Iterating on mody cf

[Jakob37]

Description and reviewer info

Changes made attempting to clarify the mody CF PR. This will be merged into the existing mody cf PR.

Will need to clarify the intended logical flow in some places prior to merge.

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

[Jakob37]

OK this ended up being a very tiny PR after looking at this for a while. Seems the current one is doing what it should. I just added two params to avoid the most convoluted where checks.

I think this one is uncontroversial, so I'll merge it into the other PR. Then we can finalize the discussion over there.