ENH: Allow pathogen-repo-ci to invoke workflow in subfolder

corneliusroemer commented 1 year ago

Current pathogen-repo-ci seems to assume that we don't need to customize workdir in nextstrain build ., i.e. we can't set nextstrain build foobar.

Our nextstrain/pathogen-repo-template, however, puts the main workflow in a folder. So we should add that feature.

A clear and concise description of what you want to happen

Tried in #57 but introduce a bug in upload-artifact. Tried to address in #62 but couldn't get it to work.

[ ] Reenable monkeypox again for augur CI once this is resolved (disabled in https://github.com/nextstrain/augur/pull/1324)

victorlin commented 8 months ago

zika no longer has a top-level workflow, increasing the need for this. I'll make PRs to disable it from all CI for now.

joverlee521 commented 3 months ago

nextstrain / .github