Y24-007 Updates to PBMC donor pooling - create plate

[yoldas]

User story
As a user of the scRNA Core pipeline, I would like updates to the PBMC Donor pooling to support GEM-X chip.

Who are the primary contacts for this story
Katy, Lesley, Abby

Who is the nominated tester for UAT
Lesley, Abby

Acceptance criteria
To be considered successful the solution must allow:

• Replace the lookup table for the number of source samples according to the chip type decided. Currently, this table (copy of Cardinal's) is used for 1-96 samples and a default number (16) for the number of pools is assumed for more samples.
• Add the constraint around the collection sites, as with Cardinal (if any) to donor pooling. At the time of writing this story, the requirement is not specified.
• Update pooling algorithm for an even distribution of samples across pools. For example, for 32 samples with same study and project, and unique donors, it generates 3 pools as expected but the sizes are 8, 8, and 16. It is because of the halving of the biggest pools for distribution done by the algorithm. They should be 11, 11, and 10 instead. Only the distribute_groups_across_pools method needs changing.
• Consider removing the pooling config file (look up table; Interim scRNA Core pooling config). A pooling strategy based on a suggested number of cells in a pool and a maximum may be better. For example, suggested size could be 10 and maximum could be 20.

Dependencies
This story is blocked by the following dependencies:

• DPL-916 PBMC donor pooling - create plate #1390

Additional context
Only one chip type is supported in this step. The lookup table to configure the number of pools based on the number of samples is affected by the decision of which chip to use and additional chip-specific considerations. We need to change code and configuration to use 10X Chromium 8-well GEM-X chip instead of 10X Chromium 16-well chip.

[KatyTaylor]

Still on hold, awaiting discussion around pooling strategy in Thursday's working group.

[SujitDey2022]

@KatyTaylor @yoldas is this story still on hold?

[KatyTaylor]

Yes, I believe so. We're still waiting to hear from R&D about it.

[KatyTaylor]

Update from Abby last Friday (26th July) was that they have made some progress on this but still haven't finalised the strategy.