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Y24-376 - Pooling algorithm changes #1985

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KatyTaylor opened this issue Oct 10, 2024 · 2 comments · May be fixed by #1734 or #2081
Open
7 of 8 tasks

Y24-376 - Pooling algorithm changes #1985

KatyTaylor opened this issue Oct 10, 2024 · 2 comments · May be fixed by #1734 or #2081
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scRNA - cDNA prep scRNA Size: L Large - large effort & risk

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@KatyTaylor
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KatyTaylor commented Oct 10, 2024

User story
As a user of the scRNA Core cDNA Prep pipeline, I would like some changes to the pooling algorithm (allocating samples into wells on the LRC PBMC plate) to increase the flexibility and robustness of the pipeline.

Who are the primary contacts for this story
Katy, Abdullah, Andrew

Who is the nominated tester for UAT
Abby

Acceptance criteria
Pooling algorithm (creating LRC PBMC Pools plate) is adjusted so that:

  • 'Number of pools' is pulled from the submission/requests (for each study-project group), rather than being calculated.
  • All pools within a study/project/donor group have the same number of samples (or differ by one if not exactly divisible).
  • The requested number of pools can vary between study-project groups in the same run.
  • The result of the algorithm is shown to the user in a success message after the plate is created (see format in additional context).
  • Plate creation fails with an informative error if any of the following conditions are not met:
    • Total number of pools on the destination plate must be between 1 and 8 (inclusive).
    • Number of samples in each pool must be between 5 and 25 (inclusive).
    • Each pool should have unique donor IDs.

References
Follows on from:

'Number of pools' won't be present in the request metadata until sanger/sequencescape#4423 has been done. However, this story can still be done first - we would need to do the request metadata migration as part of this story.

The 'number of samples per pool' field added to request_metadata as part of sanger/sequencescape#4337 is now obsolete - so we could change the name of this field rather than adding a new one?

Additional context
Output of the pooling algorithm is (e.g.), to display to the user:

Study/project/donor group Pools (num samples) Well
Study X - Project A - Donor group 1 4, 4, 3 A1
Study Y - Project B - Donor group 2 10, 10 B1
@KatyTaylor KatyTaylor added scRNA scRNA - cDNA prep Size: L Large - large effort & risk labels Oct 10, 2024
@psd-issuer psd-issuer bot changed the title Pooling algorithm changes [DRAFT] Y24-376 - Pooling algorithm changes [DRAFT] Oct 10, 2024
@KatyTaylor KatyTaylor linked a pull request Oct 11, 2024 that will close this issue
@KatyTaylor
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Have linked Abdullah's draft PR where he was playing around with algorithm changes to solve "All created pools have the same number of samples (or differ by one if not exactly divisible)."

@KatyTaylor KatyTaylor changed the title Y24-376 - Pooling algorithm changes [DRAFT] Y24-376 - Pooling algorithm changes Oct 25, 2024
@SHIV5T3R SHIV5T3R self-assigned this Nov 1, 2024
@StephenHulme StephenHulme added the Feature Flag A clean-up story for a feature flag label Nov 1, 2024
@KatyTaylor KatyTaylor removed the Feature Flag A clean-up story for a feature flag label Nov 15, 2024
@SHIV5T3R SHIV5T3R linked a pull request Nov 21, 2024 that will close this issue
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Labels
scRNA - cDNA prep scRNA Size: L Large - large effort & risk
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