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job run

Usage

Description

The job run command runs a job on a Flywheel site using the specified gear and version. The user will be prompted to provide input files and configuration values.

Configuration Options

By default, the gear's configuration values remain unchanged. However, you can use the -m/--modify-config option to modify them. When this option is used, you will be prompted to adjust each configuration value before execution. If a gear has a required configuration option for which no default value is provided, you will be prompted to enter a value.

Destination Container

A destination container can be specified using the -d/--destination option. The destination container serves different purposes depending on the job type:

Analysis Jobs

For analysis jobs, the destination container is where the newly created analysis container will be attached. Valid destinations include projects, subjects, sessions, and acquisitions.

Default behavior: If not specified, the destination will be the session of the first input file. If the gear has no inputs, you will be prompted to specify a destination container.

Utility Jobs

For utility jobs (or any non-analysis jobs), the destination container is where the job outputs will be uploaded.

Default behavior: The destination will be the parent container of the first input file.

Best practice: For utility jobs, you should only modify the destination container with caution. In most cases, the destination should be the parent container of one of the job inputs.

Input Specification

Input files and destination containers may be specified in the following formats:

  • A Flywheel container / file ID
  • A Flywheel path (i.e. fw://<group>/<project>/<subject>/<session>/<acquisition>)
  • The "fw://" portion of the string may be omitted.

Examples

flyw job run gear_name 1.0.0

Run a job with the specified gear.

flyw job run gear_name 1.0.0 -m

Modify the gear configuration before running.

flyw job run gear_name 1.0.0 -d fw://path/to/container

Specify the destination container for the job.

flyw job run gear_name 1.0.0 -y

Automatically answer yes to all prompts.