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Somehow, we never hit the case where we needed to optionally pass entire arguments to scripts. Since all arguments are always included, there is currently no way to handle #34 (closed). Some small updates to the workflow job parsing should be able to handle this, but will require changes across several spots.

Change the input structure to be a dictionary not a list. Inputs will be passed by name instead of in a list. If an argument has a value that is None, we will skip adding it entirely. This will require updating the workflow_module yaml files to similarly be dictionaries instead of lists, as well as the internals of the workflow_module class to correctly pass information to the workflow_job classes.