Let Python workflows steal the --config option name

src/toil/common.py

@@ -740,6 +740,7 @@ def parser_with_common_options(
 def addOptions(
     parser: ArgumentParser,
     jobstore_as_flag: bool = False,
+    config_option: Optional[str] = None,
     cwl: bool = False,
     wdl: bool = False,
 ) -> None:
@@ -748,11 +749,15 @@ def addOptions(
 
     Support for config files if using configargparse. This will also check and set up the default config file.
 
+    User code should consider using Job.Runner.getDefaultArgumentParser() or Job.Runner.addToilOptions() instead.
+
     :param jobstore_as_flag: make the job store option a --jobStore flag instead of a required jobStore positional argument.
 
     :param cwl: Whether CWL options are expected. If so, CWL options won't be suppressed.
 
     :param wdl:  Whether WDL options are expected. If so, WDL options won't be suppressed.
+
+    :param config_option: If set, use this string for the Toil --config option instead of "config".
     """
     if cwl and wdl:
         raise RuntimeError(
@@ -801,7 +806,7 @@ def addOptions(
         raise
 
     # Add base toil options
-    add_base_toil_options(parser, jobstore_as_flag, cwl)
+    add_base_toil_options(parser, jobstore_as_flag, cwl, config_option)
     # Add CWL and WDL options
     # This is done so the config file can hold all available options
     add_cwl_options(parser, suppress=not cwl)

src/toil/job.py

@@ -2485,14 +2485,18 @@ class Runner:
         """Used to setup and run Toil workflow."""
 
         @staticmethod
-        def getDefaultArgumentParser(jobstore_as_flag: bool = False) -> ArgParser:
+        def getDefaultArgumentParser(
+                jobstore_as_flag: bool = False,
+                config_option: Optional[str] = None,
+            ) -> ArgParser:
             """
             Get argument parser with added toil workflow options.
 
             This is the Right Way to get an argument parser in a Toil Python
             workflow.
 
             :param jobstore_as_flag: make the job store option a --jobStore flag instead of a required jobStore positional argument.
+            :param config_option: If set, use this string for the Toil --config option instead of "config".
             :returns: The argument parser used by a toil workflow with added Toil options.
             """
             parser = ArgParser(formatter_class=ArgumentDefaultsHelpFormatter)
@@ -2501,14 +2505,17 @@ def getDefaultArgumentParser(jobstore_as_flag: bool = False) -> ArgParser:
 
         @staticmethod
         def getDefaultOptions(
-            jobStore: Optional[StrPath] = None, jobstore_as_flag: bool = False
+            jobStore: Optional[StrPath] = None,
+            jobstore_as_flag: bool = False,
+            config_option: Optional[str] = None,
         ) -> Namespace:
             """
             Get default options for a toil workflow.
 
             :param jobStore: A string describing the jobStore \
             for the workflow.
             :param jobstore_as_flag: make the job store option a --jobStore flag instead of a required jobStore positional argument.
+            :param config_option: If set, use this string for the Toil --config option instead of "config".
             :returns: The options used by a toil workflow.
             """
             # setting jobstore_as_flag to True allows the user to declare the jobstore in the config file instead
@@ -2518,7 +2525,8 @@ def getDefaultOptions(
                     "to False!"
                 )
             parser = Job.Runner.getDefaultArgumentParser(
-                jobstore_as_flag=jobstore_as_flag
+                jobstore_as_flag=jobstore_as_flag,
+                config_option=config_option,
             )
             arguments = []
             if jobstore_as_flag and jobStore is not None:
@@ -2531,6 +2539,7 @@ def getDefaultOptions(
         def addToilOptions(
             parser: Union["OptionParser", ArgumentParser],
             jobstore_as_flag: bool = False,
+            config_option: Optional[str] = None,
         ) -> None:
             """
             Adds the default toil options to an :mod:`optparse` or :mod:`argparse`
@@ -2545,8 +2554,13 @@ def addToilOptions(
 
             :param parser: Options object to add toil options to.
             :param jobstore_as_flag: make the job store option a --jobStore flag instead of a required jobStore positional argument.
+            :param config_option: If set, use this string for the Toil --config option instead of "config".
             """
-            addOptions(parser, jobstore_as_flag=jobstore_as_flag)
+            addOptions(
+                parser,
+                jobstore_as_flag=jobstore_as_flag,
+                config_option=config_option,
+            )
 
         @staticmethod
         def startToil(job: "Job", options) -> Any:

src/toil/options/common.py

@@ -198,13 +198,14 @@ def parse_jobstore(jobstore_uri: str) -> str:
 
 
 def add_base_toil_options(
-    parser: ArgumentParser, jobstore_as_flag: bool = False, cwl: bool = False
+    parser: ArgumentParser, jobstore_as_flag: bool = False, cwl: bool = False, config_option: Optional[str] = None
 ) -> None:
     """
     Add base Toil command line options to the parser.
     :param parser: Argument parser to add options to
     :param jobstore_as_flag: make the job store option a --jobStore flag instead of a required jobStore positional argument.
     :param cwl: whether CWL should be included or not
+    :param config_option: If set, use this string for the Toil --config option instead of "config".
     """
 
     # This is necessary as the config file must have at least one valid key to parse properly and we want to use a
@@ -215,8 +216,8 @@ def add_base_toil_options(
     # If using argparse instead of configargparse, this should just not parse when calling parse_args()
     # default config value is set to none as defaults should already be populated at config init
     config.add_argument(
-        "--config",
-        dest="config",
+        f"--{config_option or 'config'}",
+        dest="_toil_config_file",
         is_config_file_arg=True,
         default=None,
         metavar="PATH",