Subworkflow/task import error

Tools and Workflows
1

I have a workflow calling an external task using “import wdl-path as alias”. I cannot get it validated on dockstore getting an error regarding the alias. I was wondering if I’m missing something. Here is my repo. This is the error message form docker validator:
/preprocessing.wdl : WDL file is malformed or missing, cannot extract metadata. Failed to process workflow definition ‘preprocessing_workflow’ (reason 1 of 1): Cannot lookup value ‘outsource.QueryInputs’, it is never declared. Available values are: [‘tmp’, ‘flattened_inputs’, ‘QueryInputs.json’, ‘QueryInputs.out’, ‘inputs’, ‘rt_seriesinstanceuid’, ‘ct_seriesinstanceuid’, ‘dest’, ‘patient_id’, ‘sg_seriesinstanceuid’, ‘preprocessing_task.__after’, ‘QueryInputs.__after’, ‘json_file’, ‘preprocessing_task.destination’]

2

This seems like a valid WDL error. I forked your repo and ran WomTool on it locally and got the same error:

java -jar ~/Downloads/womtool-54.jar validate preprocessing.wdl
Failed to process workflow definition 'preprocessing_workflow' (reason 1 of 1): Cannot lookup value 'outsource.QueryInputs', it is never declared. Available values are: ['tmp', 'flattened_inputs', 'QueryInputs.json', 'QueryInputs.out', 'inputs', 'rt_seriesinstanceuid', 'ct_seriesinstanceuid', 'dest', 'patient_id', 'sg_seriesinstanceuid', 'preprocessing_task.__after', 'QueryInputs.__after', 'json_file', 'preprocessing_task.destination']

I don’t know really know WDL, so I can’t give you any advice beyond trying to figure out the error message (any maybe trying it locally with WomTool first will make it easier to debug). You can get WomTool here: https://github.com/broadinstitute/cromwell/releases. I used version 54 in my command-line example above, although note Dockstore itself uses an version 41 (both versions fail with the same error locally).

3

Thx for the answer. You are right. I double-checked my code and there was a problem with the alias I used that needed to be taken care of.

4

Now that I have fixed the problem there is no validation error anymore. Yet there is no validation tick on my version and I’m unable to publish my workflow.

5

Hi,
You might be encountering https://github.com/dockstore/dockstore/issues/3812
Could you try making new branches/tags to confirm and/or workaround the issue?

6

Thx, by adding a new tag the I could get around the problem.

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