Resolve bug fro bowtie SE rule

files/Snakefile

@@ -411,8 +411,8 @@ rule bowtie_SE:
     params:
         indexPrefix = config["bowtie_index_path"]+"/index",
         mult_align_limit = config["bowtie_mult_align_limit"],
-        best = config["bowtie_best"],
-        strata = config["bowtie_strata"]
+        best = "--best" if (config["bowtie_best"]) else "",
+        strata = "--strata" if (config["bowtie_strata"]) else ""
     shell:
         "bowtie "
         "--threads {threads} "