List of input files in external yaml file

I’m trying to create a workflow which gets as input a File[] (let’s call it parameter par1) and several other inputs (booleans, ints, other File…).

Given that the quantity of Files constituting par1 is quite large, I’d like to find a way to simplify and isolate the par1 part when writing the inputs.
Currently I’m compiling a yaml file with something like:

  - {class: File, path: ../path/to/file_001.lv0}
  - {class: File, path: ../path/to/file_002.lv0}
  - {class: File, path: ../path/to/file_003.lv0}
  - {class: File, path: ../path/to/file_004.lv0}
  - {class: File, path: ../path/to/file_005.lv0}
  - {class: File, path: ../path/to/file_006.lv0}
  - {class: File, path: ../path/to/file_007.lv0}
  - {class: File, path: ../path/to/file_008.lv0}
  - {class: File, path: ../path/to/file_009.lv0}

Is there a way to get the input filenames from an external file?
I saw there’s the $include directive but I believe is not applicable to yaml file.

If it’s not possible, I’m headed towards the creation of an Expression Tool which tries to generates the File[] from a file.txt. Do you have better ideas?


You can try to pass a Directory as input instead of several files if your files are in the same directory.

Pass the directory as input and add it to the InitialWorkDirRequirement of the CWL tool.

   - '$({class: "Directory", basename: inputs.par1.location, listing: []})'
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Thanks! Interesting. Unfortunately they may not be in the same dir

That’s clever, but alas that won’t work. You can’t pull in arbitrary Files from the filesystem in CWL like that.

I recommend making a script in your language of choice to generate the input file before sending it and the workflow to your chosen CWL runner.

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