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A workflow-supplied argument can also be given in the .ini file
Some workflow generators control job-specific arguments (like times or input files). These arguments are not expected to be given in the ini file. However, one can give such options in the ini file, which will result in the option being specified twice to a job.
The code should raise an error if the workflow generator tries to add an option that is already present in the ini file. Currently this issue will not be addressed as this is being used as a "feature" for at least one code in production. So not to break things I'll either fix this after that is resolved, or at the end of O2.