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There are different schools of thought for this. I find the best way to keep your workflow organized is to group your sub processes into tool containers by the function they are performing. You can also color code your containers based on the type of sub process (Data prep, Output/Input, Check). It's also nice to give each tool a brief annotation about the tools use, in addition to a comment container that gives a more detailed overview of the sub process. Here is an example of how I organize workflows.