how to view WDL output string in Terra?

Post author
Stephanie Gogarten

I have a workflow that produces a string as output. How can I view this string in my workspace?

Comments

7 comments

  • Comment author
    Emil Furat

    Hi Stephanie,

     

    Thanks for reaching out. The outputs from your workflows are written to the Google bucket associated with your workspace. In order to find the output for a specific workflow/task you will want to click on the submission of interest in the Job History tab and navigate to the Job Manager as pictured below:

     

    From the Job Manager page you will want to click on the Outputs tab, and then click on the link to the Google bucket for the task of interest:

    You should automatically be directed to the output file/string/etc. for your task. For more information about running workflow and configuring your outputs, I recommend reading this article, especially the section titled Configuring outputs to write to the data tablehttps://support.terra.bio/hc/en-us/articles/360026521831-Configure-a-workflow-to-process-your-data

     

    If you have any other questions please let us know!

     

    Kind regards,

    Emil

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  • Comment author
    Emil Furat
    • Edited

    Hi Stephanie,

     

    I forgot to mention - the outputs from your workflows will also be written to your data tables if you provided an attribute for them to be written to. You can see in the screenshot below that the output directories to your Google bucket and data tables are listed on the methods configuration page on Terra:

     

    In this example, the outputs are saved to the "/ submission unique ID / SampleToMultipleOutput / workflow unique ID" directory in the Google bucket and to the "this.fastq-header" column in the "specimen" Data table. Looking at my specimen data table we can see the out txt files in the fastq-header column:

     

    Kind regards,

    Emil

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  • Comment author
    Stephanie Gogarten

    The job manager is currently not working, I see this screen:

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  • Comment author
    Emil Furat

    Hi Stephanie,

     

    Does the job manager continue to not load?

    Instead of finding your output file by going through the job manager, you can also access your workspace bucket by clicking on the link in the Dashboard page of your workspace ("Open in browser" pictured below):

    From here you can find the outputs for your workflow/task of interest by following the "/ submission unique ID / name of Task / workflow unique ID" convention.

    If you have any other questions please let us know.

     

    Kind regards,

    Emil

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  • Comment author
    Emil Furat

    Hi Stephanie,

     

    We haven't heard from you in a couple of days so I just wanted to check-in and see how things were going. Have you had any luck finding the outputs from your workflow?

    If we can help answer any other questions please let us know!

     

    Kind regards,

    Emil

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  • Comment author
    Stephanie Gogarten

    The job manager is still not loading. I was able to find the output string in my results directory, but it's six clicks through the directory structure to get there, so much less convenient than the job manager (I assume, as I haven't been able to use it yet).

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  • Comment author
    Emil Furat

    Hi Stephanie,

     

    Have you been able to get the job manager for your submission to open?

    The error you received in the Job Manager is usually transient, however, some users have received this error because the size of the metadata for the submission they made is exceedingly larger - could this be the case for you?

     

    Kind regards,

    Emil

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