Mody-CF update

[Jakob37]

Description and reviewer info

WIP. Will be a PR towards the mody-cf-update PR. I am unsure about the intended logical flow in parts of the code, will need to double check that.

Type of change

• [ ] Documentation
• [ ] Patch
• [ ] Minor change
• [ ] Major change

Checklist

• [ ] Self-review of my code
• [ ] Update the CHANGELOG
• [ ] Tag the latest commit (vX.Y.Z format)
• [ ] Log samples used for testing in the Verification_samples_log Excel sheet

Documentation

• [ ] At least one other person has reviewed my changes (not required for trivial changes)

Patch

• [ ] Stub run completes without errors or new warnings
• [ ] At least one other person has reviewed and approved my code (not required for trivial changes)

Major / Minor change

• [ ] Stub run completes without errors or new warnings
• [ ] onco run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] wgs single run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] wgs trio run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] At least one other person has reviewed and approved my code
• [ ] I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

• [ ] Alexander
• [ ] Jakob
• [ ] Paul
• [ ] Ryan
• [ ] Viktor

(Add if missing)

Testing performed by

• [ ] Alexander
• [ ] Jakob
• [ ] Paul
• [ ] Ryan
• [ ] Viktor