Y24-136 - ANOSPP - Creation of configuration for submission and pipeline

[andrewsparkes]

User story
As R&D we would like the ANOSPP pipeline created in LIMS

Who are the primary contacts for this story
Scott T
Andrew S

Who is the nominated tester for UAT
Scott T

Acceptance criteria
To be considered successful the solution must allow:

• creation of a submission template for 'ANOSPP Lysis' on the LANS-96 Stock plate, including request type and LANS-96 Stock plate purpose (in Sequencescape)
• pipeline configuration for the ANOSPP Lysis part of the pipeline in Limber configuration (pipeline and purposes), including
  • pipeline for lysis steps
  • plate purposes LANS-96 Stock and LANS-96 Lysate
  • label printing for the LANS-96 Lysate plate will need a double label the same as in Bioscan, which includes the Partner ID + -SDC suffix on the second label (allows the customer to relate the plate back to their original on return of the plate)
  • robot bed verifications (see details in additional context below)
• config change for GBS submission to allow submission of LANS-96 Lysate plates for GBS library prep
• modification of existing robot bed verification for GBS to allow sources to be either LANS-96 Lysate or GBS-96 Stock (see details in additional context below)
• new integration suite test to cover the ANOSPP Lysis pipeline plus submission into GBS and combination with GBS-96 Stock plates to create a 384-well GBS PCR1 plate (i.e. test submission and bed verification steps are ok)

Dependencies
This story is blocked by the following dependencies:
Some interaction with story sanger/sequencescape#4155, as both need the ANOSPP LANS-96 Stock plate to be defined in Sequencescape.

References
This story has a non-blocking relationship with:
None

Additional context
See Scott Ts document on ANOSPP here

This story could be split into smaller chunks, but is mostly a duplication of existing configuration done in Bioscan.

• Pipeline config Steps:
  • LANS-96 Stock
    • robot: name ANOSPP Beckman LANS-96 Stock Preparation, equivalent of existing 'Bioscan Beckman LILYS-96 Stock Preparation' (same beds)
  • LANS-96 Stock to LANS-96 Lysate
    • simple stamp, no controls added
    • robot: name ANOSPP Beckman LANS-96 Stock => LANS-96 Lysate, equivalent of existing 'Bioscan Beckman LILYS-96 Stock => LBSN-96 Lysate' (same beds)
    • LANS-96 Lysate plate has double label with -SDC suffix like in Bioscan
  • LANS-96 Lysate - SSR creates GBS library prep submission on this plate
    • LANS-96 Lysate purpose as an acceptable purpose for current GBS submission: see limber_gbs in config/default_records/request_types/004_limber_high_throughput.yml
  • LANS-96 Lysate to GBS PCR1
    • robot: modify existing bed verification named Mosquito GBS-96 Stock => GBS PCR1 and rename to Mosquito GBS-96 Stock or LANS-96 Lysate => GBS PCR1
      • modify to allow user to combine mixture of 1-4 x LANS-96 Lysate or GBS-96 Stock plates together (use source purpose array syntax in the bed verification)
    • check existing labware creator used to make the GBS PCR1 plate does not mind having a mixture of two different source plate purposes (LabwareCreators::QuadrantStampPrimerPanel)