Balsamic 19 changes

[mathiasbio]

Description

Closes issue: #160
Required for Balsamic v19 to store new CNV report: Clinical-Genomics/BALSAMIC#1648

Also to change CNV deprecated PDF to only deliver, not Scout upload

Added

• new CNV report html to store, deliver and upload to Scout for panels
• added possibility to override housekeeper tags in workflow specific section

Changed

• changed CNV report PDF to only be delivered not upload to Scout

Testing

How to prepare for test

• ssh to Hasta
• Test your branch with

hermes-test-deploy balsamic_19_changes
hermes-test <command here>

How to test

• login to ...
• do ...

Expected test result

• check that new CNV report is stored with Scout tag, and old CNV report has Scout tag removed:

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 92.74%. Comparing base (2991fc7) to head (be24619).
⚠️ Report is 42 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #161      +/-   ##
==========================================
+ Coverage   92.72%   92.74%   +0.01%     
==========================================
  Files          28       28              
  Lines        1004     1006       +2     
==========================================
+ Hits          931      933       +2     
  Misses         73       73              

Flag	Coverage Δ
unittests	92.74% <100.00%> (+0.01%)	⬆️

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[mathiasbio]

@fevac Hi! In order to be able to override the tag I had to make a small update here: https://github.com/Clinical-Genomics/hermes/pull/161/changes#diff-4b10a22f3c28d5f84a70379020f2a8524257188fe4c6ac919b9df9902fac884e (WGS still should upload the CNV pdf to Scout).

Another way of solving it would probably be to ensure that the PANEL PDF report (deprecated) gets separate tags from balsamic, then those can be handled separately directly. But this solution seems to work. Link to Scout case: https://scout-stage.scilifelab.se/cust087/F0071554-lymf