--- a/snippy_core_wrapper.py	Mon Jan 21 15:18:21 2019 -0500
+++ b/snippy_core_wrapper.py	Mon Jan 21 15:46:37 2019 -0500
@@ -22,24 +22,25 @@
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
-    parser.add_argument('inputs', nargs='+')
+    parser.add_argument('-i', '--indirs', nargs='+')
     args = parser.parse_args()
 
     snippy_core_command_line = ['snippy-core', '--ref', args.ref]
 
-    for input in args.inputs:
-        bn = os.path.basename(input)
-        sys.stderr.write(input + '\n')
-        copyfile(input, bn)
-        sys.stderr.write('\n'.join([input, bn]) + '\n')
-        subprocess.run(['tar', '-xf', bn])
+    for indir in args.indirs:
+        base_name = os.path.basename(indir)
+        sys.stderr.write(indir + '\n')
+        copyfile(indir, base_name)
+        sys.stderr.write('\n'.join([indir, base_name]) + '\n')
+        subprocess.run(['tar', '-xf', base_name])
 
-    test_list = [f.path for f in os.scandir() if f.is_dir() ]
+    extracted_dirs = [f.path for f in os.scandir() if f.is_dir() ]
 
-    for dir in test_list:
-        snippy_core_command_line.append(dir)
+    for extracted_dir in extracted_dirs:
+        snippy_core_command_line.append(extracted_dir)
 
     print(snippy_core_command_line)
     subprocess.run(snippy_core_command_line)
+
 if __name__ == '__main__':
     main()