code: def _add_inputs_to_kwargs(args, kwargs, parser):
      
      inputs = [x for x in [args.global_config, args.fc_dir] + args.run_config
                if x is not None]
      global_config = "bcbio_system.yaml"  # default configuration if not specified
      if kwargs.get("workflow", "") == "template":
          if args.only_metadata:
              inputs.append("--only-metadata")
          if args.force_single:
              inputs.append("--force-single")
          if args.separators:
              inputs.extend(["--separators", args.separators])
          kwargs["inputs"] = inputs
          return kwargs
      elif len(inputs) == 1:
          if os.path.isfile(inputs[0]):
              fc_dir = None
              run_info_yaml = inputs[0]
          else:
              fc_dir = inputs[0]
              run_info_yaml = None
      elif len(inputs) == 2:
          if os.path.isfile(inputs[0]):
              global_config = inputs[0]
              if os.path.isfile(inputs[1]):
                  fc_dir = None
                  run_info_yaml = inputs[1]
              else:
                  fc_dir = inputs[1]
                  run_info_yaml = None
          else:
              fc_dir, run_info_yaml = inputs
      elif len(inputs) == 3:
          global_config, fc_dir, run_info_yaml = inputs
      elif args.version:
          print(version.__version__)
          sys.exit()
      else:
          print("Incorrect input arguments", inputs)
          parser.print_help()
          sys.exit()
      if fc_dir:
          fc_dir = os.path.abspath(fc_dir)
      if run_info_yaml:
          run_info_yaml = os.path.abspath(run_info_yaml)
      if kwargs.get("workflow"):
          kwargs["inputs"] = inputs
      kwargs["config_file"] = global_config
      kwargs["fc_dir"] = fc_dir
      kwargs["run_info_yaml"] = run_info_yaml
      return kwargs
docs: Convert input system config, flow cell directory and sample yaml to kwargs.
  
      Handles back compatibility with previous commandlines while allowing flexible
      specification of input parameters.