For built-in documentation of Cromwell command line usage, run the Cromwell JAR file with no arguments:

$ java -jar cromwell-<versionNumber>.jar

You will get a usage message like the following:

cromwell 29
Usage: java -jar /path/to/cromwell.jar [server|run] [options] <args>...

  --help                   Cromwell - Workflow Execution Engine
  --version                
Command: server
Starts a web server on port 8000.  See the web server documentation for more details about the API endpoints.
Command: run [options] workflow-source
Run the workflow and print out the outputs in JSON format.
  workflow-source          Workflow source file or workflow url .
  --workflow-root <value>  Workflow root
  -i, --inputs <value>     Workflow inputs file.
  -o, --options <value>    Workflow options file.
  -t, --type <value>       Workflow type.
  -v, --type-version <value>
                           Workflow type version.
  -l, --labels <value>     Workflow labels file.
  -p, --imports <value>    A directory or zipfile to search for workflow imports.
  -m, --metadata-output <value>
                           An optional directory path to output metadata.

Cromwell's Server and Run modes can be invoked with the server and run arguments respectively. More information on these Cromwell modes can be found in Modes.

The Cromwell jar file can be built as described in Building.

server

server mode accepts no arguments and runs Cromwell as a web server that accepts REST requests. See the documentation for Cromwell's REST endpoints for how to interact with Cromwell in server mode.

run

run mode executes a single workflow in Cromwell and then exits.

  • workflow-source
    The single required argument. It can be either a local path or a remote URL pointing to the workflow source file.

  • --inputs
    An optional file of workflow inputs. Although optional, it is a best practice to use an inputs file to satisfy workflow requirements rather than hardcoding inputs directly into a workflow source file.

  • --options
    An optional file of workflow options. Some options are global (supported by all backends), while others are backend-specific. See the Workflow Options for more details.

  • --type
    An optional parameter to specify the language for the workflow source. As of Cromwell 29 any value specified for this parameter is currently ignored and internally the value WDL is used.

  • --type-version
    An optional parameter to specify the version of the language for the workflow source. Currently any specified value is ignored.

  • --labels
    An optional parameter to specify a file of JSON key-value label pairs to associate with the workflow.

  • --imports
    You have the option of importing WDL workflows or tasks to use within your workflow, known as sub-workflows. If you use sub-workflows within your primary workflow then you must include a ZIP file with the WDL import files. See the documentation on Imports for more information.

  • --metadata-output
    You can specify a filename where Cromwell will write workflow metadata JSON such as start/end timestamps, status, inputs and outputs. By default Cromwell does not write workflow metadata. The metadata format in the --metadata-output file is the same as described for the REST API.

  • --version
    The --version option prints the version of Cromwell and exits.

  • --help
    The --help option prints the full help text above and exits.