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cwl-utils

A collection of scripts to demonstrate the use of the new Python classes for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.

Requires Python 3.6+

Installation

pip3 install cwl-utils

To install from source:

git clone https://github.com/common-workflow-language/cwl-utils.git
cd cwl-utils
pip3 install .

Usage

Pull the all referenced software container images

docker_extract.py is useful to cache or pre-pull all software container images referenced in a CWL CommandLineTool or CWL Workflow (including all referenced CommandLineTools and sub-Workflows and so on).

The default behaviour is to use the Docker engine to download and save the software container images in Docker format.

docker_extract.py DIRECTORY path_to_my_workflow.cwl

Or you can use the Singularity software container engine to download and save the software container images and convert them to the Singularity format at the same time.

docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl

Using the CWL Parsers

from pathlib import Path
from ruamel import yaml
import sys

from cwl_utils.parser import load_document_by_uri, save

# File Input - This is the only thing you will need to adjust or take in as an input to your function:
cwl_file = Path("testdata/md5sum.cwl")  # or a plain string works as well

# Import CWL Object
cwl_obj = load_document_by_uri(cwl_file)

# View CWL Object
print("List of object attributes:\n{}".format("\n".join(map(str, dir(cwl_obj)))))

# Export CWL Object into a built-in typed object
saved_obj = save(cwl_obj)
print(f"Export of the loaded CWL object: {saved_obj}.")

Development

Regenerate parsers

To regenerate install the schema_salad package and run:

cwl_utils/parser/cwl_v1_0.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/CommonWorkflowLanguage.yml

cwl_utils/parser/cwl_v1_1.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/main/CommonWorkflowLanguage.yml

cwl_utils/parser/cwl_v1_2.py was created via schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/1.2.1_proposed/CommonWorkflowLanguage.yml

Release

To release CWLUtils, bump the version in cwl_utils/__meta__.py, and tag that commit with the new version. The gh-action-pypi-publish should release that tag.

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