diff --git a/Snakefile b/Snakefile
index b980edd9559fe6f103727734718c0e6e27251ce3..f7e3619a1d7a60f66c6ed491c6e438c9a2f12f51 100755
--- a/Snakefile
+++ b/Snakefile
@@ -174,14 +174,14 @@ if config["bowtie2_mapping"]["do"]:
     bowtie2_index_fasta = unpack(mapping_index)
     bowtie2_index_log = "02-Mapping/bowtie2/logs/bowtie2_{REF}_indexing.log"
     if config["genome"]["host_mapping"] and config["genome"]["rRNA_mapping"] :
-        bowtie2_index_output_done = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["host_name"])
-        bowtie2_index_output_prefix = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["host_name"])
+        bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"],"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["host_name"]))
+        bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["host_name"]))
     elif not config["genome"]["host_mapping"] and config["genome"]["rRNA_mapping"] :
-        bowtie2_index_output_done = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["name"])
-        bowtie2_index_output_prefix = config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["name"])
+        bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}.1.bt2".format(config["genome"]["name"]))
+        bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{}/bowtie2/{{REF}}".format(config["genome"]["name"]))
     else:
-        bowtie2_index_output_done = config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2"
-        bowtie2_index_output_prefix = config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}"
+        bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2")
+        bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}")
                    
     include: os.path.join(RULES, "bowtie2_index.rules")