Most of the time this may be intuitive. But from time to time it’s a little ambiguous what’s best. In general, inputs are the things you provide or set on a step, and outputs are the materials created or measured in the step.
There can be some exceptions to this general rule though. For example, it’s often more intuitive to put the percent oxygen of your fermenter inlet gas on the inputs, even though you are actually measuring that oxygen with a mass spectrometer. Conversely, it may be helpful to put the target concentration of a solution on the output, even though you specify it, rather than measure it.
So overall, we recommend doing what you think is physically intuitive.