Raredisease add concatenated SNV file for loqusDB

[peterpru]

Description

For Raredisease loqusDB uploads we need to have a file that combines both the genome-wide SNVs and the MT variants. This PR adds this output to housekeeper. Parent issue here: https://github.com/Clinical-Genomics/MTP-RAREDISEASE/issues/172

To be deployed with the corresponding servers PR.

Added

• raredisease loqusdb SNV files in housekeeper

Changed

Fixed

Testing

How to prepare for test

• ssh to Hasta
• Test your branch with

hermes-test-deploy rd-store-loqus-snv-file
hermes-test --help
us
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-servers-stage.sh rd-store-loqus-snv-file
cg workflow raredisease store evolvedsalmon

How to test

• login to hasta, do the prep above
• do the store command:

Expected test result

• check that the files are included with the correct tags
• Take a screenshot and attach or copy/paste the output.
• [ ]

Review

• code approved by
• tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.92%. Comparing base (4a6315e) to head (1330df1).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #172      +/-   ##
==========================================
+ Coverage   92.91%   92.92%   +0.01%     
==========================================
  Files          28       28              
  Lines        1030     1032       +2     
==========================================
+ Hits          957      959       +2     
  Misses         73       73              

Flag	Coverage Δ
unittests	92.92% <100.00%> (+0.01%)	⬆️

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[sofiademmou]

LGTM ! 👍

[peterpru]