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include options in config file

When I run a workflow I always use an options file that makes sure the workflow outputs, logs and call-logs are copied over to my workflow output archive. I feel like it is a bit redundant to specify the same options.json file every time I run a workflow. Isnt there a better option like putting the options in the cromwell config file?

My options file looks something like:

{
    "final_workflow_outputs_dir": "/path/to/widdle/output",
    "final_workflow_log_dir": "/path/to/widdle/logs",
    "final_call_logs_dir": "/path/to/widdle/call_logs"
}

I am running with a local backend, cromwell 34, womtool 34

Best Answer

Answers

  • Irsan_KooiIrsan_Kooi Member
    edited January 3

    Hi Ruchi, thanks for helping out. I tried the following stanza, but it doesnt have any effect, outputs are not copied to specified dir. When I use -o /path/to/my/workflow-options.json then it works fine...

    Using cromwell run to submit, version 34, SGE backend

    workflow-options {
      # copy final outputs to widdle dir, which is synced every night to network
      # drive
      final_workflow_outputs_dir: "/home/ngs/widdle/output"
      final_workflow_log_dir: "/home/ngs/widdle/logs"
      final_call_logs_dir: "/home/ngs/widdle/call_logs"
    
      # 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: true
    
      # Workflow-failure-mode determines what happens to other calls when a call fails. Can be either ContinueWhilePossible or NoNewCalls.
      # Can also be overridden in workflow options. Defaults to NoNewCalls. Uncomment to change:
      #workflow-failure-mode: "ContinueWhilePossible"
    
      default {
        # When a workflow type is not provided on workflow submission, this specifies the default type.
        #workflow-type: WDL
    
        # When a workflow type version is not provided on workflow submission, this specifies the default type version.
        #workflow-type-version: "draft-2"
      }
    }
    
    
  • ChrisLChrisL Cambridge, MAMember, Broadie, Moderator, Dev admin
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