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    Jason Cerrato

    Hey Marcos Castro-Silva,

    Happy to help here! Can you provide a screenshot of your method configuration page before you run the workflow?

    Kind regards,

    Jason

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    Marcos Castro-Silva

    Hi Jason,

    Thank you for the fast response. 

    Here is a screenshot of the first part of the configuration page:

     

    Ande here is a screenshot of the second part of the configuration page:

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    Marcos Castro-Silva

    And here is a screenshot of the error message:

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    Jason Cerrato

    Hi Marcos Castro-Silva,

    Do you have any items in your output configuration that use this.<something> notation? This could be the reason you're running into the error. Would you mind providing screenshots of your output config?

    You can alternatively share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace (see the icon with the three dots at the top-right) for us to take a look.

    1. Add GROUP_FireCloud-Support@firecloud.org to the User email field
    2. Click Add User
    3. Click Save

    Kind regards,

    Jason

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    Marcos Castro-Silva

    Hi Jason,

    I have not altered any of the parameters in the output configuration, so there is nothing to see there. From what I understand I don't need to configure the output, as it has default parameters, or have I misunderstood it?

    I have shared the workspace with GROUP_FireCloud-Support@firecloud.org as you told me, I think it will be easier. 

    Thank you very much for your help.

    Marcos

     

     

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    Jason Cerrato

    Hi Marcos,

    Thank you for sharing the workspace. We'll take a look and get back to you as soon as we can.

    Kind regards,

    Jason

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    Jason Cerrato

    Hi Marcos,

    It looks like there's something finnicky happening on the backend of that method configuration state. If you click Run workflow(s) with inputs defined by data table and then click back to Run workflow(s) with inputs defined by file paths, it should allow you to save and run the submission. Our engineers are looking at why the page has a mismatch in the state.

    So that should get you off the ground as far as being able to submit the workflow. However there's an issue with the configuration that will not allow it to run, as you've provided a .bam file for the FOFN. If you try to run it in this state, you will receive the following error.

    IOException: Could not read from gs://fc-96368ca5-0efa-4277-b2ec-91fd261582a7/BBS023_unmapped.bam: File gs://fc-96368ca5-0efa-4277-b2ec-91fd261582a7/BBS023_unmapped.bam is larger than 10000000 Bytes. Maximum read limits can be adjusted in the configuration under system.input-read-limits.

    If you look at the example method configuration for this workflow, you can see that there's an unmapped bams list provided for that variable: https://app.terra.bio/#workspaces/help-gatk/five-dollar-genome-analysis-pipeline/workflows/gatk/Germline_Single_Sample_Workflow

    As such, if you are set on using this workflow, you will need to supply an appropriate file type for that variable in order to run it. If you look at the dashboard page for the workspace I just linked, you will see a note that this workspace is no longer being updated, and that the Whole-Genome-Analysis-Pipeline supersedes the five-dollar-genome-analysis pipeline. As such, our recommendation would be to clone the Whole-Genome-Analysis-Pipeline workspace and use its workflow instead, or export the workflow from Whole-Genome-Analysis-Pipeline to your current workspace and follow the spec explained on the Dashboard.

    If you have any questions about any of this, please let me know.

    Kind regards,

    Jason

     

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    Marcos Castro-Silva

    Hi Jason,

    First I would like to thank you for your help and attention. I am new to this kind of analysis, so I probably made some mistakes there and I am sorry about it. I will try to run the Whole-Genome-Analysis-Pipeline and come back to you. 

    Thank you very much again.

    Kind regards,

    Marcos

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    Jason Cerrato

    Hi Marcos,

    Not a problem at all. We are happy to help, regardless of your level of familiarity!

    If we can be of any further assistance, please let us know.

    Kind regards,

    Jason

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