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well the process we want to do is dynamic with automation on our company gallery.
Have the workflow run on a schedule where it pulls from SFTP, saves to company disk then have the workflow hit the SFTP to delete the files from the SFTP... and the idea I had was to use the formula tool to generate an R script to delete the files as the names will probably change.
Yep, that is possible too! You can either replace the entire R script from the formula that you are referring to or just have a placeholder in your R script and check the "Replace a specific string" box down at the bottom of the configuration window and only modify that part of your script. Leveraging a macro at the end of your workflow to accomplish this sounds like the way to go.