Y24-010 Options to implement the ANOSPP non-destructive extraction pipeline.

[andrewsparkes]

Description
We need to consider how the new ANOSPP non-destructive extraction (NDE) process will be implemented and create a backlog to implement the solution.

Output
A backlog of user stories to implement the NDE two step process for ANOSPP.

Who the primary contacts are for this work
Scott T
Emma D
PSD developers familiar with Bioscan

Knowledge or Stake holders
Scott T has a diagram for the ANOSPP options, here:
(updated to v3 on 18th March 2024)
Non-Destructive Extractions BIOSCAN ANOSPP v3.pdf
See ANOSSP Confluence page for up to date links

Additional context or information
Best to meet with Scott T and Emma D to go through the details for this.

[SujitDey2022]

Team Discussion 05 March 2024:

1. Not blocked by Y24-009 How to best implement faculty input points into Limber pipelines #372
2. The output of this research story will be estimates of implementing either of the 2 options proposed by Scott T.
3. Open-ended questions related to technical implementation in the Lab - Plate warping alternatives and Addition of controls
4. Can the pipeline be made more flexible allowing the option to choose the steps involving the transfer of the plate?
5. This should be treated as a separate pipeline as it is not compatible with the current Bioscan design.
6. Does the new Anospp pipeline design help simplify the Bioscan pipeline design with the Anospp not coming into the picture at Lysate plate prep stage? If yes, what could be the possible changes required in Bioscan?

Fyi... @TWJW-SANGER @andrewsparkes @KatyTaylor

[andrewsparkes]

Updated process map to v3 on 18th March 2024.
From Scott:
After having observed the process in GSLP, I have revised the process map to better reflect the LIMS process.

PCR1 creation has a single step bed verification rather than 2-step.

[TWJW-SANGER]

Updating story to reduce the scope following discussions on 28/5/2024.

[andrewsparkes]

Stories created:
Y24-135 - ANOSPP - Sample Manifest for creation of Stock plate
Y24-136 - ANOSPP - Creation of configuration for submission and pipeline

[andrewsparkes]

@SujitDey2022 Would you like to make an ANOSPP issue label for these 2 stories above in SS and Limber?
And in terms of sizes I think safest to say the first is a medium and second a large, but I would hope it's less in reality.

[KatyTaylor]

@andrewsparkes stories look good. I left a comment on the manifest one.

I've just been reading through Scott's doc again and found a few things I thought worth mentioning:

1. "New LBSN-equivalent plates will require a 2x label barcode format similar to BIOSCAN LBSN-96 Lysate plates (which includes the Partner ID + -SDC suffix on the second label)." - is this part of Y24-136?
2. Fake cherrypicking before WGS submission - this was something that they wanted to improve upon - I think this is covered already as Y24-114 As SSRs we would like to not have to perform fake cherry picks on stock plates to make submissions so that we are not recording fake data. sequencescape#4127 is in the backlog and labelled as 'ANOSPP', so can be done as part of this group of stories.
3. WGS manifest - SSR/R&D would prefer that the new manifest for registering samples that have previously undergone ANOSPP GBS validates that H12 is empty - is this in scope? If so, would need another story.

[andrewsparkes]

Have updated Y24-136 to include requirement for double label.

And asked Scott to clarify whether we need the empty H12 validation on the manifest upload.

[andrewsparkes]

Added a new story for the H12 empty manifest type requirement:

Y24-139 - ANOSPP - Add a manifest template for WGS with a restriction on use of H12

So, including the 2 above plus the one in the backlog about fake cherrypicking and this one, that is 4 stories in total.