Edited awe template to save a couple more finals for stats computation in done stage.
Overhaul and verified working copy of stage to download files from awe for completion of pipeline.
Debugging and finalizing stage to submit jobs to AWE.  Also, added pipeline logger to the stages that submit and download from awe for debugging pipeline.
Merge pull request #155 from jaredbischof/master

Finalizing stuff to handle running part of the pipeline in AWE.