Sure. Look in the Automator Files & Folder Library, and drag/drop the Ask for Finder Items action into your workflow before your Run Shell Script action.
The prompt can be anything you want. Start at: Desktop, and Type: Folders. I would not select Allow Multiple Selection unless you have a for loop construct in your Bash code to process multiple folders.
for file in "$@"
do
...
done
exit
The "$@" is the list of items being passed to the Run Shell Script action, even if it is one item. It will be in POSIX (UNIX) path format.
Review the Automator content here. Take into consideration that some things may have changed from the time this was authored until current implementations of Automator. The bigger picture at this site is here.