Verification

[Jakob37]

Not sure how to document this

This branch contains:

• Intersect bed file updates
• Sentieon version update

It will also contain:

• VEP update

Description

What is changed? What is the result of the changes?

fixes # (issue)

Type of change

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

Checklist:

• [x] My code follows the style guidelines for NF pipelines at CMD
• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] My changes generate no new warnings (Keep an eye on .nextflow.log !)
• [x] I have updated the CHANGELOG
• [ ] The latest commit in the master branch is tagged with the correct version number

Points from startup discussion

• [x] Remove Gnomad from PR (@Jakob37 )
• [x] Merge updated rank model (@alkc )
• [x] First sanity testing (@alkc )
• [x] Update checklist templates for verification (@alkc )
• [x] Update verification document (@Jakob37 )
• [x] Document groups of causative variants linked to each risk profile (find a good CMD-only spot and put document there)
• [x] Carry out risk analysis (and include in checklist template) (@alkc )
• [ ] Gather test scripts in a separate repo
• [x] GIAB single test
• [x] GIAB trio test
• [x] Dry run - Blueprint variants
• [x] Known causative variants (@Jakob37 )

Major 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
• [x] I have made corresponding changes to the documentation

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

Patch

• [ ] Stub run completes without errors or new warnings

  [Optional] Are there any post-deployment tasks we need to perform?

  • [x] Deploy new rank models

  Instructions for the reviewers

  How to test the changes

  1. Step 1
  2. Step 2

  Expected outcome

  [Optional] Additional information

  Review

  Review performed by:

  • Reviewer 1: Jakob Willforss, (@Jakob37 )
  • Reviewer 2: Alexander Koc, (@alkc )
  • ...

  Testing performed by:

  • Name 1: Jakob Willforss, (@Jakob37 )
  • Name 2: Alexander Koc, (@alkc )
  • ...

  Post-merge

  • [ ] The master branch has been tagged with the new version number.

[Jakob37]

I cleaned up the tags and the CHANGELOG

[Jakob37]

Gnomad and grpmax references are removed now from this PR.

It should be ready for further testing (when the rank models are in).