diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
new file mode 100644
index 0000000..520a4ae
--- /dev/null
+++ b/.github/workflows/ci.yaml
@@ -0,0 +1,12 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ci:
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
diff --git a/ingest/build-configs/ci/config.yaml b/ingest/build-configs/ci/config.yaml
new file mode 100644
index 0000000..4b15515
--- /dev/null
+++ b/ingest/build-configs/ci/config.yaml
@@ -0,0 +1,6 @@
+# TODO: If the ingest workflow ever runs too long, we should figure out a way
+# to subset the ingest data. Currently, the CI just runs the default ingest workflow.
+
+# Snakemake requires at least one top level key in a config file, so including
+# a bogus key here that should not be used anywhere in the Snakemake workflow
+bogus_ci_config: "bogus_ci_config"
diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml
deleted file mode 100644
index de89c67..0000000
--- a/phylogenetic/build-configs/ci/config.yaml
+++ /dev/null
@@ -1,7 +0,0 @@
-# This configuration file contains the custom configurations parameters
-# for the CI workflow to run with the example data.
-
-# Custom rules to run as part of the CI automated workflow
-# The paths should be relative to the phylogenetic directory.
-custom_rules:
-  - build-configs/ci/copy_example_data.smk