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I have been able to create temp tables and use them in joins to queries run in a Connect In-DB step, but ideally I want to reference the temp table within the query that is running in the Connect In-DB step. Is this possible?
No its not possible join temp table with a table in Connect In-DB step.
Ideally, InDb tools works like a single set of sql query that data is not fetched until all the InDb tools are executed. Even though you are doing the join with after Connect In-DB step it will try to run it as a single step with join.
With InDb tools you are just building the query you are not directly processing the actual data like normal tools.