Merge pull request #215 from keithj/devel

iRODS improvements to permissions handling
Merge pull request #216 from keithj/devel

Fluidigm integration and Collection bug fix
New prefilter report and QC refactoring
Fixed typo and changed run() arguments
Edited comments
Merge pull request #217 from iainrb/devel

New prefilter report and QC refactoring