I am generating 3 directories that will be used for in other steps.
The directories do exist, but I kept getting: “Did not find output file with glob pattern”. I’ve tried to change “basename” to others like location, but that didn’t work neither.
Thanks in advance.
If I understood correctly from your syntax, you are trying to recursively find these directories
$(inputs.input.basename)/dir in your working directory. Is that right?
If so, may I ask why are you generating these directories inside other directories and not directly in the working directory?
Thank you for replying. It’s my first time using CWL. The program that I am writting the CWL for creates temporary directories. Then it generates files/processing in those temporary directories. I am trying to write the step that generating the directories, so that the other steps have the temporary directories for input.
Hi @NDe, Could you provide an example of what you’re trying to do so it will be more clear?
Sorry for the late response. I misunderstood my task and was trying to get some clarifications.
Yes, I should just work in the working directory.
My original question was about the scenerio that Program_A creates a directory full of files. Then Program_B takes in the directory and creates another directory that contains result files.
Program_B ./result_A_dir ./result_B_dir
result_A_dir contains Version 1 results.
result_B_dir contains Version 2 results.
I think the input/output of the cwl should look like this: