Merge pull request #3 from chapmanb/master

Merge
Merge pull request #5 from chapmanb/master

Merge
Merge pull request #7 from chapmanb/master

Merge from upstream
Merge pull request #14 from mariogiov/master

Updates / bug fixes
Merge pull request #17 from mariogiov/master

Merge! Meeerrrrggeeee!!
Merge pull request #19 from mariogiov/master

Bugfixes mostly
Merge branch 'master' of https://github.com/SciLifeLab/bcbio-nextgen
Merge branch 'master' of https://github.com/guillermo-carrasco/bcbio-nextgen
Travis is not viable for bxbio-nextgen, unfortunately