Merge pull request #22 from wtsi-npg/devel

Merge in changes from wtsi-npg/devel
Remove hard-coded queue argument
Reduce number of thresholds and change timeout
Merge pull request #121 from iainrb/devel

Remove queue argument from workflow tests
Added command line arguments for setting the analysis and sample source
directories.

Added a command line argument for specifying a manifest file.