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The only way I can see to do this is to put both workflows in the same yxwz file and either combine them using detour tools or select between them with containers. If you are using the same input tool for both workflows then you could try using detour tools. If you have different inputs for each workflow, then the container option might work better for you. I've attached simple examples of each approach.
In the Detour example, I'm using a Detour End tool to bring the two workflows together and send the data to a single Browse tool. I played a bit with not using a Detour End tool and terminating each branch with an Output Data tool. That seems to work just as well.
I haven't tried running these from an Alteryx Server. I expect they will work correctly, but you'll need to do some testing.
Also, I had to put each of these workflows in a package since for some reason we can't attach yxwz files to a posting.
Great examples, really helpful. However the issue is my one workflow is a unchained app with filters and another is a chained app with filters. When I use interface tools in a containers it gives me an error message as interface tools cannot be contained in a container. Any other workaround to execute these 2 different workflows.