Simply set this script as script to run when Transmission complete a torrent and forget it. If you need to run stuff, just add scripts inside %localappdata%/transmission/scripts
This project was created on the fly and wasn't tested yet. Main purpose is to enforce this script as script to run for transmission user on my server to allow them to run whatever they wish on completion while still being able to forcibly launch an anti malware scan when something complete for any user.