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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
150 stars 46 forks source link

More LRS SV callers #4886

Open dnil opened 1 week ago

dnil commented 1 week ago

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](https://hub.docker.com/repository/docker/clinicalgenomics/scout-server-stage) 1. Fist book your testing time using the Pax software available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). The resource you are going to call dibs on is `scout-stage` and the server is `cg-vm1`. 1. `ssh @cg-vm1.scilifelab.se` 1. `sudo -iu hiseq.clinical` 1. `ssh localhost` 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps` 1. Stop the service with current deployed branch: `systemctl --user stop scout.target` 1. Start the scout service with the branch to test: `systemctl --user start scout@` 1. Make sure the branch is deployed: `systemctl --user status scout.target` 1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](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 @hasta.scilifelab.se` 1. Book your testing time using the Pax software. `us; paxa -u -s hasta -r scout-stage`. You can also use the WSGI Pax app available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `conda activate S_scout; pip freeze | grep scout-browser` 1. Deploy the branch to test: `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b ` 1. Make sure the branch is deployed: `us; scout --version` 1. 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:

codecov[bot] commented 1 week ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.80%. Comparing base (69b622d) to head (b1e8e62).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #4886 +/- ## ======================================= Coverage 84.80% 84.80% ======================================= Files 319 319 Lines 19314 19318 +4 ======================================= + Hits 16379 16383 +4 Misses 2935 2935 ```

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sonarcloud[bot] commented 5 days ago

Quality Gate Passed 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

northwestwitch commented 4 days ago

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

dnil commented 4 days ago

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.