Fixes the phylogenetic clean rule such that USVI data is not inadvert…

…ently removed #38
nextstrain · Feb 27, 2024 · 70a9f8c · 70a9f8c
2 parents 86012b2 + 06ade1e
commit 70a9f8c
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
@@ -19,7 +19,10 @@ if "custom_rules" in config:
 rule clean:
     """Removing directories: {params}"""
     params:
-        "data ",
+        "data/metadata.tsv* ",
+        "data/sequences.fasta* ",
+        "data/metadata_all.tsv ",
+        "data/sequences_all.fasta ",
         "results ",
         "auspice"
     shell: