Adding workflow steps

After loading steps and adding workflow inputs, the steps of the workflow should be specified. To add a step to a workflow, its method must be called on the WorkflowGenerator object. For example, to add a step called add [1] to the workflow, the following method must be called:

answer1 = wf.add(x=num1, y=num2)

The method expects a list of key=value pairs as input parameters. (To find out what inputs a step needs call wf.inputs(<step name>). This method prints all inputs and their types.) wf.<step name>() returns a string if the step has a single output and a tuple of strings if the step has multiple output parameters:

output1, output2 = wf.someStep(input=input)

The order of the outputs is the same as in the step specification, and can be determined by printing the step signatures using print(wf.list_steps()).

The strings returned by wf.<step name>() contain output names that can be used as input for later steps, or that can be connected to workflow outputs. For example, in a later step, answer1 can be used as input:

answer2 = wf.multiply(x=answer1, y=num2)

Scattering steps

Scriptcwl supports scattering steps. To scatter a step, keyword arguments scatter and scatter_method must be provided when a step is added to the workflow. To scatter a step called echo, which has a single input argument message, this would look like:

output = wf.echo(message=input1, scatter='message', scatter_method='dotproduct')

The type of message, should be array (e.g., an array of strings).

To scatter over multiple variables, scatter also accepts a list of input names:

output = wf.echo(message1=input1, message2=input2, scatter=['message1', 'message2'], scatter_method='dotproduct')

[1]	Scriptcwl contains two example command line tools, add and multiply. The Python and CWL files can be found in the examples folder.