Make the Tomte workflow orderable

[Vince-janv]

User story:

As a customer, I would like to be able to analyse RNA samples with Tomte, as it is a better and more moderna workflow than MIP-RNA.

Acceptance criteria:

• A customer should be able to place orders to be analysed with tomte
  • The case added to status_db should have data_analysis=tomte
  • reference_genome should be propagated from the order to status_db
  • Family relationships should be able to be set via the order (as mip-dna)
  • Status (affected/unaffected) be able to be set via the order (as mip-dna)

Priority:

• Tomte is set to be ready for production by the start of May

[Vince-janv]

Technical refinement:

cg

• In orderform 1508 add the data_analysis option tomte
• in cg/meta/orders add a TomteSubmitter that inherits from CaseSubmitter
• Add entry for tomte in cg.models.orders.constants.OrderType
• In cg/meta/orders/api.py:37 add an entry linking the aforementioned OrderType to the TomteSubmitter
• cg.meta.orders.case_submitter.CaseSubmitter._create_sample needs to pass reference_genome as a kwarg to cg.store.crud.create.CreateHandler.add_sample

[fevac]

Also, note that fibroblast should be included as an option in source

[fevac]

As long term change, it would be nice if a tissue ontology field (https://www.ebi.ac.uk/ols4/ontologies/bto) was added to replace the mixed field source

[islean]

Can we close this now @fevac @Vince-janv ?

[fevac]

Completed in https://github.com/Clinical-Genomics/cg/pull/3119