Common Workflow Language (CWL) is another workflow specification (similar to WDL). Below will outline how to run the
02_download_collection_files workflow in the
CWL format locally using
CWLtool and Docker.
The following software and workflow are required and will be downloaded, installed, and used as part of this tutorial:
Download the worked examples repository by one of the following methods.
- Clone with Git
git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git
- Or download and unzip
It is assumed that all commands will be run from the root directory of this repository on your local machine. From the directory where you’ve downloaded the examples repository.
Download and install cwltool by one of the following methods.
aptfor Debian, Ubuntu, and similar Linux distributions
sudo apt-get install cwltool
pip3 install cwlref-runner cwltool
Running the workflow
To run the workflow:
Output files can be found in the current directory.