Multiome: include paired/unpaired assay check in process-fragment instead of as a separate cli command

[brianraymor]

Context

Reported by @brian-mott on sci-data-eng:

For local validation, it makes sense to have the paired/unpaired assay check as part of process-fragment instead of a separate cli command. I could also spend all that time validating, not realize the assay terms are incorrect, then fail at upload/ingestion, and it would have been easy to catch in one cli call early in the validation process