CommandlineTool Directory outputs can't be found

CWL Questions
1

Hi,
I am generating 3 directories that will be used for in other steps.

outputs:
  dir:
    type: Directory
    outputBinding:
      glob: "*/$(inputs.input.basename)/dir"

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.

2

Hey @NDe,
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?

3

Hi HrishiDhondge,

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.

Thank you.

4

Hi @NDe, Could you provide an example of what you’re trying to do so it will be more clear?

5

Hi @HrishiDhondge,

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.

For instance:

Program_A     ./result_A_dir
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:

A.cwl:

......

inputs:
  Dir:
    type: Directory
    inputBinding:
      position: 1

outputs:
  Results_A:
    type: Directory
    outputBinding:
      glob: result_A_dir/**

B.cwl:

......

inputs:
  A_results:
    type: Directory
    inputBinding:
      position: 1

outputs:
  Results_B:
    type: Directory
    outputBinding:
      glob: result_B_dir/**