illusional / cwl-utils

Python 3.6+ utilities for CWL

cwl-utils

A collection of scripts to demonstrate the use of the new Python classes for loading and parsing CWL v1.0 documents.

cwl_utils/parser_v1_0.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/master/v1.0/CommonWorkflowLanguage.yml

Install

Requires Python 3.6.x or Python 3.7

git clone https://github.com/common-workflow-language/cwl-utils.git
virtualenv -p python3.6 venv3.6
source venv3.6/bin/activate
pip install cwl-utils

Usage

Pull the image with Docker

This is the default behaviour:

python docker_extract.py DIRECTORY path_to_my_workflow.cwl

Pull the image with Singularity

python docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl

Regenerate

To regenerate install schema_salad package and run:

schema-salad-tool --codegen python \
    https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/CommonWorkflowLanguage.yml