Y26-005 - LCM Triomics - assign Project / Cost Code to automated submissions

[KatyTaylor]

User story

I have suggested that when setting up the 'automated' submissions in Limber for #2665, that we hardcode a dummy Project, so as to avoid holding up the rest of the pipeline development.

This story is to work out how to get the correct project into those submissions. We can't hardcode a project (as we did for Heron, which used the same 'choose workflow' screen), because this pipeline will be used across multiple projects (cost codes).

A few options I've thought of:

• Include it on the sample manifest (there is an existing project_id field on sample manifest we could use) - but would it work for repeats, where they may want to use a different cost code?
• Get the lab users to specify it in the 'Choose Workflow' screen (this information would probably need to be passed onto them by the SSR - perhaps another piece of information in a comment on the Labware).
• A hybrid of the above - able to specify it in the UI, but provide a suggestion based on the manifest, or based on previous library prep runs from the same plate.

But there may be other, better options.

Who are the primary contacts for this story

Scott G, Katy

Who is the nominated tester for UAT

Scott G, ...

Acceptance criteria

Consider if these features can be featured flagged to decouple testing and deployment.
To be considered successful the solution must allow:

• Decide on a design for getting the project id into the LCM Triomics submissions
• Implement it
• Update Automated Submission documentation if needed

Dependencies

This story has a blocking dependency on:

• Y26-004 - LCM Triomics - choose workflow (EMSeq & RNASeq) #2665

Update: believe this can be picked up now with use of the Limber epic branch and careful communication with devs on the related stories.

Additional context

Deployment notes

[TWJW-SANGER]

Thanks @KatyTaylor.
My preference is probably entry at the Choose Workflow screen.

Other possible acceptance criteria might be:

• Consider how the project/cost code can be corrected once set. (Probably FreshService ticket but best to be explicit).
• Identify where cost codes would need to be updated for correction in downstream system or not e.g. mlwh_events ?
• Document/Share knowledge of how this might be done with Neil.

[KatyTaylor]

@TWJW-SANGER thanks for the ideas. I think that correction of the project/cost code for these submissions will be the same as for any other submissions - because the data in the backend is all the same - the only difference is how we are creating that data (from Limber via API, rather than in SS via spreadsheet). Worth making sure Neil knows this though as he'll be less familiar with 'automated' submissions. I'll add a note on this documentation page and an acceptance criteria to update the page where needed as part of the story.

[KatyTaylor]

From Liz E email:

For this one, we can use the system we already use for the SSR to provide us with the project information we need. They provide us with request details now via a Google Sheet schedule, and we create paperwork from this, so no need to engineer a way to convey the information from SSR to us. But will would still need a place to add the cost code for the work we are currently undergoing.

[KatyTaylor]

Ticked off acceptance criteria "Decide on a design for getting the project id into the LCM Triomics submissions" because it feels from above comments like the way to go is a box on the Limber submission UI asking them to enter the project / cost code. Easiest for us would be the project - but if it's easier for the users we could do a cost code search instead.

Update:

Looked into the data. 421 cost codes relate to multiple projects - it is very much not a 1:1 relationship. For instance, searching for cost code 'S4699' in Sequencescape gives 20 related projects https://training.sequencescape.psd.sanger.ac.uk/searches?type=Project&q=S4699.

Had a conversation with Liz E. They can ask the SSR to supply them with project id, cost code or whatever we need. My suggested solution would be to get them to enter project id, then query and display the cost code so they can double check it's correct. (Entering project id with no feedback seems risky as typos could be dangerous). Alternative is to let them enter cost code and then query and display a dropdown of related projects for them to pick - but could be awkward UX with a dropdown of 20 or more.