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final_workflow_outputs_dir in cromwell.conf ?

Is it possible to set a default final_workflow_outputs_dir in cromwell.conf so that is used for every workflow that is executed? I know that it is possible to add this settings in the workflow options.json file, but we always want to copy the final outputs so we would prefer to have this setting in the global config file.

I have tried adding it in my config file like this, but that did not appear to have any effect:

workflow-options {
  # These workflow options will be encrypted when stored in the database
  #encrypted-fields: []

  # AES-256 key to use to encrypt the values in `encrypted-fields`
  #base64-encryption-key: "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="

  # Directory where to write per workflow logs
  #workflow-log-dir: "cromwell-workflow-logs"

  # When true, per workflow logs will be deleted after copying
  workflow-log-temporary: false

  final_workflow_outputs_dir: "results"

  # Workflow-failure-mode determines what happens to other calls when a call fails. Can be either Con
  # Can also be overridden in workflow options. Defaults to NoNewCalls. Uncomment to change:
  #workflow-failure-mode: "ContinueWhilePossible"
}
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Answers

  • jamespjamesp Member
    I have the same question. It doesn't seem to work in Cromwell 40, from what I can tell?
  • jamespjamesp Member
    Because the formatting wasn't clear to me, I tried all of the following combinations, none of which worked (but supplying the options.json file does work) in Cromwell 40:

    ```
    workflow-options {
    final-workflow-outputs-dir = "gs://ukbb_v2/projects/jamesp/cromwell_output"
    final_workflow_outputs_dir: "gs://ukbb_v2/projects/jamesp/cromwell_output"
    "final-workflow-outputs-dir": "gs://ukbb_v2/projects/jamesp/cromwell_output"
    "final_workflow_outputs_dir": "gs://ukbb_v2/projects/jamesp/cromwell_output"

    default {
    final-workflow-outputs-dir = "gs://ukbb_v2/projects/jamesp/cromwell_output"
    final_workflow_outputs_dir: "gs://ukbb_v2/projects/jamesp/cromwell_output"
    "final-workflow-outputs-dir": "gs://ukbb_v2/projects/jamesp/cromwell_output"
    "final_workflow_outputs_dir": "gs://ukbb_v2/projects/jamesp/cromwell_output"
    }
    }
    ```
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