Update Nallo to 0.11.0

[fellen31]

Description

This PR contains the changes needed to run Nallo 0.11.0 in production. To be tested with Clinical-Genomics/cg#4948.

Added

• Paraphrase outputs for TSV and JSON (it's unclear at the moment which file we will use in Scout)

Changed

• Changed to store paraphase jsons per sample (as is output from Paraphase)

Fixed

Testing

How to prepare for test

• ssh to Hasta
• Test your branch with

hermes-test-deploy <branch-name>
hermes-test <command here>

How to test

• login to ...
• do ...

Expected test result

• check that ...
• 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 92.82%. Comparing base (12b1edd) to head (861b80a).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #159   +/-   ##
=======================================
  Coverage   92.81%   92.82%           
=======================================
  Files          28       28           
  Lines        1016     1017    +1     
=======================================
+ Hits          943      944    +1     
  Misses         73       73           

Flag	Coverage Δ
unittests	92.82% <100.00%> (+<0.01%)	⬆️

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