diff --git a/ingest/README.md b/ingest/README.md
index b7116b7..ce5068d 100644
--- a/ingest/README.md
+++ b/ingest/README.md
@@ -7,6 +7,18 @@ If you have another data source or private data that needs to be formatted for
 the phylogenetic workflow, then you can use a similar workflow to curate your
 own data.
 
+## Run
+
+From within the `ingest` directory, run the workflow with:
+
+```
+nextstrain build .
+```
+
+This produces a `results` directory with the following outputs:
+- sequences.fasta
+- metadata.tsv
+
 ## Config
 
 The config directory contains all of the default configurations for the ingest workflow.
diff --git a/ingest/Snakefile b/ingest/Snakefile
index fb0a17a..121fe54 100644
--- a/ingest/Snakefile
+++ b/ingest/Snakefile
@@ -1,9 +1,31 @@
 # Use default configuration values. Override with Snakemake's --configfile/--config options.
 configfile: "config/defaults.yaml"
 
+rule all:
+    input:
+        "results/sequences.fasta",
+        "results/metadata.tsv",
+
 
 include: "rules/fetch_from_ncbi.smk"
 include: "rules/curate.smk"
 
+
+# If included, the nextclade rules will create the final metadata TSV by
+# joining the Nextclade output with the metadata.
+# However, if not including nextclade, we have to rename the subset metadata TSV
+# to the final metadata TSV.
 if "nextclade" in config:
     include: "rules/nextclade.smk"
+
+else:
+
+    rule create_final_metadata:
+        input:
+            metadata="results/subset_metadata.tsv"
+        output:
+            metadata="results/metadata.tsv"
+        shell:
+            """
+            mv {input.metadata} {output.metadata}
+            """