Y25-100 - CITE-seq pipeline variation

[KatyTaylor]

User story

As a lab user of the scRNA Core (cDNA Prep) pipeline, I would like to be able to distinguish GEMs plates that are going for just gene expression from those that are going for CITE-seq library prep as well, so that I remember to use a different primer when creating the PCR plates.

Who are the primary contacts for this story

Katy, Andrew, Abby

Who is the nominated tester for UAT

Abby

Acceptance criteria

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

• New plate purpose 'LRC GEM-X 5p GEMs Input CITE'
• Test that the purpose name is not too long for the barcode label (discuss with Abby if it is)
• Above plate purpose can be uploaded by the "scRNA Core Pools Plate" manifest (must be a 'stock plate')
• Above plate purpose can be used in a 'Limber-Htp - scRNA Core cDNA Prep GEM-X 5p GEMs Input' submission (add to 'acceptable purposes' of the request type)
• Above plate purpose can enter the 'scRNA Core cDNA Prep GEM-X 5p GEMs Input' Limber pipeline (see suggested config in Additional Context)
• Any bed verifications or driver files that are associated with the existing 'LRC GEM-X 5p GEMs Input' plate purpose are also associated with the new one.

Additional context

Suggested change to pipeline config:

scRNA Core cDNA Prep GEM-X 5p GEMs Input:
  pipeline_group: scRNA Core cDNA Prep
  filters:
    request_type_key: limber_scrna_core_cdna_prep_gem_x_5p_gems_input
  relationships:
    LRC GEM-X 5p GEMs Input: LRC GEM-X 5p cDNA PCR
    LRC GEM-X 5p GEMs Input CS: LRC GEM-X 5p cDNA PCR     # new line
    LRC GEM-X 5p cDNA PCR: LRC GEM-X 5p cDNA PCR XP

Story illustrated in diagram form:

The plan for the future is to build the CITE-seq line properly into the LIMS (the dotted lines on the diagram), including being able to specify at an earlier entrypoint whether CITE-seq is requested. This story is a quick fix to avoid lab mistakes.