Hi guys,

I made a very small code change so that the workflows API will display
all the steps in a workflow, not just the inputs (these are still
displayed separately, as before).  I made a pull request even though
the change is small, just to learn what I'm doing:

But in doing so I noticed something in the workflows I don't
understand. I can't see a connection between workflow "input datasets"
and the steps they are inputting to. I doubt this is a bug, I just
don't know how it's supposed to work, so I'm not sure if my API change
is sufficient.

So for instance, if I create a small workflow with steps
Input Dataset -> TopHat (accepted_hits bam file) -> Cufflinks
and call the API on this workflow, I now see

    "id": "f2db41e1fa331b3e",
    "inputs": {
        "1": {
            "label": "Input SE fastq",
            "value": ""
    "name": "Tophat + cufflinks",
    "steps": {
        "1": {
            "id": 1,
            "input_steps": {},
            "tool_id": null,
            "type": "data_input"
        "2": {
            "id": 2,
            "input_steps": {},
            "tool_id": "tophat",
            "type": "tool"
        "3": {
            "id": 3,
            "input_steps": {
                "input": {
                    "source_step": 2,
                    "step_output": "accepted_hits"
            "tool_id": "cufflinks",
            "type": "tool"
    "url": "/api/workflows/f2db41e1fa331b3e"

The "inputs" field was there before, the "steps" field is the new bit.
So as expected, step 3 lists step 2 as an input. However step 2 does
not list step 1 as an input, even though the GUI shows that they are
connected and the workflow works. From other testing it seems that
"Input Dataset" steps never appear wired up in my API response. I'm
just iterating over all input_connections, so apparently steps of type
data_input are not in the list of WorkflowStep.input_connections .

Is this how it should be? How can I find out which steps an Input
Dataset is connected to?



Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759
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