Swgs

[Istaisa]

SWGS app still in development, changes needed for showing initial data to clinical scientists.

Changes in this pull request:

• Scripts to upload/update panels from either the panelapp API or a CSV list of genes
• Gene lists for initial somatic panels
• Set up for indications (lots of many to many fields so we can add multiple panels to a tier)
• Updated tiering display so now there's 4 tables: Tier 1 somatic, Tier 2 somatic, Tier 1 germline, Tier 3 germline - closes #132
• We can talk about this one but off the back of Joseph's artefact checking training there were some questions in the chat about MNVs and things being missed which I've realised we could also be at risk of, so I've also displayed non-intronic possible MNVs in their respective tiers - the lists are already really short and it's only added one to my test data but we can tweak this later on

Still to come!

• Tests
• Refactoring basically everything
• Documentation

[erikwaskiewicz]

Got it to work, I needed to link the panels to my indication. Can you update the fixtures and give a quick install guide in the readme to cover it? Doesnt have to be comprehensive for now

I like the MNV feature :)

[Istaisa]

• Addressed inline comments
• Added requests to env - builds from scratch locally but might be safest to pip install in the existing environment on Viglen
• Added some initial documentation

What specifically do you mean by update the fixtures?

[Istaisa]

Also just to note - I am going to do some long term versioning on the indications so that previous analyses maintain their original panel versions, but it's not a necessary to get this data for now