Version 1.0.7 - May 2014

1. Check for existence of required input directories and give a warning if they
don't exist.
Version 1.0.8 - May 2014

1. Updated to configurationClass to allow defining files/directories as temporary.
This ensures that these files do not appear in the list of outputs for a tool/pipeline.

2. Updated help.

3. Checked that input files have the correct extension prior to constructing output filenames.