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Y24-321 - Cell counting driver file for pools plate #1915

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KatyTaylor opened this issue Sep 13, 2024 · 1 comment · Fixed by #1943
Closed
4 tasks done

Y24-321 - Cell counting driver file for pools plate #1915

KatyTaylor opened this issue Sep 13, 2024 · 1 comment · Fixed by #1943
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scRNA - cDNA prep scRNA Size: S Small - low effort & risk

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@KatyTaylor
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KatyTaylor commented Sep 13, 2024

User story
As a user of the scRNA Core pipeline, I would like the LIMS to generate a driver file for the transfer from the LRC PBMC Pools plate to the Cellaca plate.

Who are the primary contacts for this story
Abby, Katy

Who is the nominated tester for UAT
Abby

Acceptance criteria

  • Cell counting driver file download available on LRC PBMC Pools plate.
  • Based on hamilton_lrc_pbmc_defrost_pbs_to_cellaca_count (as on 'LRC PBMC Defrost PBS' plate).
  • Includes columns 'Plate Barcode', 'Well Position', 'Well Name' as in above file.
  • Includes additional column, 'Source well volume', which is calculated as:
    • (Number of samples in pool x 30,000 x 0.95238) / 2,400
    • Where:
      • 30,000 is the required number of cells
      • 0.95238 is accounting for wastage of material when transferring between labware
      • 2,400 is the desired chip loading concentration

References
Uses same calculation as in #1914

Additional context
This is for the 'pre-MVP' version, to be used for R&D's end to end test. For the MVP version, we may want to refactor to store the constants in a more central place, or do the calculation once and use the stored result for both #1914 and this story.

All wells are counted, like on the LRC PBMC Defrost PBS plate, and unlike on the LRC PBMC Bank plate.

@dasunpubudumal
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Integration suite PR (well, "Merge Request" to be precise): https://gitlab.internal.sanger.ac.uk/psd/integration-suite/-/merge_requests/168

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scRNA - cDNA prep scRNA Size: S Small - low effort & risk
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