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.
multiply (these are available
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 (
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.
Install using pip:
pip install scriptcwl
git clone firstname.lastname@example.org:NLeSC/scriptcwl.git cd scriptcwl python setup.py develop
Run tests (including coverage) with:
python setup.py test
To use scriptcwl for creating CWL workflows, you need CWL
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
Copyright (c) 2016-2018, Netherlands eScience Center, University of Twente
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