Merge pull request #79 from iainrb/devel

Option for post filtering samples with low Gencall CR from Illuminus input
Merge pull request #80 from iainrb/devel

Corrections to CR filter on illuminus input
Merge pull request #82 from iainrb/devel

Corrected bug in placeholders for metric values
Merge pull request #83 from iainrb/devel

Record version number in output
Fixed bug where files could be counted multiple times. Added the ability to recover from some errors
Added --days-ago CLI option
Avoid undefs when invalid files are found
Merge pull request #84 from iainrb/devel

Changes from iainrb/devel for version 0.7.0
Merge remote branch 'wtsi-npg/devel' into devel
Merge pull request #87 from keithj/devel

Fixed bug where files could be counted multiple times.  Added --days-ago CLI option
Added ability to make irods groups

Added methods to find objects and collections by their metadata
Added iRODS group creation to publishing script

Added genotyping project title to sample metadata

Added --force option to pipeline setup for a special case where mixed chips are really desirable in an analysis
Replaced --force argument with --chip_design argument
Merge remote branch 'wtsi-npg/devel' into devel
Merge pull request #88 from keithj/devel

iRODS groups and chip design selection
Merge pull request #13 from wtsi-npg/devel

Latest iRods changes from keithj