Specify current runtime arguments using wdl?

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Bryan Cosca

• October 26, 2020 15:26
• Edited

Hi! I'm a CWL user coming into using WDL.

Is there a way in wdl to specify the runtime arguments like memory, CPU in the command? Like ${runtime.cpu}? Also is there a way to specify the current working directory or output directory or a temporary directory?

For example, in a command

java -Xmx${runtime.memory}m -Djava.io.tmpdir=${runtime.tmpdir}

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  Jason Cerrato

  • October 26, 2020 17:33

  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 Cerrato

  • October 26, 2020 17:47

  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

  • October 26, 2020 18:07

  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 Cerrato

  • October 26, 2020 20:29

  Hi Bryan,

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

  Kind regards,

  Jason

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