Job argumnet creation is now actually legible AND works with the new style of inputs/outputs as well as job definition files.

Heavily updated workflow_job parsing & validation.  Addeded several tests to confirm the validity of new parsing.  additional_inputs no longer exist, and input / output files are defined as dicts instead of lists.  References refer directly to the dict key names instead of a list index.

Added initial sphinx doc tree & build stuff.  Using the sphinx markdown theme.  Use 'make html' to build the docs.

Updated validation, error parsing, and param parsing.  Params specific to the job are now expected to be passed by the workflow.  file list arguments MUST have file_type defined.

Updated all yaml files to support type argument.  Heavily updated workflow_job parsing and verbosity.

Updated workflow_job validation.  Added rawfile type.  Added gem wrapper script, yaml, and chromsome conversion script.

Create save_result function in workflow.  Updated workflow_job & module to provide additional necessary info to save database results.

Added db_save_results yaml job, and script.  Updated workflow information tracking to create correct meta data files for saving information to the database.  Conf adjusted to support yaml files, and arbitrary result files.  workflow_job can now return a dictionary of all arguments used.

Updated stdout & stderr redirection.  Includes adjustments in individual job yaml files, module yaml files, and workflow generation handling.