nextstrain-internal: Add docs for automating pathogen workflows

docs/nextstrain-internal/README.md

@@ -10,4 +10,5 @@ This directory holds documentation that is intended to be used by the internal N
 
 Docs on how the team uses GitHub Action workflows to automate pathogen repos.
 
+- [Automated pathogen workflows](automated-pathogen-workflows.md)
 - [Pathogen repo CI](pathogen-repo-ci.md)

docs/nextstrain-internal/automated-pathogen-workflows.md

@@ -0,0 +1,30 @@
+# Automated pathogen workflows
+
+GitHub Action workflows can be scheduled to run at a specific cadence which is
+useful for automating pathogen workflows.
+
+## Using `pathogen-repo-build`
+
+Nextstrain maintains a reusable [pathogen-repo-build][] GH Action workflow that
+can be used to set up automated pathogen workflows.
+
+The [pathogen-repo-build][] is very flexible to allow running of a variety of
+pathogen workflows. The main input option `run` allows the GH Action workflow
+to run any shell command, usually `nextstrain build ...`. See the description
+for other input options in the [pathogen-repo-build][] workflow.
+
+### Set up AWS credentials
+
+The [pathogen-repo-build][] is able to automatically generate short-lived AWS
+credentials for a [list of supported pathogens][]. Please follow
+[instructions in the infra repo][] to add a new pathogen to the list.
+
+Once this is done, the GH Action workflow will have credentials to run `aws s3`
+commands within the build runtime for a [specific list of S3 paths for the pathogen][]
+and have the option to run jobs using the Nextstrain `aws-batch` runtime.
+
+
+[instructions in the infra repo]: https://github.com/nextstrain/infra?tab=readme-ov-file#how-to-add-a-new-pathogen-repository-for-use-with-pathogen-repo-build
+[list of supported pathogens]: https://github.com/nextstrain/infra/blob/main/env/production/locals.tf
+[pathogen-repo-build]: https://github.com/nextstrain/.github/blob/HEAD/.github/workflows/pathogen-repo-build.yaml
+[specific list of S3 paths for the pathogen]: https://github.com/nextstrain/infra/blob/main/env/production/aws-iam-policy-NextstrainPathogen%40.tf