Separate out state-specific subsampling

[j23414]

Context

Separate out Washington-specific subsampling into a separate config

Description

Ideally the default build will be a global view of WNV, and focused builds (e.g. state specific subsampling) have more fine tuned subsampling in separate config files.

Examples

# Global build
nextstrain build ingest
nextstrain build phylogenetic

# WA specific builds
nextstrain build ingest --configfile wa-specific-config.yaml
nextstrain build phylogenetic --configfile wa-specific-config.yaml

Possible solution

Possible places to put the focused build configs based on prior art:

• ncov - config/{buildname}.yaml files
• mpox - phylogenetic/defaults/{buildname}/config.yaml
• use the custom configs folder based on pathogen-repo-guide - phylogenetic/build-configs/{build}/config.yaml
• another example of custom configs used for nextstrain-automation - phylogenetic/build-configs/*/config.yaml

[j23414]

After chatting with @DOH-LMT2303 about automating global and WA public facing trees, we're leaning towards the mpox style:

defaults/
  |_ global/
  | |_ auspice_config.json
  | |_ reference.gb
  | |_ include.txt
  |_ WA/
    |_ auspice_config.json
    |_ reference.gb
    |_ include.txt

Not necessarily as part of #30, since we may need to discuss some more design decisions and can reorganize the files in later PR(s).