The "home directory" is where PGP Command Line expects to find its preferences (where the license information is stored) and keyring files. It doesn't have anything to do with where it finds its input files. You can also specify a directory where the output file can go.
E.g.:
pgp -er [recipient] $current-input-directory/* --output $output-directory
and change the value of $current-input-directory in your script, for each location.
or
cd $current-input-directory
pgp -er [recipient] [file name or *] --output $output-directory
Make sure that $output-directory is an absolute path (e.g. "/data/pgp/encrypted"). It can certainly be the same as your input directory. If the file always has the same name, and you want to put the outputs in the same place, you will also need to change "--output" to specify something unique.
Regards,