Chromograph ideograms for hg38

[dnil]

This PR adds a functionality or fixes a bug.

• Fix hg38 Chromograph ideograms #5863

Testing on cg-vm1 server (Clinical Genomics Stockholm)

Prepare for testing

1. Make sure the PR is pushed and available on Docker Hub
2. First 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@<name_of_currently_deployed_branch>
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

[dnil]

There is a risk that these hardcoded values won't cut it for the hg38, but not much to do but test and adjust. 🤷‍♂️

[dnil]

Ideograms generated like

chromograph -i cytoBandIdeo.igv.hg38.bed -d hg38_ideo
for file in `ls -1 *png`; do mv $file ${file//cytoBandIdeo.igv.hg38_chr/chromosome-}; done

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 83.78%. Comparing base (9d75872) to head (5909d9d).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #5883   +/-   ##
=======================================
  Coverage   83.78%   83.78%           
=======================================
  Files         336      336           
  Lines       20960    20960           
=======================================
  Hits        17561    17561           
  Misses       3399     3399           

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[northwestwitch]

Couple of suggestions. Just because I realised at the end that this PR was still a draft 😃

[northwestwitch]

Ah sorry, I wanted to update this one but I marked it as ready for review

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

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

See analysis details on SonarQube Cloud