diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 6fa98cd..12ce718 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
+      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 d599360..30c4777 100644
--- a/phylogenetic/Snakefile
+++ b/phylogenetic/Snakefile
@@ -1,5 +1,4 @@
-if not config:
-    configfile: "config/config_zika.yaml"
+configfile: "config/config_zika.yaml"
 
 rule all:
     input:
@@ -22,6 +21,12 @@ 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 0000000..495d778
--- /dev/null
+++ b/phylogenetic/profiles/ci/copy_example_data.smk
@@ -0,0 +1,21 @@
+rule copy_example_data:
+    input:
+        sequences="example_data/sequences.fasta",
+        metadata="example_data/metadata.tsv",
+        usvi_sequences="example_data/sequences_usvi.fasta",
+        usvi_metadata="example_data/metadata_usvi.tsv",
+    output:
+        sequences="data/sequences.fasta",
+        metadata="data/metadata.tsv",
+        usvi_sequences="data/sequences_usvi.fasta",
+        usvi_metadata="data/metadata_usvi.tsv",
+    shell:
+        """
+        cp -f {input.sequences} {output.sequences}
+        cp -f {input.metadata} {output.metadata}
+        cp -f {input.usvi_sequences} {output.usvi_sequences}
+        cp -f {input.usvi_metadata} {output.usvi_metadata}
+        """
+
+ruleorder: copy_example_data > decompress
+ruleorder: copy_example_data > decompress_usvi
\ 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 0000000..17bad21
--- /dev/null
+++ b/phylogenetic/profiles/ci/profiles_config.yaml
@@ -0,0 +1,2 @@
+custom_rules:
+  - profiles/ci/copy_example_data.smk