Update Gnomad

[Jakob37]

Description

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

Close #95

Type of change

• [x] Minor change

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

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
• [ ] At least one other person has reviewed and approved my code
• [x] I have made corresponding changes to the documentation

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: Alexander Koc, (@alkc )

Testing performed by:

• Jakob Willforss, (@Jakob37 )

Post-merge

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

[Jakob37]

First run went through with similar looking AFs, but looks like not all information is yet there in the minified updated version.

New:

1       pos rs707475        G       A       .       PASS    AF=0.399787 

Old:

1       pos rs707475        G       A       .       PASS    AF=0.399921;popmax=afr;AF_popmax=0.498193 

Next, check if this is a banta.pl issue, and/or whether format of the original data differs

[Jakob37]

This is ready for testing now. I realized my final test run was performed using the wrong branch, so I will need to restart the testing when back from parental-leave-week.

[Jakob37]

Test samples successfully completed. I will do some comparisons of the results. Then this PR should be ready for preparation for validation.

[Jakob37]

Rank score changes looks OK