pathogen-repo-ci: add tests for `nextstrain run`

[joverlee521]

Context

Motivated by accidentally breaking nextstrain run compat in measles (nextstrain/measles#73, nextstrain/measles#100).

Description

Ideally, we'd check the nextstrain-pathogen.yaml file for nextstrain run compatibility and automatically test the workflows that are marked as compatible. Maybe a dynamic matrix of workflows?

Then set up and run the workflows with the currently commit hash of the CI run.

nextstrain setup <pathogen>@<commit>
nextstrain run <pathogen> <workflow> /tmp/<workflow>-output

Open questions

1. how do we limit the runtime of the nextstrain run tests, e.g. use example data?
2. related to [1], should we limit how many workflows to test?

[victorlin]

Could we add another job in pathogen-repo-ci named nextstrain-run, analogous to nextstrain-build? It can use the same example data and be conditional on nextstrain run support.

[joverlee521]

Could we add another job in pathogen-repo-ci named nextstrain-run, analogous to nextstrain-build?

Ah, so similarly limit testing to only ingest, phylogenetic, and nextclade workflows? One small issue with that is the nextstrain run workflows can be arbitrarily named (e.g. nextstrain/mpox#330 uses phylogenetic/all-clades). We could add an input that defines the exact workflows to test for nextstrain run.

It can use the same example data and be conditional on nextstrain run support.

It can use the same example data if it exists. I think we'd have to move the example files from the repo source to the analysis directory or resolve paths to the example data somehow for nextstrain run to have access.