From 06ade1e2bbe4e5bf07cd1043affaf96a60976226 Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Mon, 26 Feb 2024 11:02:18 -0800
Subject: [PATCH] fix: phylo: clean rule removes the USVI data

---
 phylogenetic/Snakefile | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/phylogenetic/Snakefile b/phylogenetic/Snakefile
index da7fdd9..3612286 100644
--- 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: