Handle deprecated cohorts

[MattWellie]

Deletion for reference: https://github.com/populationgenomics/seqr-private/issues/215#issuecomment-2261973125

• Custom Cohorts are designed to be an immutable set of SG IDs, using a set of criteria.
• When samples & their relevant sequence data need to be deleted, we currently remove the corresponding CPG IDs from any cohorts that contain them
• The Cohorts are not marked as altered/deprecated - future analyses using the cohorts will use the new, reduced, sample set. The notion that the underlying cohort has changed is not stored anywhere.
• My understanding of the original CustomCohort design was that immutability was designed for this exact purpose - the pipeline wouldn't tolerate a CC where any of the component samples were withdrawn/inactive. By removing the samples from the cohorts completely we lose the ability to make this check

Questions:

1. Can we do the sample removal without removing the CPG ID from the CustomCohort? I'm not sure if this is valid within the database structure we have

   • when the pipeline pulls each custom cohort, it can check if each of the CPG IDs is still a current/valid sequencing group

2. If we do need to remove from a CustomCohort, can we mark the whole Cohort as inactive

   • we have an active boolean on a few other entities in the database, but not CCs (AFAIK).
   • If we need to pull samples/CPG IDs out of a Cohort, we should be able to mark the whole cohort as inactive, possibly with a reason to go with it

[vivbak]

Note @dancoates, to be moved to Metamist.