Move Nextstrain automation rules and configs to the ingest/build-conf…

…igs directory
nextstrain · Mar 8, 2024 · 85fae8f · 85fae8f
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diff --git a/ingest/README.md b/ingest/README.md
@@ -31,7 +31,7 @@ This will produce two files (within the `ingest` directory):
 Run the complete ingest pipeline and upload results to AWS S3 with
 
 ```sh
-nextstrain build . --configfiles defaults/config.yaml defaults/optional.yaml
+nextstrain build . --configfiles defaults/config.yaml build-defaults/nextstrain-automation/config.yaml
 ```
 
 ### Adding new sequences not from GenBank

diff --git a/ingest/defaults/optional.yaml → ...configs/nextstrain-automation/config.yaml b/ingest/defaults/optional.yaml → ...configs/nextstrain-automation/config.yaml
diff --git a/ingest/rules/upload.smk → ...-configs/nextstrain-automation/upload.smk b/ingest/rules/upload.smk → ...-configs/nextstrain-automation/upload.smk