scriptcwl

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.

Installation

Install using pip:

pip install scriptcwl

For development:

git clone [email protected]:NLeSC/scriptcwl.git
cd scriptcwl
git checkout develop
pip install -r requirements.txt
python setup.py develop

Run tests (including coverage) with:

python setup.py develop test

Useful tools

To use scriptcwl for creating CWL workflows, you need CWL CommandLineTools. There are some software packages that help with generating those for existing command line tools written in Python:

• argparse2tool: Generate CWL CommandLineTool wrappers (and/or Galaxy tool descriptions) from Python programs that use argparse. Also supports the click argument parser.
• pypi2cwl: Automatically run argparse2cwl on any package in PyPi.
• python-cwlgen: Generate CommandLineTool and DockerRequirement programmatically