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collect the exit status and output path of each task

Here is part of the stdout to screen from Cromwell run. Is there a good way to collect the exit status and output path of each task, besides parsing the whole stdout?

[2019-01-08 09:40:48,06] [info] SingleWorkflowRunnerActor workflow finished with status 'Succeeded'.
{
  "outputs": {
    "bwawf.runBwa.oBam": "/user/jack/pipeline/cromwell-executions/bwawf/b9501cd7-9443-4161-a4b3-89f6a8fc1609/call-runBwa/execution/S1.bam"
  },
  "id": "b9501cd7-9443-4161-a4b3-89f6a8fc1609"
}

Thanks!

Answers

  • ChrisLChrisL Cambridge, MAMember, Broadie, Dev admin

    @blueskypy if you're running Cromwell in server mode, there's the outputs endpoint which I think is exactly what you're hoping for

  • blueskypyblueskypy Member ✭✭

    Thanks @ChrisL for the help! Could you show me how to run the server mode in a SGE cluster that I can only access through ssh? I tried the following command in the cluster, but got error:

    java -Dconfig.file=../sge.conf -jar /site/ne/home/e0380702/tool/cromwell-36.jar server ../bwa2.wdl -i ../input2.json
    Error: Unknown argument '../bwa2.wdl'
    Error: Unknown option -i
    Error: Unknown argument '../input2.json'
    

    It runs successfully if I change the server to run.

    Also I need to run the pipeline hundreds of times on different samples, is the Server mode appropriate?

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