Download

We finished all the changes and set up the config file so that everything works. I also merged the two reference.conf files into one because it seems we can, so all the config stuff is together.  Might we want to move this file to the parent module since it's universal?  Lastly, I wrote a runpipeline.sh script in the parent module that runs through the entire process. It supplies no parameters (except the -t and -i) to any of the classes.  Instead, we set each class up so that they individually retrieve a default value from the reference.conf file.  I tested the script (with latin specified so it would go quickly) and it ran fine.