Using `Directory` as an output type
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0
Entering edit mode
8 months ago
Anton • 0

I'm creating a pipeline and one of my tools (let's call it Tool 2) accepts Directory as an input, like so:

    "inputs": [
        {
            "id": "analysis_inputs_id",
            "type": "Directory",
            "inputBinding": {
                "position": 11,
                "shellQuote": true
            }
        }
    ],

My preceding tool (Tool 1) performs some analysis and outputs several files into /tmp/

My question is how do I write the Tool 1's CWL specification so that it outputs the directory /tmp/ into the input of Tool 2?

So far I've tried this for Tool 1:

    "outputs": [
        {
            "id": "outdir",
            "type": "Directory",
            "outputBinding": {
                "path": "/tmp"
            }
        }
    ]

and it fails like so:

Job error:
Error validating output record. the `outdir` field is not valid because
  is not a dict
 in {
    "outdir": null
}

What is the correct way to specify directory outputs in CWL?

directory glob cwltool output • 299 views
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Entering edit mode

CWL support is now provided via a different forum. Please post this at: https://cwl.discourse.group/

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