CWL: How to add multiple files from two input parameters of type FILE and DIRECTORY to InitialWorkDirRequirement

Question

[awilke1972]

I am struggling creating a tool definition which has multiple files as InitialWorkDirRequirement. The problem is that I have two input parameters, one is of type File and the other one of type Directory. I need all files from the Directory to be staged into the working directory. Below is a simple tool definition for testing. The example below is clearly not working since one expression in "listing" evaluates to a list, resulting in [ [File] , File].

{
  "cwlVersion": "v1.0",
  "class": "CommandLineTool",
  "baseCommand": [
    "ls",
    "-l",
    "."
  ],

  "requirements": [
    {
      "class": "InitialWorkDirRequirement",
      "listing": [
        "$(inputs.in.listing)" ,
        "$(inputs.fasta)"
      ]
    }
  ],
  "stdout": "ls.log",
  "stderr": "error.log",
  "inputs": {
    "in": "Directory",
    "fasta": "File"
  },
  "outputs": {
    "output": "stdout",
    "error": "stderr"
  }
}

Answer 1

[Michael R. Crusoe]

Hello awilke1972,

Thank you for your question. As you have discovered, CWL v1.0 does not allow for specifying other than a File, Directory, Dirent, or Expression when providing an array to the listing of a InitialWorkDirRequirement; specifically an array of Files can't be a member of that array response.

http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement

As a workaround, you can use InlineJavascriptRequirement and an expression like so:

  "requirements": {
    "InlineJavascriptRequirement": {},
    "InitialWorkDirRequirement": {
       "listing": "${var listing = inputs.in.listing; listing.push(inputs.fasta); return listing; }"
    }
  },

[and again in our typical YAML formatting]

requirements:
  InlineJavascriptRequirement: {}
  InitialWorkDirRequirement:
    listing: |
      ${
        var listing = inputs.in.listing;
        listing.push(inputs.fasta);
        return listing;
       }

I've created an issue so we can fix this in a future revision of the specification. Thank you for bringing this to our attention!

https://github.com/common-workflow-language/common-workflow-language/issues/412