Port AmpliconAssembly to pbsmrtpipe.
Updated resources to have new SMRT files.
Port P_SAT.py. This won't work until the makeSATReport.py uses pbreports json data file as an input.
Add autopep8 to dev req.txt file.
Remove CCS filter. bas files in 2.1 don't have CCS. CCS/Reads of Insert is done in secondary now.
Port P_AssemblyPolishing. Still needs work. Some oddness going on with the smrt files.
Port P_Bridgemapper to new setup.
Add P_MotifFinder. Base mods should work now.
Port P_AHA. Update resources.py
Update P_BridgeMapper to load the reference in the 'standard' way.
Ported P_GMAP.
Port P_GATKVC. Still needs some integration fixes to work.
Update tests to handled disabled CCS task in P_Filter.