Adjust naming to make parsing easier
Allow GFF and hierarchy to become optional

If GFF and hierarchy file are not supplied then the script will now run
RepeatMasker to generate these
Remove RepeatMasker step from PoPoolationTE run

Since a RepeatMasker step is present in the main pipeline a RM separate
RM step is no longer needed for PoPoolationTE
Correct test script and inputs for new pipeline