Add flag to only output BAM files

[alkc]

Description and reviewer info

This update adds a flag --alignment_only to instruct the pipeline to only output BAMs and QC data.

Will be used to regenerate BAM files for /access/wgs/bam and whambam.

Type of change

• [x] Minor change

Checklist

• [ ] Self-review of my code
• [x] Update the CHANGELOG
• [ ] Tag the latest commit (vX.Y.Z format)
• [x] Log samples used for testing in the Verification_samples_log Excel sheet

Specific tests

• [x] Bam + QC only run for onco works
• [x] Bam + QC only run for wgs works

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
• [ ] At least one other person has reviewed and approved my code
• [x] I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

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

(Add if missing)

Testing performed by

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

[alkc]

Put on hold while I deal with the reruns, but what I'd like to do next is to test run this a final time after merging master into this branch, then it should be ready to merge and deploy