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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
150 stars 46 forks source link

Unify codebase with molecuar diagnostics Lund #2324

Closed mhkc closed 3 years ago

mhkc commented 3 years ago

We in Lund has made the following changes to Scout code base. For more information please look at our fork.

Most things are minor changes and could be solved by allowing to add custom fields. The "edit metadata and submit for reanalysis" is more elaborate and should be an optional feature. However it would require that we define a "standard RESTapi" which Scout uses to communicate with a custom service that each site is responsible for setting up. This might be a feature that could be implemented in the future.

northwestwitch commented 3 years ago

OK! I was afraid it would be much more different, but this is very mergeable I think! That note on the other hand .. 😆

mhkc commented 3 years ago

How do you think the very Lund specific changes (Gens & rerunner) should be implemented?

I guess the easiest solution would be to only display the integration if related variables are set in the config. Another, more involved, method could be to expand the ability to define custom data fields in the case yaml file.

dnil commented 3 years ago

Display-if-available sounds the absolute best! That way everyone else can also use the integration as soon as they get off their butts and start using Gens & rerunner! 😸

northwestwitch commented 3 years ago

I wouldn't mind start using Gens in Stockholm as well, and fixing rerunner to be general enough to send requests to our cg software

dnil commented 3 years ago

Same here.. Gems is a little complicated for us as it is right now with how cases are stored, but it would be changeable if someone has the interest. We could have a a project student on that one - @moonso, wouldn't you like to supervise one formally before you are defending perhaps? Or you C? You know array data well enough!

northwestwitch commented 3 years ago

Yes, that would be fun!

bjhall commented 3 years ago

This PR fixes the DECIPHER button confusion: https://github.com/Clinical-Genomics/scout/pull/2347

So you can scratch that from the list @mhkc

bjhall commented 3 years ago

And this fixes the Sanger ordering emails: https://github.com/Clinical-Genomics/scout/pull/2348

bjhall commented 3 years ago

I realized there is one more thing that needs to be sorted out related to this issue. We've discussed this before, but I don't think we found a good solution.

It relates to CALLERS in scout/constants/__init__.py. To me this is configuration stuff and should not be hardcoded (since different sites will always be using different callers).

Similarly we've changed the DISSMISS_VARIANT_OPTIONS in scout/constants/variant_tags.py. In this case I do, however, think it would be nice if the geneticist of the different sites could agree on a set of terms that would work for everyone... But that might be easier said than done.

dnil commented 3 years ago

Much agree! The latter one would be an interesting exercise; it took our different clinics a while to converge even though they were borrowed fairly cleanly from previous lab systems for classical techniques (Sanger, aCGH). We will have to alter handling of those in a few places I guess, especially thinking ahead to potentially sharing case- and classification data. Then we may need a mapping between the different site classifications if we can't agree. Still, ACMG will be interchangeable so not the end of the world.