[User Story] Annotated, ranked and Scout compatible SVs

[jemten]

Need

As a clinician or researcher, I want SNVs to be annotated, ranked and compatible with Scout.

Suggested approach

Draw upon inspiration from the nf-core/rd pipeline: SVDB annotation --> VEP --> Genmod

Can be closed when

• Call structural variants
  • Add Severus nf-core/modules#5951
  • Implement nf-test for structural_variant_calling #188
  • Replace sniffles multisample with bcftools merge #280
  • Add Severus as the default SV caller #279
  • Add FOUND_IN tags to SV calling #336
• Add annotate structural variants workflow #281
  • Add SVDB QUERY #383
  • Add VEP for SVs #384
  • Implement nf-test for annotate_structural_variants #282
• Merge CNV and SV calls #400
• Add rank variants for SVs #413
  • Implement nf-test for rank_variants #283
    • Update genmod to 3.8.3 #406

Additional considerations

• Sniffles2 multisample is currently used to merge samples and create a SV "database".