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Project description
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.
Install
Requires Python 3.6+
virtualenv -p python3.6 venv3.6 # Python 3.7, 3.8, or 3.9 would also work
source venv3.6/bin/activate
pip install cwl-utils
or install the latest development version of cwl-utils
git clone https://github.com/common-workflow-language/cwl-utils.git
cd cwl-utils
virtualenv -p python3.6 venv3.6 # Python 3.7, 3.8, or 3.9 would also work
source venv3.6/bin/activate
pip 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.
python 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.
python docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl
Development
Regenerate parsers
To regenerate install the schema_salad package and run:
cwl_utils/parser_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_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_v1_2.py was created via
schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/main/CommonWorkflowLanguage.yml
Release
To release CWLUtils, bump the version in cwl_utils/__meta__.py, and tag that
commit with the new version. TravisCI should release that tag.
Release history Release notifications | RSS feed
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