Less error-prone and simplify handling of `variant_catalog` for Nallo and Raredisease

[fellen31]

As a bioinformatics pipeline developer,
I want the variant catalog copied to the case analysis directory on config-case, that file stored in the HK bundle on store and the HK bundle file uploaded to Scout for Nallo and raredisease,
So that updates to the reference directory can happen while there are cases running without uploading the wrong versions to a case.

Work impact

Answer the following questions:

• Is there currently a workaround for this issue? If so, what is it?
  • Remember that updates to the reference directory cannot be done while cases are running/pending in production (we have no documentation for it).
• How much time would be saved by implementing this feature on a weekly basis?
  • 0.1 headaches
• How many users are affected by this issue?
  • Pipeline developers
• Are customers affected by this issue?
  • Yes, see description in Move cg/cg/resources/*_bundle_filenames.yaml to another repo #4777 (comment)

Acceptance Criteria

• Paths to the variant catalog in the reference direcotory is set in the cg config, not hardcoded in the deliverables file.
• The variant catalog is copied to the case analysis directory on config-case so we know which variant catalog was used for a specific case.
• The variant catalog is stored in the HK bundle on store.
• The variant catalog is uploaded to Scout from the files stored in the HK bundle
• There exists documentation on how the upload of the variant catalog file to Scout works (we can discuss who is responsible for maintaining this)
  ...

Notes

• Additional information.
• Dependencies.
• Related user stories:
  • Original issue: Move cg/cg/resources/*_bundle_filenames.yaml to another repo #4777
  • Similar flow: Harmonize rank model submissions to Scout #5186