Cromwell

Workbench supports submitting workflows to cromwell deployed in many different environments. While there are some configuration options that are different depending on the environment, there are some common parameters that are supported across all environments.

Available Parameters

workflow_failure_mode=STRING

Determines what happens when a call fails. Valid options are "NoNewCalls" and "ContinueWhilePossible". "NoNewCalls" will stop execution of all remaining calls in the workflow, while "ContinueWhilePossible" will continue executing other calls in the workflow as long as their dependencies are satisfied.

write_to_cache=BOOLEAN

Specifies whether to write the outputs of successful calls to the call cache. Default is true.

read_from_cache=BOOLEAN

Specifies whether to read the outputs of previously successful calls from the call cache. Default is true.

delete_intermediate_output_files=BOOLEAN

Specifies whether to delete intermediate output files. Default is false.

final_workflow_outputs_dir=STRING

Specifies a directory to which final output files should be copied. This can be a local path or a URI.

final_call_logs_dir=STRING

Specifies a directory to which call logs should be copied. This can be a local path or a URI.

final_workflow_log_dir=STRING

Specifies a directory to which the final workflow log should be copied. This can be a local path or a URI.

final_workflow_metadata_dir=STRING

Specifies a directory to which the final workflow metadata should be copied. This can be a local path or a URI.

use_relative_output_paths=BOOLEAN

Specifies whether to use relative output paths in workflow outputs. Default is false.

call_caching=OBJECT

A JSON object containing the call caching configuration. Example:

{
  "call_caching": {
    "enable": true,
    "read_from_cache": true,
    "write_to_cache": true
  }
}

default_runtime_attributes=OBJECT

A JSON object containing the default runtime attributes. Example:

{
  "default_runtime_attributes": {
    "maxRetries": 1
  }
}

default_backend=STRING

Specifies the default backend to use for workflow execution. Default is "Local".

allow_result_reuse=BOOLEAN

Specifies whether to allow reuse of previously calculated results. Default is true.

disallow_result_reuse=BOOLEAN

Specifies whether to disallow reuse of previously calculated results. Default is false.

imported_file_metadata=STRING

Specifies the metadata file for imported files. This can be a local path or a URI.