Issue Launching Tool

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8 comments

  • Sushma Chaluvadi

    Sahar -

    Did you choose a specific set of pairs or are you Launching analysis with the default settings?

     

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  • Sahar Alkhairy

    I tries both selecting pairs to run and the default.

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  • Sushma Chaluvadi

    Sahar -

    Can you try to export the Tool to your workspace and before doing so, renaming it to have no "." in the name?

    If this does not work can you share your workspace name and workspace with

    GROUP_FireCloud-Support@firecloud.org so we can take a closer look.

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  • Sahar Alkhairy

    I deleted the task then reimported it to exclude ".". So, no the tool is able to launch.

    However, it is failing as it is unable to find attributes it requires to run (it runs on pairs) and it is giving me the attached errors.

    I understand that there is an issue linking pairs to samples and this maybe the cause of the problem. So, I am awaiting a response on that.

    I also, emailed my workspace link to GROUP_FireCloud-Support@firecloud.org .

    Thanks,

    Sahar

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  • ericco92

    I'm having similar issues on sample_sets. Clicking "select data" causes the Terra interface to completely crash. Clicking the error bubble details button shows this message:

     

    I assume this is some sort of broken assumption in the data model. This workflow runs fine in classic FireCloud, and I've run a previous version of it in Terra.

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  • Sushma Chaluvadi

    Hi Sahar and Ericco92 -

    Can you email your workspace link to Terra-support@broadinstitute.zendesk.org.

     

    Can you confirm if this is the case with all Tools that you are running with sample_sets or if this is simple with the CGA WES pipeline. Essentially, I am trying to determine for sure if the issue is a linking issue for pairs and samples in the data model.

     

    Sushma

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  • Sushma Chaluvadi

    Hi Sahar -

    I tried to replicate uploading the Data Model to link pairs and it seems that I was unable to do this either. I tested the same .tsv files in FireCloud which was successful. I am checking with the team to determine if the steps I followed are incorrect or if there is perhaps a bug. As soon as I hear back I will make sure to update this post.

    Thanks for your patience.

     

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  • Sushma Chaluvadi

    Sahar and Ericco92 -

    I have asked the Terra team and it looks like the Data Model in Terra does not show Pair and Sample associations as links the way it does in FireCloud. Previously, we had errors with linking not working but have recently implemented a fix that allows you to manually choose to link the uploading .tsv.

    When you choose a .tsv to upload you will be prompted to "Create participant, sample, and pair associations". For participant, sample, and pair .tsv files this box should be checked to make sure that the Data Model knows to create the links.

    Some small formatting rules to keep in mind:

    Sample table needs to have a participant column.

    Pair table needs to have the case, control, and participant columns labeled as case_sample, control_sample, and participant respectively. The documentation here (https://software.broadinstitute.org/firecloud/documentation/article?id=9772) shows that you are required to add "_id" after case_sample, control_sample, and participant but that is not necessary as long as you check the box to explicitly tell the data model to make the association.

    Lastly, it is possible that your current data models were uploaded to the workspaces prior to the addition of the ""Create participant, sample, and pair associations" and therefore will need to be re-uploaded while selecting the box for each of the three tables. 

    Would you both be able to confirm that the Tool is working/not working after re-uploading your .tsv tables (with selection of the make associations box)?

    Thank you!

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