Automate stub runs

[alkc]

Description and reviewer info

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

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)

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
• GIAB single (wgs) finishes and differences to current master branch have been investigated (using PipeEval)
• GIAB trio (wgs) finishes and differences to current master branch have been investigated
• Seracare (onco) sample finishes and differences to current master branch have been investigated
• Output from processes with altered code have been inspected (i.e. in the work folder: .command.sh, .command.log, .command.err and result files)
• All three samples 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

[alkc]

Container spec (wgs_active.sif must be destroyed) needs to be sorted before this can proceed