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Hi @mattlukoff! To my knowledge, it is not possible to run part of a workflow. However, you can put the various parts of your workflow into a Tool Container and then disable the tool container. Any tools contained in a disabled tool container will not be processed.
There isn't really a good way to do this yet. The best way would be to move the pieces you don't want to run to a seperate workflow. Another way is to simply disconnect the components you aren't using. this will throw an error, but the rest of the flow will still run. handy if you're just troubleshooting.
Questions like this typically are from the desire to not have to run through the early parts of a workflow each time.
While using the containers to eliminate the need for the later (or parallel) parts of a workflow can work, for avoiding the rerun of the early parts, I'd check out the Cache macro that is available on the Alteryx Gallery.