Hopefully this will save others some headaches.
When performing Unix commands, Automator does not seem to do tilde expansion for directory paths. Thus, if you were building an arbitrary workflow to send the output of ls to a textfile, for instance, directories must be entered as:
/Users/yourUsername/yourDirectoryChoice
as opposed to:
~/yourDirectoryChoice
Mac OS X Hints
http://hints.macworld.com/article.php?story=20050504035814120