Apologies for the newbie question. I am trying to set up CWL with my set of tools so I am going through a kind of boot camp now.
One of my tools works by having a directory specified in a config file (a config file for the inner program) which will contain many files that the program will read. So for example the program will have a config file with:
I pass in this settings file itself through the usual CWL “class: File” method which works as expected. What I need to do is also pass in as input the data directory. So for example, I may have in the config file that is passed in:
And then include an input in the CWL file like:
(and in settings)
This runs without error, but the actual data directory does not seem to be passed, or at least I think I am using “Directory” incorrectly. I have tries testing with “tree” and “ls” commands and only one temp file is shown - no directory. How can I make this directory location available to the program either by copying it or using a symlink? Is there a way to include a whole directory?
Thanks for reading and have an awesome day!