diff --git a/Snakefile b/Snakefile
index 8843c4740b377d7c4e582d4565d7d1335920d0d9..a2c0133a9a811f9c7d120a0b25e201cd3fd9fe7e 100755
--- a/Snakefile
+++ b/Snakefile
@@ -41,7 +41,7 @@ RULES = os.path.join("workflow", "rules")
 #-------------------------------------------------------
 # list of all files in the directory 'input_dir'
 
-filenames = [f for f in glob.glob(config["input_dir"]) if match(r'.*'+config["input_mate"]+config["input_extension"]+'', f)] 
+filenames = [f for f in glob.glob(config["input_dir"]+"*") if match(r'.*'+config["input_mate"]+config["input_extension"]+'', f)] 
 
 if not filenames :
     raise ValueError("Please provides input fastq files")