diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 9252f756..12ce7187 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -5,7 +5,24 @@ on:
   - pull_request
 
 jobs:
-  ci:
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@dec0880059017dac7facf100435c5737bf1386c8
+  pathogen-ci:
+    strategy:
+      matrix:
+        runtime: [docker, conda]
+    permissions:
+      id-token: write
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    secrets: inherit
     with:
-      workflow-root: phylogenetic
\ No newline at end of file
+      runtime: ${{ matrix.runtime }}
+      run: |
+        nextstrain build \
+          phylogenetic \
+          --configfile profiles/ci/profiles_config.yaml
+      artifact-name: output-${{ matrix.runtime }}
+      artifact-paths: |
+        phylogenetic/auspice/
+        phylogenetic/results/
+        phylogenetic/benchmarks/
+        phylogenetic/logs/
+        phylogenetic/.snakemake/log/
\ No newline at end of file
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
index a2ced232..9b8f998f 100644
--- a/phylogenetic/Snakefile
+++ b/phylogenetic/Snakefile
@@ -1,5 +1,4 @@
-if not config:
-    configfile: "config/config_dengue.yaml"
+configfile: "config/config_dengue.yaml"
 
 serotypes = ['all', 'denv1', 'denv2', 'denv3', 'denv4']
 
@@ -12,6 +11,12 @@ include: "rules/construct_phylogeny.smk"
 include: "rules/annotate_phylogeny.smk"
 include: "rules/export.smk"
 
+# Include custom rules defined in the config.
+if "custom_rules" in config:
+    for rule_file in config["custom_rules"]:
+
+        include: rule_file
+
 rule clean:
     """Removing directories: {params}"""
     params:
diff --git a/phylogenetic/profiles/ci/copy_example_data.smk b/phylogenetic/profiles/ci/copy_example_data.smk
new file mode 100644
index 00000000..4f11a7cd
--- /dev/null
+++ b/phylogenetic/profiles/ci/copy_example_data.smk
@@ -0,0 +1,14 @@
+rule copy_example_data:
+    input:
+        sequences="example_data/sequences_{serotype}.fasta",
+        metadata="example_data/metadata_{serotype}.tsv",
+    output:
+        sequences="data/sequences_{serotype}.fasta",
+        metadata="data/metadata_{serotype}.tsv",
+    shell:
+        """
+        cp -f {input.sequences} {output.sequences}
+        cp -f {input.metadata} {output.metadata}
+        """
+
+ruleorder: copy_example_data > decompress
\ No newline at end of file
diff --git a/phylogenetic/profiles/ci/profiles_config.yaml b/phylogenetic/profiles/ci/profiles_config.yaml
new file mode 100644
index 00000000..17bad213
--- /dev/null
+++ b/phylogenetic/profiles/ci/profiles_config.yaml
@@ -0,0 +1,2 @@
+custom_rules:
+  - profiles/ci/copy_example_data.smk