--- a/CSP2/bin/chooseRefs.py	Tue Dec 03 16:35:35 2024 -0500
+++ b/CSP2/bin/chooseRefs.py	Wed Dec 04 12:50:59 2024 -0500
@@ -83,9 +83,9 @@
     return [file_path,contig_count,assembly_bases,n50,n90,l50,l90]
 
 parser = argparse.ArgumentParser(description='Choose reference isolates based on FASTA metrics and mean distances.')
-parser.add_argument('--ref_count', type=int, help='Number of reference isolates to select')
+parser.add_argument('--ref_count', type=int, default=1, help='Number of reference isolates to select')
 parser.add_argument('--mash_triangle_file', type=str, help='Path to the mash triangle file')
-parser.add_argument('--trim_name', type=str, help='Trim name')
+parser.add_argument('--trim_name', type=str, default="", help='trim name')
 args = parser.parse_args()
 
 ref_count = args.ref_count