Mody CF (clean)

[Jakob37]

Description and reviewer info

What is changed? How does this update improve the pipeline? (For reviewers) How to test it?

Close #162

Clean copy of the PR #82

Type of change

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

Checklist

• [x] Self-review of my code
• [x] Update the CHANGELOG
• [x] Tag the latest commit (vX.Y.Z format)
• [x] 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

• [x] Stub run completes without errors or new warnings
• [x] onco run finishes without any new warnings/errors and the results can be loaded into scout
• [x] wgs single run finishes without any new warnings/errors and the results can be loaded into scout
• [x] wgs trio run finishes without any new warnings/errors and the results can be loaded into scout
• [x] 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
• [x] Viktor

(Add if missing)

Testing performed by

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

[Jakob37]

I'll copy this from the old PR

Ready for review @ViktorHy

I have stub-run it in the master branch and here for all profiles, and checked that the executed processes are exactly the same.

Would like to discuss the part of the code around freebayes and the subsequent split_normalize at some point. But that is more for my understanding.

Removing the sensitive data is a different story. That will require some thought prior to merge.

[Jakob37]

Thanks for the review! The tests went through fine. Let's discuss the institute details when we get the chance and wrap things up.