Changes made to pipeline to prepare for Integration into seemless framework. Also, creation of a master script and several source folders
Merge branch 'master' of github.com:rusalkaguy/uab_ngs
remove 'sensitive' files before running BFG
Merge branch 'master' of github.com:rusalkaguy/uab_ngs
Merge branch 'master' of github.com:rusalkaguy/uab_ngs
Remove cohort* files, change some paths, remove some other accidentally checked in files