oicr-gsi/robust-paper

Explain why config files don't satisfy rule 8

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Reviewer 3: I would tend to suggest generalizing the rule somewhat to suggest externalizing parameters rather than necessarily requiring them to be available as command line options. For example if a configuration file is used to provide all parameter values, this could accomplish the task of separating the parameters out from the code as well as providing a record of the values used for a run as they describe through echoing parameters to a log file.

We should have a callout explaining why config files don't satisfy this - yes, they can be script-generated and then used as input, but scripts to do that are usually more complex than scripts that pass command-line parameters, so designing for the latter constraints the program to be easier to use.