sprocket run

Individual tasks and workflows can be run with the sprocket run subcommand. We outline a few of the important considerations below, but we encourage you to run sprocket run --help to see all available arguments and options.

Entrypoints

The task or workflow to run can be provided explicitly with the --entrypoint argument.

sprocket run --entrypoint main example.wdl

Whether or not this argument is required is based on whether inputs are provided to Sprocket from which the entrypoint can be inferred (e.g., providing an input of main.is_pirate implies an entrypoint of main). Conversely, if you supply an --entrypoint, you don't have to prefix your inputs with the entrypoint fully qualified name.

Sprocket will indicate when it cannot infer the entrypoint.

Inputs

Inputs to a Sprocket run are provided as arguments passed after the WDL document name is provided. Each input can be specified as either

• a key value pair (e.g., main.is_pirate=true)
• a JSON file containing inputs (e.g., a hello_defaults.json file where the contents are { "main.is_pirate": true })
• a YAML file containing inputs (e.g. a hello_defaults.yaml file where the contents are main.is_pirate: true)

Inputs are incrementally applied, meaning that inputs specified later override inputs specified earlier. This enables you to do something like the following to use a set of default parameters and iterate through sample names in Bash rather than create many individual input files.

sprocket run example.wdl hello_defaults.json main.name="Ari"

An example

Using the the WDL document from the guided tour, we can specify the name parameter as a key-value pair on the command line.

sprocket run example.wdl --entrypoint main name="World"

After a few seconds, this job runs successfully with the following outputs.

{
  "main.messages": [
    "Hello, World!",
    "Hallo, World!",
    "Hej, World!"
  ]
}

If you wanted to override some of the defaults for the workflow, you could do so by defining the input in a hello_overrides.json file:

{
  "main.greetings": [
    "Good morning",
    "Good afternoon",
    "Good evening"
  ],
  "main.is_pirate": true
}

Then providing that file in the set of inputs to the workflow.

sprocket run example.wdl hello_overrides.json main.name="Sprocket"

This produces the following output.

{
  "main.messages": [
    "Good morning, Sprocket!",
    "Good afternoon, Sprocket!",
    "Good evening, Sprocket!",
    "Ahoy, Sprocket!"
  ]
}