minor

Author: gitliver

pandora.py

@@ -156,7 +156,7 @@ def check_arg_scan(args):
     if '1' in args.steps and not ((args.mate1 and args.mate2) or args.bam or (args.single and (args.mate1 or args.bam))):
         print('[ERROR] Need --mate1 and --mate2 arguments OR --bam argument OR --single argument for Step 1')
         sys.exit(1)
-    if '1' in args.steps and ((not args.refstar) or (not args.refbowtie)):
+    if '1' in args.steps and not args.bam and ((not args.refstar) or (not args.refbowtie)):
         print('[ERROR] Need --refstar and --refbowtie arguments for Step 1')
         sys.exit(1)
     if '3' in args.steps and (not args.blastdb):