Submitting a workflow where symbolic links are used for directories, such as on fog

[pagrubel]

When I submit a workflow using . (or the current directory) on fog the script ends up with --cd /yellow/users//... in the ch-run command. It is picking up the incorrect path for the container.

I think it should be --cd /home//...

[jtronge]

We may have to add something to the config file, like a comma separated list of aliases for the the homedir. The main problem is related to os.getcwd() giving a different result than pwd in the shell. There could also be a way to set the user-environment to avoid this, but I'm not sure.

[pagrubel]

It works fine if I don't use . for the workdir but instead put in the path upon submit such as /users/username/dir