Define workflow dependencies

[victorlin]

Context

This workflow only works with specific versions of software. There is a Conda environment file (workflow/envs/nextstrain.yaml) however this has issues:

1. It is only meant for use within Snakemake (--use-conda, rule.conda)
2. It acts more like a "lock" file with exact version pins
3. It doesn't document the version constraint on Snakemake (the workflow doesn't support Snakemake 8.x)

Possible solutions

1. Create a list of workflow dependencies as supported ranges. Drafting that here:

   • Augur: >= 22.0.1 (ref)
   • Snakemake: ?? <= 8.0.0
   • ?

2. Check at the start of running the workflow. This is what's already done in other workflows such as nextstrain/mpox@d9f6d47

3. [from @tsibley on Slack] We can put that declaration in nextstrain-pathogen.yaml and then use that information in the Snakefile if we desire. This then also lets nextstrain build and/or nextstrain run (and other tooling) verify it too.

Related issues

• Workflow fails on Snakemake 8.x #1114
• Report Augur versions on error without --use-conda #611
• Introduce minimum augur version check #1070