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+# Nextstrain automation
+
+> [!NOTE]
+> External users can ignore this directory!
+> This build config/customization is tailored for the internal Nextstrain team
+> to extend the core ingest workflow for automated workflows.
+
+## Update the config
+
+Update the [config.yaml](config.yaml) for your pathogen:
+
+1. Edit the `s3_dst` param to add the pathogen repository name.
+2. Edit the `files_to_upload` param to a mapping of files you need to upload for your pathogen.
+The default includes suggested files for uploading curated data and Nextclade outputs.
+
+## Run the workflow
+
+Provide the additional config file to the Snakemake options in order to
+include the custom rules from [upload.smk](upload.smk) in the workflow.
+Specify the `upload_all` target in order to run the additional upload rules.
+
+The upload rules will require AWS credentials for a user that has permissions
+to upload to the Nextstrain data bucket.
+
+The customized workflow can be run from the top level pathogen repo directory with:
+```
+nextstrain build \
+    --env AWS_ACCESS_KEY_ID \
+    --env AWS_SECRET_ACCESS_KEY \
+    ingest \
+        upload_all \
+        --configfile build-configs/nextstrain-automation/config.yaml
+```
+
+## Automated GitHub Action workflows
+
+Additional instructions on how to use this with the shared `pathogen-repo-build`
+GitHub Action workflow to come!