add allele registry step in update vat with samples task

[jklugherz]

options for where in pipeline to register the alleles (I implemented option B here):

A) in a new airflow/luigi task downstream of the annotations table tasks

• doesn't really jive with luigi expecting a file output, and I'm not sure how to get the variants to register (I could pass the variants to register between tasks with the airflow xcom, or use the callset from the input variable to re-create the new_variants_ht)

B) within the update annotations table task

• I can easily use the new_variants_ht to get what I need to call the register endpoint with
• However, this logic doesn't necessarily belong in the task and really a new step should mean a new pipeline task

[bpblanken]

yeah, just in a brief look at this, my gut is leaning towards option A. The UpdateAnnotations task is already more crowded than it should be (VEP at some point was its own task... but got moved here when we moved things around).

rather than Xcoms I'd recommend a new intermediate file, similar to what we're doing with the WriteImportedCallset, of just the new variants. It probably also makes sense for VEP to be there!