Phylogenetic updates to match pathogen-repo-guide

joverlee521 commented 4 months ago

Includes major file restructuring within the phylogenetic workflow to match the pathogen-repo-guide:

rename workflow/snakemake_rules/ to rules/
rename config/ to defaults/
separation of custom build-configs
split cores.smk into separate snakefiles
misc. small updates - see commits for details

I had originally wanted to create a default config YAML as part of this PR. Then remembered this was already done in https://github.com/nextstrain/mpox/pull/173 and changed back to not use a default config in https://github.com/nextstrain/mpox/pull/171/commits/50194209c1163d0d3e1f7dbe22a228fd7ce27258...

I'll leave this potentially controversial change to another PR. It will most likely involve some changes to the config schema as well as I was finding some potentially confusing uses of the config parameters (e.g. other_filters for non_b1 vs b1).

joverlee521 commented 4 months ago

Rebased to pull in changes from #239.

Running trial builds for

[x] mpxv -> deployed to staging
[x] hmpxv1 -> deployed to staging
[x] hmpxv1-big -> deployed to staging

joverlee521 commented 4 months ago

Thanks for the review @j23414! I'll merge and monitor the automatic builds over week.

If there are issues with the removal of LAPIS, we can always revert the change in the future.

nextstrain / mpox

Phylogenetic updates to match pathogen-repo-guide #238