When running a pipeline programmatically (i.e. using Pipeline.pm and calling ->run) the pipeline needs the Ergatis.ini (for Workflow settings). There are cases where this situation is not ideal, namely when the Ergatis.ini file is on your webserver and the run subroutine is being called on the machine you are running the pipeline from.
We spoke about moving the relevant options required in Ergatis.ini as parameters in the constructor of the pipeline (or some where else) to allow the running of a pipeline without Ergatis.ini config file.
