Y26-104 - Bed Verification for SPRI on Hamilton "Porkins" and "Hamlet" Post Amplification AA209

[Stan1520]

Context
The current SPRI protocol in Post Amplification AA209 does not include bed verification in LIMBER. This removes an important quality control checkpoint between SPRI and PCR steps, increasing the risk of historical quality issues reoccurring when the process is brought back online. Bed verification is required between defined protocol steps to safeguard the process.

User story
As a laboratory operator, I want bed verification checkpoints added to the SPRI workflow in LIMBER for Hamilton "Porkins" and "Hamlet" in Post Amplification AA209, So that plate positioning is verified between SPRI and PCR steps to prevent process errors and protect sample quality.

Who are the primary contacts for this story
Joanna C

Who is the nominated tester for UAT
Joanna C

Acceptance criteria
To be considered successful the solution must allow:

• Bed verification steps are added in LIMBER between each defined SPRI and PCR step in the AA209 Post Amp workflow.
• The workflow prevents progression to the next step unless bed verification is successfully completed.
• Bed verification is implemented for both Hamilton instruments "Porkins" and "Hamlet".

Dependencies

This story is blocked by the following dependencies:

• #<issue_no.>
• sanger/#<issue_no.>

References
This story has a non-blocking relationship with:

• #<issue_no.>
• sanger/#<issue_no.>

Additional context

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.

[KatyTaylor]

Which Limber pipeline are we talking about here? See https://limber.psd.sanger.ac.uk/pipelines?group=true for the whole list.

Can you describe the relevant transfer in terms of source and target plate purposes (also shown on the above diagram)?

What are the details of the bed verification i.e. which plate purposes should be on which beds?

[me12-WSI]

Hi Katy,

Pipelines:

• scRNA Core Library Prep
• scRNA Core BCR Library Prep
• scRNA Core TCR Library Prep

I've attached pictures of which steps these go between

[KatyTaylor]

@me12-WSI That's great thank you. Could you also please provide, for each of the 3 bed verifications:

• Source plate bed number(s)
• Destination plate bed number(s)

[Stan1520]

Refinement Notes: 31/03/2026
Meg to come back on the story with details of the bed verification i.e. which plate purposes should be on which beds?, Robot type,

Then Sized as a small

[KatyTaylor]

Update: checked the existing bed verifications in Limber config and found the following. So they seem to be present already. Are they not working?

hamilton LRC GEM-X 5p TCR Post Lig 1XSPRI => LRC GEM-X 5p TCR Post PCR

bed 7: LRC GEM-X 5p TCR Post Lig 1XSPRI
bed 10: LRC GEM-X 5p TCR Post PCR

hamilton LRC GEM-X 5p BCR Post Lig 1XSPRI => LRC GEM-X 5p BCR Post PCR

bed 7: LRC GEM-X 5p BCR Post Lig 1XSPRI
bed 10: LRC GEM-X 5p BCR Post PCR

However: there is no existing bed verification for the LRC GEM-X 5p GE LigXP --> LRC GEM-X 5p GE PCR 2XP step, so we can add one here.

[me12-WSI]

Hi,

Apologies for the slow reply! The beds are the same for GEX so:
bed 7: LRC GEM-X 5p GE LigXP
bed 10: LRC GEM-X 5p GE PCR 2XP

This line is not currently running so I can't check if the BCR/TCR verifications are working