GPL-246 Add Chromium Visium library type

[KatyTaylor]

User story As an SSR user I would like the Chromium Visium library type to be available in Sequencescape

Who the primary contacts are for this story

1. Liz E - original requester.
2. Matt Jones - Limber Bespoke user who knows about Chromium Visium
3. Mike Quail - R&D user who already input the tag groups.

Acceptance criteria To be considered successful the solution must allow: 1 - When creating a submission, 'Chromium Visium' library type should be available in the list when I select any submission templates starting with 'Limber-bespoke - PCR' (apart from ones that say PCR Free) - this corresponds to the 'Limber PCR Bespoke' request type 2 - I should be able to process the LBB Cherrypick plates that have been through the above submission in Limber, using the existing 'PCR Bespoke' pipeline 3 - I should be able to choose the 'VisiumUDI_i7' and 'VisiumUDI_i5' tag groups (already created by Mike in production) while processing in Limber 4 - Ideally I can also scan a tag plate instead of selecting the tag groups manually (the tag plates will have to be created in Gatekeeper

[KatyTaylor]

Mike Quail had already inserted the relevant Tags and Tag Groups into production when I started this story, but here's a script for inserting them in case useful (used in UAT to bring that up to date, for instance). Pulled this data from training/snapshot database.

script for inserting Tags and Tag Groups.txt

[KatyTaylor]

Script to run in order to insert the new Library Type and link it to the correct Request Type:

Script for adding 'Chromium Visium' library type.txt

[KatyTaylor]

Spent some time investigating how we would make it possible to scan a tag plate instead of selecting the tag groups manually in Limber.

Decided not to implement this feature for now as Matt Jones isn't sure if it would be useful or not. They don't currently have this functionality for the existing Chromium pipelines and tag plates. The reason it is useful for the high throughput pipelines is that they use the entire tag plate and transfer the library into the tag plate itself, so the tag plate then becomes the main plate going through the pipeline and needs to be carefully tracked. With the Chromium plates, they only use some of the tags at a time and come back to it several times. Also, the IDT plates have some QC checking done on them at Sanger, whereas the Chromium ones are QC checked already when they arrive on site, so we don't need to track that.

Summary of stuff learned about Sequencescape & Gatekeeper:

• Data model: https://www.lucidchart.com/invitations/accept/36bbac45-8469-4cfb-b456-16d05050eb9e
• Data changes:
  • would have to create a new Lot Type, probably similar to the 'IDT Tags' one
  • would have to create a new Tag Layout Template, referencing the 2 new Tag Groups and with direction 'in columns'
• Gatekeeper changes:
  • Home page would need link to allow you to create Lots of the new Lot Type
  • 'Lot' page - you can upload a spreadsheet to create IDT plates - this is basically the functionality we would need for Chromium ones as they are pre-barcoded and the barcodes pulled out of the spreadsheet (column 3) - however, might want to allow a wider range of spreadsheet formats and change the UI not to read 'Create IDT Plates'
• Barcode format changes:
  • Gatekeeper always creates barcodes of format 'external' - this is in 'external_barcode=' method in 'barcodeable', called by 'create_asset!' method in 'qcable' model - maybe should change this to avoid barcode clashes within the 'external' format?
  • If wanted to create a new barcode format in Sequencescape, would probably be like this - https://github.com/KatyTaylor/sequencescape/commit/f2718a2ff6903e31a95840cf282cf5536b89c7bd - but haven't figured out the Chromium barcode format.