Moved the RNASeq comparison sheet to the more generic AnnotationSheet class.
Added support for column 'Comparison name' to explicitly specify, rather than automatically assemble a comparison name from group or sample names. Since file names are based on comparison names, automatic name assembly does not scale for large comparisons as the maximum length of a file name string could be exceeded.
A comparison sheet is now optional. If none has been provided, all Sample objects will be added from the Collection objects and only the first stage of the pipeline will be run.
Changed Python docstrings to use Epytext annotation rather than reStructuredText.
Corrected the syntax in type fields, where types are now separated by pipe characters.
Removed empty lines after function definitions.