Workflow

A workflow is a process consisting of one or more steps. Each step has input and output parameters defined by the inputs and outputs fields. A workflow executes as described in execution model.

WorkflowOutputParameterList(...)

Arguments

...	element or list of the element.

Value

a Workflow object.

Fields

outputs

(WorkflowOutputParameterList) Defines the parameters representing the output of the process. May be used to generate and/or validate the output object. Inherited from Process

steps

(WorkflowStepList) The individual steps that make up the workflow. Steps are executed when all input data links are fufilled. An implementation may choose to execute the steps in a different order than listed and/or execute steps concurrently, provided that dependencies between steps are met.

WorkflowOutputParameter Class

Describe an output parameter of a workflow. The parameter must be connected to one or more parameters defined in the workflow that will provide the value of the output parameter.

source

[character] Specifies one or more workflow parameters that will provide this output value.

linkMerge

[LinkMergeMethod] The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested:

Dependencies

Dependencies between parameters are expressed using the source field on workflow step input parameters and workflow output parameters.

The source field expresses the dependency of one parameter on another such that when a value is associated with the parameter specified by source, that value is propagated to the destination parameter. When all data links inbound to a given step are fufilled, the step is ready to execute.

Extensions

ScatterFeatureRequirement and SubworkflowFeatureRequirement are available as standard extensions to core workflow semantics.

Examples

# need better examples here
ws <- WorkflowStepList(
    WorkflowStep(
        id = "step1", label = "align-and-sort",
        description = "align and sort",
        inputs = WorkflowStepInputList(
            WorkflowStepInput(id = "id1"),
            WorkflowStepInput(id = "id2")
        )
    )
)
Workflow(steps = ws)
#> id: '#'
#> inputs: []
#> outputs: []
#> requirements: []
#> hints: []
#> class: Workflow
#> steps:
#> - id: '#step1'
#>   inputs:
#>   - id: '#id1'
#>   - id: '#id2'
#>   outputs: []
#>   hints: []
#>   label: align-and-sort
#>   description: align and sort
#>