DPL-914 Create tube rack containing banked PBMC tubes

[KatyTaylor]

User story As a user of the scRNA Core pipeline, I would like to be able to create a plate (that represents a tube rack) in the LIMS that holds tubes containing banked PBMCs, so that I can track it and use it in bed verifications.

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

Who is the nominated tester for UAT Lesley, Abby

Acceptance criteria

• [x] The LIMS supports the creation of "LRC PBMC Cryostor" tube racks (represented as a plate in the LIMS for now) from a group of "LRC Bank Seq" and "LRC Bank Spare" tubes.
• [x] UX will look like:
  • User goes to tube page
  • Clicks green 'add an empty...' button to go to next labware in pipeline
  • Uploads rack scan to tell Limber which tubes are being transferred into which wells
  • Page checks all tubes exist in the LIMS already - error if not
  • Page checks all tubes have active requests of the correct type (limber_scrna_core_donor_pooling, from https://github.com/sanger/sequencescape/issues/3900)
  • Lands on plate page (user will print out plate barcode and stick on tube rack)
• [x] Update Integration Suite test to include this transfer.

[Lesley84]

1) How will they make sure they've got the same selection of tubes as specified on the submission? Tubes will be in FluidX tubes and scanned on a 2D rack scanner. Perhaps discussion to be had as to whether this activity sits within Bioresource or DNAP?

2) What should the interface look like? Ideally, the submission will align with the plate layouts of the stored PBMCs for easy retrieval. It would rely on the SSRs having access to the plate rack scan that was used for submission to the Bioresource Team.

[andrewsparkes]

Could we treat this as a kind of manual cherrypick + auto-submission? Upload a tube rack scan in the Thaw plate labware creator, then auto-submission on the resulting plate?

[KatyTaylor]

Needs more discussion, but some notes from today's meeting:

A selection of tubes will be retrieved from the freezer - between 100 and 160 donors - enough for one 10X chip. They can know in advance how many tubes this will be, however the exact pooling arrangement on the 10X chip will be determined based on cell count data.

Sounds like it would make sense for a submission to include this batch of tubes.

They will be transferred into plates - however many needed - presumably normally 2.

[KatyTaylor]

We decided in the meeting with Lesley 5/12/23 to represent the tube rack as a plate for MVP, to reduce the scope of Phase 2 development.

Pasting previous section from story description below in case useful in the future:

2 UX options:

1. If representing tube rack properly:

   • User goes to tube page
   • Clicks 'add tube rack' or similar
   • Uploads rack scan
   • Page checks all tubes exist in the LIMS already
   • Lands on tube rack page
   • tube rack has now been associated with all the correct tubes
   • no new transfers, links between labware or wells etc. have been created

2. If representing tube rack as a plate: - do this for first version

   • User goes to tube page
   • Clicks green 'add an empty...' button to go to next labware in pipeline
   • Uploads rack scan
   • Page checks all tubes exist in the LIMS already
   • Page checks all tubes have active requests of the correct type
   • Lands on plate page (print out plate barcode and stick on tube rack)

[andrewsparkes]

To raise in UAT: Would users like an export file download on the plate to list the original tube barcodes?