Workflow¶

A Workflow definition is one or more yaml files that follow the Common Workflow Language specification

A full example of a generator task as a workflow CWL file is as follows:

cwlVersion: v1.2
class: Workflow

id: workflow_me_type_property
label: mock-generator-workflow

inputs:

    - id: cell_composition
      type: NexusType

    - id: output_dir
      type: Directory

outputs:

    partial_circuit:
        type: NexusType
        outputSource: register/resource_file

steps:
    - id: stage
      run: ./staging.cwl
      in:
        cell_composition: cell_composition
        output_dir: output_dir
      out:
        - composition_file

    - id: place
      run: ./place.cwl
      in:
         cell_composition: stage/composition_file
         output_dir: output_dir
      out:
         - nodes_file

    - id: register
      run: ./register.cwl
      in:
        cell_composition: cell_composition
        nodes_file: place/nodes_file
      out:
        - resource_file

Inputs¶

Workflow inputs are similar to CommandLineTool inputs, with the difference that only the id and the type of the input are specified. These inputs will then be used to be chanelled to the workflow steps where needed.

Outputs¶

Workflow outputs utilize the outputSource key to specify the step and output file that the workflow will address as a final output.

Steps¶

Each Workflow step connects the workflow inputs and outputs to a CommandLineTool handled by that step.

Mapping a workflow step to a CommandLineTool requires the following keys:

Attention

Workflow step ids must be unique within a Workflow

run¶

The run key is used to specify either the path to the definition of the CommandLineTool or directly embed it.

When a Variant is registered as a NEXUS resource, all definitions specified as files will be embedded so that a single Workflow definition is registered. However, when added in the registry, relative paths in the same directory are allowed for readability.

Note

Relative paths, e.g. ./file.cwl are resolved with respect to the location of the Workflow cwl file.

in¶

Defines the input parameters to the workflow step. To channel the output of another step the id of the task should be followed by the output id separated by a forward slash as task/output.

If an output name is specified without a forward slash, then it is assumed a workflow global input is given.

out¶

The out section is a list where all the outputs that are needed within the worklow are listed. It is not necessary to specify all possible outputs that the CommandLineTool produces, only those that are going to be used by other tasks or the workflow global outputs.