Many reference databases are out of date

[willbradshaw]

Many of the reference databases used in the index workflow are out-of-date, typically from late 2022. We need to update them to newer versions.

Reference files to update:

• ref/human_viruses.tsv
• Reference genomes (human, cow, etc)
• SILVA rRNA databases
• NCBI taxdump file
• Kraken reference db

[willbradshaw]

As of 2024-06-19, these have all been updated in the dev branch, and will be updated in master as soon as that branch is ready to merge.

I'd like to add more information about these references, and how to check for new ones, to the documentation, but that's a separate issue.