/Optimus.changelog.md Co-authored-by: Elizabeth Kiernan <[email protected]> * Update pipelines/skylab/slideseq/SlideSeq.changelog.md Co-authored-by: Elizabeth Kiernan <[email protected]> * Update pipelines/skylab/smartseq2_single_nucleus_multisample/MultiSampleSmartSeq2SingleNucleus.changelog.md Co-authored-by: Elizabeth Kiernan <[email protected]> * Update pipelines/skylab/paired_tag/PairedTag.changelog.md Co-authored-by: Elizabeth Kiernan <[email protected]> * Updated pipeline_versions.txt with all pipeline version information * updating indexing for pairedtag and changing index file name * Updated outputs to reflect the csi index. Renamed the index from tbi to index * Update Multiome.wdl changed JoinBarcodes task index file name * Update pipelines/skylab/atac/atac.wdl Co-authored-by: Elizabeth Kiernan <[email protected]> --------- Co-authored-by: GitHub Action <[email protected]> Co-authored-by: Elizabeth Kiernan <[email protected]> Co-authored-by: ekiernan <[email protected]>
dev -> staging
|
DO NOT SQUASH MERGE!!! |
🔍Changelog Validation Results: |
🔍Version Validation Results: |
|
Multiome, optimus, and paired tag are failing due to nondetermism affecting the doublet_score metric: Multiome Optimus PairedTag CheckFingerprint failed with a transient error. Rerunning here: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/88299/console UltimaGenomicsJointJenotyping is failing due to some slight wiggles but @meganshand has given us the ok to update the truth for this pipeline https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/88301/ |
ekiernan
approved these changes
Nov 8, 2024
khajoue2
approved these changes
Nov 8, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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 team by tagging @broadinstitute/warp-admins in a comment on this PR.