Error loading WDL and importing workflow

Post author
Jessime Kirk

I'm attempting to launch the GiraffeDeepVariantLite workflow, which has a Launch with Terra link. The link takes me to an "Import Workflow" page in Terra, which immediately hits a "Error loading WDL" error. The details just say:

[object Object]

If I attempt to fill out the form by choosing a "Destination Workspace" and clicking "IMPORT", I get a "Error importing workflow" error, with the following details:

Bad Request
Full error:
{
  "causes": [],
  "exceptionClass": "cromwell.client.ApiException",
  "message": "Bad Request",
  "source": "rawls",
  "stackTrace": [
    {
      "className": "cromwell.client.ApiClient",
      "fileName": "ApiClient.java",
      "lineNumber": 1030,
      "methodName": "handleResponse"
    },
    {
      "className": "cromwell.client.ApiClient",
      "fileName": "ApiClient.java",
      "lineNumber": 946,
      "methodName": "execute"
    },
    {
      "className": "cromwell.client.api.WomtoolApi",
      "fileName": "WomtoolApi.java",
      "lineNumber": 179,
      "methodName": "describeWithHttpInfo"
    },
    {
      "className": "cromwell.client.api.WomtoolApi",
      "fileName": "WomtoolApi.java",
      "lineNumber": 155,
      "methodName": "describe"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.dataaccess.CromwellSwaggerClient",
      "fileName": "CromwellSwaggerClient.scala",
      "lineNumber": 27,
      "methodName": "$anonfun$describe$2"
    },
    {
      "className": "scala.util.Try$",
      "fileName": "Try.scala",
      "lineNumber": 217,
      "methodName": "apply"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.dataaccess.CromwellSwaggerClient",
      "fileName": "CromwellSwaggerClient.scala",
      "lineNumber": 25,
      "methodName": "$anonfun$describe$1"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.dataaccess.CromwellSwaggerClient",
      "fileName": "CromwellSwaggerClient.scala",
      "lineNumber": 24,
      "methodName": "describe"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.jobexec.wdlparsing.CachingWDLParser",
      "fileName": "CachingWDLParser.scala",
      "lineNumber": 78,
      "methodName": "inContextParse"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.jobexec.wdlparsing.CachingWDLParser",
      "fileName": "CachingWDLParser.scala",
      "lineNumber": 54,
      "methodName": "parseAndCache"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.jobexec.wdlparsing.CachingWDLParser",
      "fileName": "CachingWDLParser.scala",
      "lineNumber": 47,
      "methodName": "parse"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.jobexec.MethodConfigResolver",
      "fileName": "MethodConfigResolver.scala",
      "lineNumber": 16,
      "methodName": "parseWDL"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.jobexec.MethodConfigResolver",
      "fileName": "MethodConfigResolver.scala",
      "lineNumber": 70,
      "methodName": "getMethodInputsOutputs"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.workspace.WorkspaceService",
      "fileName": "WorkspaceService.scala",
      "lineNumber": 2080,
      "methodName": "$anonfun$getMethodInputsOutputs$2"
    },
    {
      "className": "org.broadinstitute.dsde.rawls.util.MethodWiths",
      "fileName": "WithSupport.scala",
      "lineNumber": 53,
      "methodName": "$anonfun$withMethod$1"
    },
    {
      "className": "slick.basic.BasicBackend$DatabaseDef",
      "fileName": "BasicBackend.scala",
      "lineNumber": 172,
      "methodName": "$anonfun$runInContextInline$1"
    },
    {
      "className": "scala.concurrent.impl.Promise$Transformation",
      "fileName": "Promise.scala",
      "lineNumber": 470,
      "methodName": "run"
    },
    {
      "className": "java.util.concurrent.ForkJoinTask$RunnableExecuteAction",
      "fileName": null,
      "lineNumber": -1,
      "methodName": "exec"
    },
    {
      "className": "java.util.concurrent.ForkJoinTask",
      "fileName": null,
      "lineNumber": -1,
      "methodName": "doExec"
    },
    {
      "className": "java.util.concurrent.ForkJoinPool$WorkQueue",
      "fileName": null,
      "lineNumber": -1,
      "methodName": "topLevelExec"
    },
    {
      "className": "java.util.concurrent.ForkJoinPool",
      "fileName": null,
      "lineNumber": -1,
      "methodName": "scan"
    },
    {
      "className": "java.util.concurrent.ForkJoinPool",
      "fileName": null,
      "lineNumber": -1,
      "methodName": "runWorker"
    },
    {
      "className": "java.util.concurrent.ForkJoinWorkerThread",
      "fileName": null,
      "lineNumber": -1,
      "methodName": "run"
    }
  ],
  "statusCode": 400
}

Is the implication here that the GiraffeDeepVariantLite WDL file is invalid?

Comments

2 comments

  • Comment author
    Emily Barnes
    • Official comment

    Hi Jessime,

    Thanks for writing in with this issue! After taking a closer look we found that giraffe_and_deepvariant_lite.wdl does not exist in the underlying github repo:

     

    The creator of these workflows would need to resolve this issue for users to be able to import the workflows.

    Please let us know if you have any questions!

    Best,

    Emily

  • Comment author
    Jessime Kirk

    GiraffeDeepTrio imports just fine, so the issue is likely with the workflow. 

    0

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