Y24-327 - scRNA Core bulk test

[KatyTaylor]

User story As a user of the scRNA Core pipeline, I would like to be confident that the pipeline will work for the volume of samples and size of pools that I'm planning to put through the end to end test.

Who are the primary contacts for this story Abby, Andrew, Katy

Who is the nominated tester for UAT This doesn't need UAT, it just needs the test to pass in the UAT and/or training envs.

Acceptance criteria To be considered successful the solution must allow:

• [ ] Discuss this story with Abby when she's back on 23/9/24. If she is planning to do a realistic test manually for UAT, then it's probably not worth creating this new automated test, and we should focus on completing the other stories.
• [ ] Create or update the scRNA Core Integration Suite tests to be close to what R&D are planning for their end to end test:
  • [ ] 10 samples per pool, 8 pools per chip
  • [ ] 24 samples per pool, 8 pools per chip

Dependencies The development of the test is not blocked by the following, however we need to check it passes after the following are done:

• https://github.com/sanger/limber/issues/1909
• https://github.com/sanger/limber/issues/1914

[yoldas]

For recent UAT sessions, we have used the following integration suite branch: scrna_core_pipeline_volume_test, particularly the test spec/limber/scrna_core_volume_spec.rb

It allows specifying parameters for number of runs, number of vac tubes each run, etc. However it only covers the usual 'scRNA Core entry point 1 - LRC Blood Vac tubes' scenario. It has all steps in separate methods so disabling calls to them becomes easy in the main flow.

I am looking into

• Well failing makes it difficult to track later stages and causes an error in full plates.
• Getting updates from the original scRNA Core tests, such as adding bulk submission step.