I recently wanted to automate cleanup of my WSUS server. A lot of posts around the web advocate using strange PowerShell scripts that make .NET calls to work with WSUS or even use third-party applications to do so. That information all seems outdated. On server 2012 R2 you only need Invoke-WsusServerCleanup.
In my case I created a scheduled task on my WSUS server to run
powershell with the arguments
-command Invoke-WsusServerCleanup -CleanupObsoleteComputers -CleanupObsoleteUpdates -CleanupUnneededContentFiles -CompressUpdates -DeclineExpiredUpdates -DeclineSupersededUpdates on a weekly basis.