diff --git a/ingest/Snakefile b/ingest/Snakefile
index 97e010c..2569ce6 100644
--- a/ingest/Snakefile
+++ b/ingest/Snakefile
@@ -25,3 +25,8 @@ rule clean:
         """
         rm -rfv {params.targets}
         """
+
+# Import custom rules provided via the config.
+if "custom_rules" in config:
+  for rule_file in config["custom_rules"]:
+    include: rule_file
diff --git a/ingest/build-configs/nextstrain-automation/README.md b/ingest/build-configs/nextstrain-automation/README.md
deleted file mode 100644
index 9175569..0000000
--- a/ingest/build-configs/nextstrain-automation/README.md
+++ /dev/null
@@ -1,47 +0,0 @@
-# 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][] 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][] 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:
-
-```bash
-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!
-
-[config.yaml]: ./config.yaml
-[upload.smk]: ./upload.smk
diff --git a/ingest/build-configs/nextstrain-automation/config.yaml b/ingest/build-configs/nextstrain-automation/config.yaml
index c24191c..aefd2fa 100644
--- a/ingest/build-configs/nextstrain-automation/config.yaml
+++ b/ingest/build-configs/nextstrain-automation/config.yaml
@@ -1,9 +1,5 @@
-# This configuration file should contain all required configuration
-# parameters for the ingest workflow to run with additional Nextstrain
-# automation rules.
-
-# Custom rules to run as part of the Nextstrain automated workflow The
-# paths should be relative to the ingest directory.
+# Custom rules to run as part of the Nextstrain automated workflow.
+# The paths should be relative to the ingest directory.
 custom_rules:
   - build-configs/nextstrain-automation/upload.smk
 
@@ -13,7 +9,7 @@ custom_rules:
 cloudfront_domain: "data.nextstrain.org"
 
 # Nextstrain AWS S3 Bucket with pathogen prefix
-s3_dst: "s3://nextstrain-data/files/workflows/seasonal-cov"
+s3_dst: "s3://nextstrain-data/files/workflows/yellow-fever"
 
 # Mapping of files to upload
 files_to_upload:
@@ -21,4 +17,3 @@ files_to_upload:
   metadata.tsv.zst: results/metadata.tsv
   sequences.fasta.zst: results/sequences.fasta
   alignments.fasta.zst: results/alignment.fasta
-  translations.zip: results/translations.zip
diff --git a/ingest/build-configs/nextstrain-automation/upload.smk b/ingest/build-configs/nextstrain-automation/upload.smk
index cf1c2c5..0c21284 100644
--- a/ingest/build-configs/nextstrain-automation/upload.smk
+++ b/ingest/build-configs/nextstrain-automation/upload.smk
@@ -28,7 +28,7 @@ rule upload_to_s3:
         s3_dst=config["s3_dst"],
         cloudfront_domain=config["cloudfront_domain"],
     shell:
-        """
+        r"""
         ./vendored/upload-to-s3 \
             {params.quiet} \
             {input.file_to_upload:q} \
@@ -39,6 +39,9 @@ rule upload_to_s3:
 
 rule upload_all:
     input:
-        uploads=[f"results/upload/{remote_file}.upload" for remote_file in config["files_to_upload"].keys()],
+        uploads=[
+            f"results/upload/{remote_file}.upload"
+            for remote_file in config["files_to_upload"].keys()
+        ],
     output:
         touch("results/upload_all.done"),