diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ff430bc
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,6 @@
+auspice/*
+logs/*
+benchmarks/*
+results/*
+.snakemake
+downloads
\ No newline at end of file
diff --git a/Snakefile b/Snakefile
new file mode 100644
index 0000000..05fe976
--- /dev/null
+++ b/Snakefile
@@ -0,0 +1,31 @@
+import datetime
+
+if "builds" in config:
+    rule all:
+        input:
+            expand("auspice/ncov_{build_name}.json", build_name=config["builds"].keys())
+
+    # Include rules to handle primary build logic from multiple sequence alignment
+    # to output of auspice JSONs for a default build.
+    include: "workflow/snakemake_rules/core.smk"
+
+    if "build_type" in config and config["build_type"]=="reference_build":
+        include: "workflow/snakemake_rules/reference_build.smk"
+
+rule clean:
+    message: "Removing directories: {params}"
+    params:
+        "results",
+        "auspice"
+    shell:
+        "rm -rfv {params}"
+
+rule clean_all:
+    message: "Removing directories: {params}"
+    params:
+        "results",
+        "auspice",
+        "downloads"
+    shell:
+        "rm -rfv {params}"
+    
\ No newline at end of file