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When publishing a workflow to Gallery or Scheduler (Designer + Desktop Automation) or when packaging a workflow for export, checking the boxes for what to include and what to exclude seems to work inconsistently as of Designer 2020.2. Here is a workaround to cover you until the issue is resolved in a future release.
While trying to connect to Snowflake from Alteryx Designer, using Input Data tool, the following error is thrown after running the workflow:
Error: Input Data (1): Error SQLExecute: No active warehouse selected in the current session. Select an active warehouse with the 'use warehouse' command.