Non-functional refactoring of VEP

[vladsavelyev]

Proposed Changes

• [x] Use new cpg_utils.workflows module for batch resources and other utilities
• [x] Use cpg_utils.Path instead of CloudPath (it would make it work for local paths)
• [x] Update split_intervals, use the source intervals lists from config
• [ ] Move split_intervals and gather_vcfs into cpg_utils?
• [x] Sync with Seqr Loader to potentially make the former import AIP
• [ ] One issue in Seqr Loader importing AIP is that AIP strictly pins packages, which means that packages would conflict. @MattWellie, what do you think of dropping pins and releasing AIP as a pypi package?

Checklist

• [ ] Related Issue created
• [ ] Tests covering new change
• [ ] Linting checks pass

[MattWellie]

@vladsavelyev following last week's discussion, is this still a live PR, or are we going to move to a dependency directly on production-pipelines?

[MattWellie]

@vladsavelyev I'm going to merge this, but eventually I think this code will be imported from production-pipelines

[vladsavelyev]

Oh sorry @MattWellie, I missed your question question 6 days ago... I'm going to look into importing this from prod-pipes!