fix: make cadd snv optional

[mathiasbio]

This PR:

WIP. Missing issue at the moment.

Created this branch to make cadd_snv optional as the balsamic cache for hg38 did not have this file which prevented starting cases on hg38. But maybe I just have an incomplete cache...

Added: for new features.
Changed: for changes in existing functionality.
Deprecated: for soon-to-be removed features.
Removed: for now removed features.
Fixed: for any bug fixes.
Security: in case of vulnerabilities.

Review and tests:

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

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Files	Coverage Δ
BALSAMIC/commands/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/config/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/config/case.py	100.00% <100.00%> (+3.44%)	⬆️
BALSAMIC/commands/config/pon.py	100.00% <100.00%> (+4.87%)	⬆️
BALSAMIC/commands/init/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/options.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/base.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/deliver.py	100.00% <100.00%> (ø)
BALSAMIC/commands/report/status.py	100.00% <100.00%> (ø)
BALSAMIC/commands/run/analysis.py	100.00% <100.00%> (ø)
... and 20 more

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[ivadym]

I'm building the cache for hg38, so we can test it. I don't think it's missing but let's see :)
/home/proj/stage/cancer/balsamic_cache/develop/hg38

The hg19 should be up to date (/home/proj/stage/cancer/balsamic_cache/develop/hg19). To use the develop cache just add a --cache-version develop flag to the config case

[khurrammaqbool]

The file is here:
https://github.com/Clinical-Genomics/BALSAMIC/blob/develop/BALSAMIC/constants/cache.py#L394

[ivadym]

It is generated. You can update your cache with the one we have in the develop/hg38 folder

{
    "cadd_snv": "variants/hg38.cadd_snv.tsv.gz",
}