[TheiaProk] upgrade ANI database to RGDv3 to match PN2.0

[kapsakcj]

🆒

📌 Explain the Request

Currently the ANI task in TheiaProk uses CDC EDLB's Reference Genome Database version 2 (RGDv2) for ANI on enteric pathogens.

• Docker image and some info https://github.com/StaPH-B/docker-builds/tree/master/mummer/4.0.0-RGDv2
• paper describing database: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1225207/full

However, a new version (v3) is being used in PN2.0 platform that includes more reference genomes for various taxon (more salmonella, more Vibrio, probably others that I'm unaware of)

A PHL partner requested that we upgrade to the v3 database so they will be reaching out to CDC about getting the updated list of NCBI accessions for these genomes. I don't believe the db is described publicly in a paper or elsewhere

This will require:

• creating a new docker image with RGDv3 genomes via StaPH-B/docker-builds
  • copy docker image to our GAR
• updating the ANI task to utilize this new docker image
• test TheiaProk with variety of enteric pathogens

[kapsakcj]

waiting to receive details on the database