Refactor Optimus Parameterization with respect to input chemistry

[kbergin]

Why do we want to do this?

Required to release this pipeline to production

The Optimus pipeline work done during the pipeline surge to support 10X V3 as a boolean V2 vs V3. We know that we plan to extend Optimus to analyze more datatypes, so we think we should extend this parameterization to more easily support more assays.

Where to start?

• Follow up discussion with Saman and Rex to confirm agreement with parametrization
• Modify Optimus WDL to accept the new parametrization (default to V2 to avoid breaking pipeline)

AC:

• Optimus is more extensible to other assay inputs
• A string parameter dictates the input data chemistry, instead of Boolean

┆Issue is synchronized with this Jira Dev Task

[kbergin]

➤ Nick Barkas commented:

I’ve done this, but adding a second PR test for the same pipeline is not currently supported. Need to talk with other team members to find out best way to do this

[kbergin]

➤ Nick Barkas commented:

Added functionality to support multiple types of tests in our tests (not just ‘PR’). The tests default to ‘PR’ so no change necessary to existing code. Added new test. Currently blocked by requirement to modify circleci config (approvers are away), lack of CB review and Eng review.

[kbergin]

➤ Nick Barkas commented:

Need CB approval from [~accountid:5ba003187ec0fb2e420b1942] or [~accountid:557058:f258569c-acb2-4486-a9e8-96dc2d9ec8d1] and response on eng review from [~accountid:557058:36e7f1cd-a074-4b69-8e9d-730ffdc144e9] to be able to proceed

[kbergin]

➤ Nick Barkas commented:

QA Instructions: Check the current merged code and confirm that the chemistry parameter is the in optimus: https://github.com/HumanCellAtlas/skylab ( https://github.com/HumanCellAtlas/skylab|smart-link )

[kbergin]

➤ Trevyn Langsford commented:

Chemistry parameter is there