How do you run cronjobs

[eluser]esset[/eluser]
I have a question on how you do when running cronjobs w/ CI.

Since CI routes everything through the URL scheme (segments) which are public I was wondering how YOU do to best protect your cron related calls. For best security I would like to run cron related calls away from the public_html directory, so they aren't even accessable from the public domain.

Any tips&tricks; would be appreciated.

Thanks