This is the better way of implementing #9.
The idea is to add a CWL step to the MDStudio CWL API that takes a File and a str as inputs, and saves the file contents at the remote path indicated by the string. The microservice would then take a remote path, and if it is specified, run a version of the workflow that contains this step to save the trajectory.
Ideally, there would be a step in the other direction, that loads a file from a remote directory and returns it as a File for use in other steps, but that's not the immediate use case here.