update to R 4.4.0

[alexvpickering]

Description

• updates R to 4.4.0 and all packages
• updates code for Seurat V5 (current)

Things tested:

• Default pipeline with 10x dataset
• "within" and "between" DE with 10x and Seurat datasets
• All integration methods with 10x dataset
• ScType automated clustering with new 10x dataset
• leiden clustering with new 10x dataset
• Upload of Seurat object with Assay5 RNA
• trajectory analysis with new 10x dataset

staging:

https://ui-alex-worker357-pipeline363.staging.single-cell-platform.net

Details

URL to issue

N/A

Link to staging deployment URL (or set N/A)

N/A

Links to any PRs or resources related to this PR

hms-dbmi-cellenics/worker#357

Integration test branch

master

Merge checklist

Your changes will be ready for merging after all of the steps below have been completed.

Code updates

Have best practices and ongoing refactors being observed in this PR

• Migrated any selector / reducer used to the new format.

Manual/unit testing

• Tested changes using InfraMock locally or no tests required for change, e.g. Kubernetes chart updates.
• Validated that current unit tests for code work as expected and are sufficient for code coverage or no unit tests required for change, e.g. documentation update.
• Unit tests written or no unit tests required for change, e.g. documentation update.

Integration testing

You must check the box below to run integration tests on the latest commit on your PR branch.
Integration tests have to pass before the PR can be merged. Without checking the box, your PR
will not pass the required status checks for merging.

• Started end-to-end tests on the latest commit.

Documentation updates

• Relevant Github READMEs updated or no GitHub README updates required.
• Relevant Wiki pages created/updated or no Wiki updates required.

Optional

• Staging environment is unstaged before merging.
• Photo of a cute animal attached to this PR.

[gerbeldo]

looks good to me, left some comments and questions.

[gerbeldo]

looks good to me, left some comments and questions.