refactor: Update QC criteria

[ivadym]

This PR:

Updates QC criteria for panel and wgs analysis.
Removes outdated balsamic report files (balsamic_report.html & balsamic_report.md).

Review and tests:

• Tests pass
• Code review
• New code is executed and covered by tests, and test approve

[codecov]

Codecov Report

Merging #952 (9937b1c) into develop (d202a40) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop     #952   +/-   ##
========================================
  Coverage    99.24%   99.24%           
========================================
  Files           28       29    +1     
  Lines         1713     1714    +1     
========================================
+ Hits          1700     1701    +1     
  Misses          13       13           

Flag	Coverage Δ
unittests	99.24% <100.00%> (+<0.01%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
BALSAMIC/constants/qc_metrics.py	100.00% <ø> (ø)
BALSAMIC/utils/cli.py	99.69% <ø> (-0.02%)	⬇️
BALSAMIC/commands/init/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py	100.00% <100.00%> (ø)
BALSAMIC/utils/io.py	100.00% <100.00%> (ø)
BALSAMIC/utils/rule.py	94.21% <100.00%> (+0.19%)	⬆️

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[ivadym]

Tested metric extraction for TN WGS case (different conditions for tumor & normal samples):

ACC6307A1: normal sample
ACC5821A7: tumor sample

[keyvanelhami]

Great work Vadym, I have some few comments

[keyvanelhami]

@ivadym Let me know when ready and I will merge the PR

[ivadym]

I think we still need approval from @ashwini06 and/or @khurrammaqbool as code owners. Maybe they can also come up with some ideas, suggestions on the implementation of this.

[ashwini06]

Looks good 💯

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication