Workflow Metadata Files and Directories

[jtronge]

BEE workflows include a number of options that can point to particular file paths. These include dockerFile, beeflow:useContainer and beeflow:copyContainer, but there may be others that I'm forgetting.

Depending on how and where the workflow manager is started and where the workflow is submitted from, paths may or may not be accessible. We need to figure out some set of rules for finding these files, or maybe require that the user wrap everything up into the workflow tarball. We can probably easily wrap up small metadata files, like docker files, but I don't think that this is feasible for large container images. Container images aren't really an issue right now since we've been using absolute paths, but it may be a problem if the client no longer runs on the same machine as the workflow manager. Or maybe we can just require that paths are specified relative to a specific location? I'm not sure that's a good idea since it may not go along with the CWL standard.