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.
Merge pull request #122 from keithj/devel

Added command line arguments
Removed MANIFEST
Fixed manifest and skip file
Fixed manifest and skip file
Merge branch 'release-0.8.0' of github.com:wtsi-npg/genotyping into release-0.8.0
Restored PDF files; these are required indirectly by tests
Merge pull request #123 from keithj/devel

Restored PDF files; these are required indirectly by tests
Fixed incorrect method name in error logging
Removed a file readability test that misreported on mounted Windows shares
Merge pull request #124 from keithj/devel

Post user-testing fixes
Enable UTF8 on Mysql client
Enable UTF8 on Mysql client.

Add validation of sample ID
Enable UTF8 on Mysql client
Use joins via aliquot to relate samples to wells
Add utility methods to report install path
Added defaults for sqlite executable and DDL
Added test for base_dir and config_dir methods

Bumped version
RT 335864. Fix for exception raised when the pipeline run name is a number