Y25-598 - Add New Tube and Plate Purposes to scRNA Core Pipeline #2597
Description
Context
In the current scRNA Core Cdna Prep GEM-X 5p pipeline (entry point 2), the LIMS does not distinguish between different tube types received in the lab. The team plans to start processing two tube types — 1ml FluidX tubes and 0.8ml FluidX tubes — which require slightly different thawing procedures.
1ml tubes follow a specific INTEGRA instrument thawing protocol.
0.8ml tubes require an additional post-thaw plate creation step (aliquoting 100µl per well) to standardize the input for cell counting and downstream processing.
Currently, the lack of differentiation between these tube types in LIMS increases the risk of lab errors, such as skipping the additional aliquoting step for 0.8ml tubes or performing unnecessary steps for 1ml tubes. Furthermore, both the parent tube and the new aliquot plate contain material that may be revisited for same-day processing (counting and pooling), making accurate tracking and unique identification essential.
Implementing new tube and plate purposes within LIMS will ensure correct process deviations depending on tube type, enhance traceability, and minimize human error.
User story
As a laboratory technician, I want LIMS to distinguish between 1ml and 0.8ml FluidX tube types and define corresponding plate purposes in the scRNA Core pipeline, So that the correct thawing and aliquoting processes are automatically applied, and all related materials are uniquely tracked and identifiable.
Who are the primary contacts for this story
Abby C
Who is the nominated tester for UAT
Abby C
Acceptance criteria
To be considered successful the solution must allow:
-
LIMS must allow configuration of two tube types for entry point 2 of the scRNA Core Cdna Prep GEM-X 5p pipeline:
- 1ml FluidX tubes
- 0.8ml FluidX tubes -
When 0.8ml tubes are processed, LIMS must trigger the creation of an additional plate (aliquoting step) with a unique identifier.
-
The LIMS workflow must automatically associate the new aliquot plate with its parent tube for full traceability.
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Both parent and child plates/tubes must remain available in the system for same-day processing (counting and pooling).
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The workflow must clearly indicate which thawing protocol (INTEGRA) applies to each tube type.
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The system must prevent users from performing unnecessary steps (e.g., skipping aliquot creation for 0.8ml tubes or adding extra steps for 1ml tubes).
Dependencies
This story is blocked by the following dependencies:
None
References
This story has a non-blocking relationship with:
None
Additional context
I have a request for some changes to the existing LIMS process for entry point 2 of our pipeline (scRNA Core Cdna Prep GEM-X 5p).
We are planning to receive 2 different tube types (1ml or 0.8ml FluidX tubes). Each tube type needs slightly different treatment in the lab at the thawing stage:
- 1ml tubes have a different set of INTEGRA instrument thawing protocols to 0.8ml tubes
- 0.8ml tubes have an additional plate after thawing (extra step to aliquot out 100ul/well) to standardise input into post-thaw cell count between tube types
specifics of what would need to change are at option 1b in red of the lucidchart diagram link:
https://lucid.app/lucidchart/0807c1aa-0650-4bbc-b0cd-fcafb9d52420/edit?viewport_loc=-5055%2C-3351%2C7703%2C3655%2C0_0&invitationId=inv_51fc8d21-05da-4db5-8e6c-d76c72be8756
Integration Suite Test
https://gitlab.internal.sanger.ac.uk/psd/integration-suite/-/merge_requests/298
Deployment notes
Add any details that should be noted when deploying this feature. For example, is a database migration needed, a specifc rake task or other script that needs to be run, a dependency on another application or service that needs to be released first etc?
These notes are intended to ensure the developers releasing the feature know what needs to be done.
Add any other context or screenshots about the feature request here.
The request type limber_scrna_core_cdna_prep_gem_x_5p has had it's acceptable purposes modified.
acceptable_purposes are now:
- LRC Bank Seq
- LRC Bank Spare
- LRC Bank Input 1ml
- LRC Bank Input 0.8ml
We are losing the LRC Bank Input one.
After deployment may need to check this in the rails console.
rt = RequestType.find_by(name: 'scRNA Core cDNA Prep GEM-X 5p')
pp = Purpose.find_by(name: 'LRC Bank Input')
rt.acceptable_purposes.delete(pp)