generate_input.sh no longer expands symbolic links.

Some computing facilities store data that can be accessed through symbolic links. This becomes an issue if generate_input.sh is used to create the input file for the pipeline, which expands these links before writing the paths to file. The data paths in this file would then be in disagreement with the symbolic link paths used to mount data. The script no longer expands any symbolic links.

Original issue was reported by Deepika Venkattu.