diff --git a/tools/snap/snap.rule.snakefile b/tools/snap/snap.rule.snakefile
index 212ea9161828666ff32b0502b405c707ab20b7ff..ae8a8a4936ad068474f5d83552526198db08a04b 100755
--- a/tools/snap/snap.rule.snakefile
+++ b/tools/snap/snap.rule.snakefile
@@ -11,8 +11,6 @@ if config["SeOrPe"] == "PE":
             config["<step_name>__snap_threads"]
         params:
             command = config["<step_name>__snap_PE_command"],
-            #indexPrefix =  config["<step_name>__snap_index_output_dir"]+"/index",
-            #/patho_index/indexName.fna.hash 
             indexDir = lambda w, input: os.path.dirname([x for x in input.index if 'GenomeIndexHash' in x]),
             snap_seed_number = config["<step_name>__snap_seed_number"],
             snap_min_insert_size = config["<step_name>__snap_min_insert_size"],
@@ -47,7 +45,7 @@ elif config["SeOrPe"] == "SE":
             command = config["<step_name>__snap_PE_command"],
             snap_seed_number = config["<step_name>__snap_seed_number"],
             snap_disable_alt_awareness = "-A-" if config["<step_name>__snap_disable_alt_awareness"] else "",
-            snap_max_score_gap = config["<step_name>__snap_max_score_gap"]
+            snap_max_score_gap = config["<step_name>__snap_max_score_gap"],
             indexDir = lambda w, input: os.path.dirname([x for x in input.index if 'GenomeIndexHash' in x]),
         shell:
             "{params.command} "