rm intermediate files
TagsToSNPByAlignmentPlugin requires -e Start Chr, -s End chr
Merge pull request #8 from mdavy86/feature/cleanoutFiles

Feature/cleanout files
prepare git subtree
Added local template files as the Moa installation procedure seems to be broken.

TODO: Remove these template files and install templates from git once Moa works correctly again.
Merge remote branch 'upstream/master'