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Specify current runtime arguments using wdl?

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    Jason

    Hey Bryan,

    Thanks for writing in - happy to help here! To start, I will point you to the current WDL spec which lives here: https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md

    In WDL workflows, you would specify the runtime arguments in the runtime block rather than in the command. Here is some documentation with descriptions and examples: https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/

    Additional information: https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#runtime-section

    The current working directory is set to the /cromwell_root/ in the Google VM by default. If you localize directories to the VM, you can cd to those directories within the task block before running the commands.

    You set outputs in the outputs block of the workflow, as shown here: https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md#outputs-section

    Finally, it may help to review actual WDL code to get a handle on how it works. I recommend checking out the workflows of our Featured workspaces to get a better sense of how these pieces fit together! You can find those here: https://app.terra.bio/#workspaces?tab=featured

    If you have any other questions, please let us know.

    Kind regards,

    Jason

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    Jason

    Hi Bryan,

    To follow-up on that matter of changing the working directory, you will want to remember to move any needed output files back to the /cromwell_root directory because that is where Cromwell is expecting all outputs and inputs to be stored.

    Kind regards,

    Jason

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    Bryan Cosca

    Hi Jason,

    Thanks for the thorough response and all your help. With your answers and the examples on Terra, I think I am all set for now. I'll be sure to reach back on this forum if I have any more questions.

    Thanks,

    Bryan

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    Jason

    Hi Bryan,

    Glad to hear - do let us know if we can be of any further assistance!

    Kind regards,

    Jason

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