DPL-251 Improve automatic sample sheet generation [L]

[JamesGlover]

User story

As a traction user, I would like the sample sheets to contain updated information to assist with run setup.

Sequencing of Microbial, HiFi and ULI libraries. If binding kit v2.2 is used we need to be able to specify Adaptive Loading/ Loading Target ‘Loading Target (P1 + P2)’ in run design, per well (Default set to: 0.85). I mentioned to Ben a while ago in an email when we were initially looking at the incompatibility with the latest version of SMRTLink. There is now a new option available as part of the run design/ csv setup (I think has been available since SMRTLink 10.0), We can now set ‘Application’. With our current csv file output this defaults to ‘custom’. However, we could for IsoSeq samples or any sample once we have appropriate flags in place, set the application to ‘IsoSeq Method’ or appropriate other application. I was hoping that this would automatically set the correct default values for other aspect for the run design but on further testing this does not appear to be the case. I have now played around with the traction generated sample sheet csv and currently SMRTLink detects that v2.2 binding kit is being used so automatically sets ‘Use Adaptive Loading’ to YES and ‘Loading Target (P1+ P2) to 0.75 but I think we need to be able to control these settings within TRACTION. These will require additional options to be present when we set up the run per well. Once we have library flags in place it would be good to define specific defaults for each library type to minimise run setup errors.

Who are the primary contacts for this story
Craig C
James W

Acceptance criteria
To be considered successful the solution must allow:

• Y24-308 - As developers we would like to Migrate existing library_type column on pacbio_request to an association as currently it is a text column which is less maintainable #1429
• DPL-251-1 - Add Use Adaptive Loading and Loading Target (P1+ P2) to CSV [M] #731

Dependencies
We will have a matching story in traction UI to add the corresponding fields.

Additional context

Currently library types for a given pipeline are stored in the front-end, however we may wish to move this to traction-service to allow these options to be updated without redeployment. This will involve creating libraries as first class citizens, associated with pipelines. This would also allow us to associate tag-groups with library-types, rather then pipelines, streamlining library creation.