More LRS SV callers

[dnil]

This PR adds a functionality or fixes a bug.

Add new potential Nallo additions Severus (https://github.com/KolmogorovLab/Severus) and HiFiCNV (https://www.pacb.com/blog/hificnv/) plus a missing tag for TRGT (https://github.com/PacificBiosciences/trgt).

Testing on cg-vm1 server (Clinical Genomics Stockholm)

Prepare for testing

1. Make sure the PR is pushed and available on Docker Hub
2. Fist book your testing time using the Pax software available at https://pax.scilifelab.se/. The resource you are going to call dibs on is scout-stage and the server is cg-vm1.
3. ssh <USER.NAME>@cg-vm1.scilifelab.se
4. sudo -iu hiseq.clinical
5. ssh localhost
6. (optional) Find out which scout branch is currently deployed on cg-vm1: podman ps
7. Stop the service with current deployed branch: systemctl --user stop scout.target
8. Start the scout service with the branch to test: systemctl --user start scout@<this_branch>
9. Make sure the branch is deployed: systemctl --user status scout.target
10. After testing is done, repeat procedure at https://pax.scilifelab.se/, which will release the allocated resource (scout-stage) to be used for testing by other users.

Testing on hasta server (Clinical Genomics Stockholm)

Prepare for testing

1. ssh <USER.NAME>@hasta.scilifelab.se
2. Book your testing time using the Pax software. us; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.
3. (optional) Find out which scout branch is currently deployed on cg-vm1: conda activate S_scout; pip freeze | grep scout-browser
4. Deploy the branch to test: bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>
5. Make sure the branch is deployed: us; scout --version
6. After testing is done, repeat the paxa procedure, which will release the allocated resource (scout-stage) to be used for testing by other users.

How to test:

1. how to test it, possibly with real cases/data

Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.

Review:

• code approved by
• tests executed by

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.78%. Comparing base (c37c486) to head (f57d8d7).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4886   +/-   ##
=======================================
  Coverage   84.77%   84.78%           
=======================================
  Files         319      319           
  Lines       19322    19326    +4     
=======================================
+ Hits        16381    16385    +4     
  Misses       2941     2941           

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[northwestwitch]

Looks good to me 👍🏻

Consider starting using constants in callers lists

[northwestwitch]

Do we want to include this one in the the release?

[dnil]

It's not a rush. I'll try to make a test case based on the examples from @fellen31. I'm sure the tags as such work, but it would be nice to see that the caller output actually load and show something useful in Scout when adding them.

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[fellen31]

It's not a rush. I'll try to make a test case based on the examples from @fellen31. I'm sure the tags as such work, but it would be nice to see that the caller output actually load and show something useful in Scout when adding them.

Taking a bit longer to get a real test case, but variants from both (without annotation) seem to be able to be uploaded to Scout.

[dnil]

Ok, that is good enough for me! Annotation is reasonably proven. We can get back to nitty gritty details on specific keys for these callers later as needed.