scriptcwl 0.7.0

scriptcwl is a Python package for creating workflows in Common Workflow Language (CWL). If you give it a number of CWL CommandLineTools, you can create a workflow by writing a Python script. This can be done interactively using Jupyter Notebooks. The full documentation can be found on Read the Docs.

Given CWL CommandLineTools for add and multiply (these are available in scriptcwl), a CWL specification of this workflow can be written as:

from scriptcwl import WorkflowGenerator

with WorkflowGenerator() as wf:
  wf.load(steps_dir='/path_to_scriptcwl/scriptcwl/examples/')

  num1 = wf.add_input(num1='int')
  num2 = wf.add_input(num2='int')

  answer1 = wf.add(x=num1, y=num2)
  answer2 = wf.multiply(x=answer1, y=num2)

  wf.add_outputs(final_answer=answer2)

  wf.save('add_multiply_example_workflow.cwl')

The workflow has two integers as inputs (num1 and num2), and first adds these two numbers (wf.add(x=num1, y=num2)), and then multiplies the answer with the second input (num2). The result of that processing step is the output of the workflow. Finally, the workflow is saved to a file. The result looks like:

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
  num1: int
  num2: int
outputs:
  final_answer:
    type: int
    outputSource: multiply/answer
steps:
  add:
    run: add.cwl
    in:
      y: num2
      x: num1
    out:
    - answer
  multiply:
    run: multiply.cwl
    in:
      y: num2
      x: add/answer
    out:
    - answer

The Python and CWL files used in the example can be found in the examples folder.

pip install scriptcwl

git clone git@github.com:NLeSC/scriptcwl.git
cd scriptcwl
git checkout develop
pip install -r requirements.txt
python setup.py develop

python setup.py develop test