Try piping the job script and its arguments into qsub like this. Use the debug queue for this experiment! Note that you have to specify all PBS settings to qsub directly on the command line, NOT in the cuffidd.sh.
echo "cuffidd.sh -d yymmdd -n 'file1 file2 ... fileN'" | qsub -q debug -P myproject -l walltime=00:10:00 ....(whatever)...
Another possibility is to set environment variables. Here is a made-up example:
qsub -v INFILE=fileX,OUTFILE=fileY myjobscript.sh
and then you can refer to $INFILE and $OUTFILE in myjobscript.sh.