[User Story] Ensure pipeline compatibility with CG production

[fellen31]

Need

As a bioinformatician, I want to be able to run the pipeline in production at CG.

Suggested approach

Make the pipeline ready for implementation at CG.

Can be closed when

Must have

• Replace family_id with case_id #48

Should have

• Consistent output file naming compatible with Housekeeper #154
• [User Story] Consistent naming of pipeline parameters #324
• [User Story] Annotated, ranked and Scout compatible SNVs #23
• [User Story] Annotated, ranked and Scout compatible SVs #104
• Annotated and Scout compatible repeat expansions
• Add deepvariant/vcf_stats_report.py #309 (I think production would very much like to have)