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 [It can be configured to do this]

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

• Y24-313 - PBMC donor pooling - use requested number of samples per pool #1909
• Y24-319 - Pooling driver file tweaks #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.

[yoldas]

I have written a volume test which covers Blood Banking, cDNA Prep, and Library Prep. It can be configured using the let blocks. I have set the config to make 7 banking runs. From each run we pick 8 Seq and 2 Spare tubes. We also add 10 Input tubes to those to make 80 tubes going into pooling.
GitLab MR: https://gitlab.internal.sanger.ac.uk/psd/integration-suite/-/merge_requests/177

Local Run: ENVIRONMENT=local DEBUG_ON_FAIL=true bundle exec rspec spec/limber/scrna_core_volume_spec.rb

Running it against uat and training environments needs Sequencescape UAT action for randomised FluidX barcodes to be deployed (merged into develop already).

[yoldas]

The Sequencescape UAT action for generating FluidX barcodes is deployed to UAT. I will run the bulk test against UAT using GitLab.