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Clinical-Genomics / cg

Glue between Clinical Genomics apps
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Panel handling for orders #1832

Open dnil opened 1 year ago

dnil commented 1 year ago

Description

A large and increasing number of rd wgs orders are for low-usage in silico panels, that are not on the master list. While we could theoretically add these to master, it defeats some of the purpose as it would be very rare that any of the other cases need to use it.

Suggested solution

Add options to orders to order arbitrary low-use panels from Scout, and to use master list plus these panels for processing these.

Note that panels for ordering are also mirrored in status db, for what appears mostly to be historical reasons. Perhaps we can work around that, or just add a write panels there. Hence we may need to also write them there or scrap that.

This can be closed when

Orders for low-use panels can conveniently be placed from the order portal through to processing without CG personel hands on.

ChrOertlin commented 1 month ago

added to refinement 19-06-2024

Vince-janv commented 2 weeks ago

@dnil I don't quite understand this issue. Can these low-usage panels not be ordered in the orderportal under the panel field?

dnil commented 2 weeks ago

If you now have the option to order a small panel PLUS master, that is fine. Previously non-master order would cancel master inclusion.

dnil commented 2 weeks ago

Oh, also if you automatically import these from scout? I think you may still need someone to add to a constant in cg?

Vince-janv commented 2 weeks ago

I see. I did not know that. Is it true to say that we always want to include the master panel plus any others added? It would make the logic a lot more clean

dnil commented 2 weeks ago

This issue can be closed when a scout and order portal user can herself make a new small volume panel in scout, order it and have it run pipeline with master list, without affecting other case orders ie without adding the low volume panel to master list.

dnil commented 2 weeks ago

I see. I did not know that. Is it true to say that we always want to include the master panel plus any others added? It would make the logic a lot more clean

I think that would make a lot of sense! It should normally mean only a slight overhead in processing at the gain of fewer reruns. Possibly there are a few non-core customers who do not wish this? Perhaps an explicit option to exclude master?

Vince-janv commented 2 weeks ago

I think that would make a lot of sense! It should normally mean only a slight overhead in processing at the gain of fewer reruns. Possibly there are a few non-core customers who do not wish this? Perhaps an explicit option to exclude master?

What overhead would that be? Would the solution somehow negatively impact how the users work in scout? In general I'm in favour for as few extra options as possible