Centralize existing pathogen build workflows

[joverlee521]

Context

We now have a centralized reusable GitHub Action workflow for running pathogen builds.

We should update existing pathogen build workflows to use the centralized workflow to make future maintenance easier for ourselves and to discover any pitfalls in reusable workflow that may have been overlooked during development.

Hopefully there shouldn't be any huge changes that need to happen to the reusable workflow, but better to discover them now than later when it's widely used.

Description

Here's a list of repos that should be updated to use the new workflow:

• monkeypox (Use pathogen-repo-build workflow for builds mpox#190)
• Overhaul GH Action workflows ncov-ingest#440
• ncov
• rsv (updated as part of ingest: Switch to NCBI Datasets CLI to fetch data rsv#37)
• seasonal-flu
• forecasts-ncov (Seq counts workflow forecasts-ncov#60 + Clean up workflows forecasts-ncov#62)

Examples

See example use of the reusable workflow in seasonal-flu

[genehack]

@joverlee521 looks like the only unticked box in the original TODO list is for ncov, and I see a merged PR against ncov ...is this issue maybe done?

[joverlee521]

@genehack The merged PR is for ncov-ingest which is a separate repo than ncov. The ncov GH Action workflows still need to be migrated.

[genehack]

The need to update the CI workflow in ncov has been moved to a new issue in the ncov repo.

Closing this issue out.

[joverlee521]

@genehack, I completely misread your previous issue! This is actually regarding the use of the pathogen-repo-build workflow. I've made a new issue to track the separate task: nextstrain/ncov#1113