WorkflowStepInput-class: WorkflowStepInputList

Description

WorkflowStepInputList

WorkflowStepOutputList

WorkflowStepList

A workflow step is an executable element of a workflow. It specifies the underlying process implementation (such as CommandLineTool) in the run field and connects the input and output parameters of the underlying process to workflow parameters.

Usage

WorkflowStepInputList(...)
WorkflowStepOutputList(...)
WorkflowStepList(...)

Arguments

...

element or list of the element.

Value

a WorkflowStep object or subclass object.

Fields

id: [character] The unique identifier for this workflow step.
inputs: (WorkflowStepInputList) Defines the input parameters of the workflow step. The process is ready to run when all required input parameters are associated with concrete values. Input parameters include a schema for each parameter and is used to validate the input object, it may also be used build a user interface for constructing the input object.
outputs: (WorkflowStepOutputList) Defines the parameters representing the output of the process. May be used to generate and/or validate the output object.
requirements: [ProcessRequirement] Declares requirements that apply to either the runtime environment or the workflow engine that must be met in order to execute this workflow step. If an implementation cannot satisfy all requirements, or a requirement is listed which is not recognized by the implementation, it is a fatal error and the implementation must not attempt to run the process, unless overridden at user option.
hints: [ANY] Declares hints applying to either the runtime environment or the workflow engine that may be helpful in executing this workflow step. It is not an error if an implementation cannot satisfy all hints, however the implementation may report a warning.
label: [character] A short, human-readable label of this process object.
description: [character] A long, human-readable description of this process object.
run: (CommandLineToolORExpressionToolORWorkflow) Specifies the process to run.
scatter: [character]
scatterMethod: [ScatterMethod] Required if scatter is an array of more than one element.

WorkflowStepInput Class

merge_nested: The input shall be an array consisting of exactly one entry for each input link. If merge_nested is specified with a single link, the value from the link is wrapped in a single-item list.
merge_flattened: 1) The source and sink parameters must be compatible types, or the source type must be compatible with single element from the "items" type of the destination array parameter. 2) Source parameters which are arrays are concatenated; source parameters which are single element types are appended as single elements.
id: (character) A unique identifier for this workflow input parameter.
source: [character] Specifies one or more workflow parameters that will provide input to the underlying process parameter.
linkMerge: [LineMergeMethod] The method to use to merge multiple inbound links into a single array. If not specified, the default method is merge_nested:
default: [ANY] The default value for this parameter if there is no source field.

WorkflowStepOutput Class

id: (character) A unique identifier for this workflow output parameter. This is the identifier to use in the source field of WorkflowStepInput to connect the output value to downstream parameters.

Scatter/gather

To use scatter/gather, ScatterFeatureRequirement must be specified in the workflow or workflow step requirements. A "scatter" operation specifies that the associated workflow step or subworkflow should execute separately over a list of input elements. Each job making up a scatter operaution is independent and may be executed concurrently. The scatter field specifies one or more input parameters which will be scattered. An input parameter may be listed more than once. The declared type of each input parameter is implicitly wrapped in an array for each time it appears in the scatter field. As a result, upstream parameters which are connected to scattered parameters may be arrays. All output parameters types are also implicitly wrapped in arrays; each job in the scatter results in an entry in the output array. If scatter declares more than one input parameter, scatterMethod describes how to decompose the input into a discrete set of jobs.

dotproduct specifies that each the input arrays are aligned and one element taken from each array to construct each job. It is an error if all input arrays are not the same length.
nested_crossproductspecifies the cartesian product of the inputs, producing a job for every combination of the scattered inputs. The output must be nested arrays for each level of scattering, in the order that the input arrays are listed in the scatter field.
flat_crossproductspecifies the cartesian product of the inputs, producing a job for every combination of the scattered inputs. The output arrays must be flattened to a single level, but otherwise listed in the order that the input arrays are listed in the scatter field.

Subworkflows

To specify a nested workflow as part of a workflow step, SubworkflowFeatureRequirement must be specified in the workflow or workflow step requirements.

Examples

Run this code

ws <- WorkflowStepList(WorkflowStep(id = "step1", label = "align-and-sort",
             description = "align and sort", 
             inputs = WorkflowStepInputList(
                 WorkflowStepInput(id = "id1"),
                 WorkflowStepInput(id = "id2")
             )))

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