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Clinical-Genomics / cg

Glue between Clinical Genomics apps
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Add a new field "Platform" to Application in statusdb #3395

Open annagellerbring opened 2 months ago

annagellerbring commented 2 months ago

The field will be used to specify the sequencing platform applicable for the application. It will be located next to the field "prep category".

"Platform" needs a drop down list with the following options:

annagellerbring commented 2 months ago

FYI @pbiology @Vince-janv

Vince-janv commented 2 months ago

Should there really be 4 Illumina short-read options? It feels weird that WGSPCFC030 should be locked to eg NovaSeq X

pbiology commented 2 months ago

I was thinking this more in the context to be able to follow which platform has been used to process a given data set. Perhaps this is already solved by the new flowcell tables coming to cg?

Vince-janv commented 2 months ago

Yes, it will have the types pacbio, Illumina, bionano, oxford_nanopore. (Names can be changed in the future if we decide to buy other tech from these companies...)

pbiology commented 2 months ago

And it will have sequencer_type which will hold which exact platform, right?

Vince-janv commented 2 months ago

For illumina that will remain. for the others we haven't added it. Would it make sense even if we only have the revio, saphyr and promethion?

pbiology commented 2 months ago

Well. We will most likely soon have other platforms there as well. The case at hand would be the external data sent to us by clin mic for the 16S project. That will most likely come from the GridION platform (and perhaps minION).

To me it makes sense to accommodate this already now

Edit: And also for PacBio we are already talking about Ontos...

annagellerbring commented 5 days ago

is this on hold @Karl-Svard ? If yes, can you put a label on it.

Karl-Svard commented 4 days ago

It probably will be. I'll add the label after confirming it during the meeting next week