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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.

Project details

Release history Release notifications | RSS feed

0.35

Oct 14, 2024

0.34

Sep 8, 2024

0.33

Apr 10, 2024

0.32

Dec 1, 2023

0.31

Nov 13, 2023

0.30 yanked

Oct 26, 2023

Reason this release was yanked:

broken format field parsing and other issues

0.29

Sep 2, 2023

0.28

Jun 1, 2023

0.27

May 17, 2023

0.26

May 11, 2023

0.25

May 2, 2023

0.24

Apr 13, 2023

0.23

Feb 1, 2023

0.22

Jan 26, 2023

0.21

Nov 28, 2022

0.20

Sep 27, 2022

0.19

Sep 13, 2022

0.18

Sep 7, 2022

0.17

Sep 2, 2022

0.16

Aug 25, 2022

0.15

Aug 19, 2022

0.14

Jul 15, 2022

0.13

Nov 11, 2021

0.12

Nov 7, 2021

0.11

Jul 2, 2021

0.10

Jun 16, 2021

This version

0.9

Dec 11, 2020

0.8

Dec 11, 2020

0.7

Aug 11, 2020

0.6

Jul 9, 2020

0.5

Jun 13, 2020

0.4

Jun 9, 2020

0.3

Jan 10, 2020

0.2

Jan 8, 2020

0.1

Jan 23, 2019

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