Toil and toil-vg both want the `--config` option

[adamnovak]

I'm trying to update the old toil-vg workflow to current Toil, and I am getting errors like this because of a duplicate --config option:

Traceback (most recent call last):
  File "/Users/anovak/workspace/vg/.env/bin/toil-vg", line 7, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/anovak/workspace/vg/.env/lib/python3.12/site-packages/toil_vg/vg_toil.py", line 434, in main
    args = parse_args(sys.argv[1:])
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/anovak/workspace/vg/.env/lib/python3.12/site-packages/toil_vg/vg_toil.py", line 81, in parse_args
    pipeline_subparser(parser_run)
  File "/Users/anovak/workspace/vg/.env/lib/python3.12/site-packages/toil_vg/vg_toil.py", line 169, in pipeline_subparser
    add_common_vg_parse_args(parser_run)
  File "/Users/anovak/workspace/vg/.env/lib/python3.12/site-packages/toil_vg/vg_common.py", line 85, in add_common_vg_parse_args
    parser.add_argument('--config', default=None, type=str,
  File "/Users/anovak/workspace/vg/.env/lib/python3.12/site-packages/configargparse.py", line 1403, in add_argument
    action = self.original_add_argument_method(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/python@3.12/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/argparse.py", line 1500, in add_argument
    return self._add_action(action)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/python@3.12/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/argparse.py", line 1885, in _add_action
    self._optionals._add_action(action)
  File "/opt/homebrew/Cellar/python@3.12/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/argparse.py", line 1705, in _add_action
    action = super(_ArgumentGroup, self)._add_action(action)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/homebrew/Cellar/python@3.12/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/argparse.py", line 1514, in _add_action
    self._check_conflict(action)
  File "/opt/homebrew/Cellar/python@3.12/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/argparse.py", line 1654, in _check_conflict
    conflict_handler(action, confl_optionals)
  File "/opt/homebrew/Cellar/python@3.12/3.12.11/Frameworks/Python.framework/Versions/3.12/lib/python3.12/argparse.py", line 1663, in _handle_conflict_error
    raise ArgumentError(action, message % conflict_string)
argparse.ArgumentError: argument --config: conflicting option string: --config

Toil added ConfigArgParse and its --config option after the workflow was already using a --config option itself.

We should let the workflow rename Toil's config option out of the way. (We might actually want an option namespacing system for all of Toil's options, somehow.)

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1795