CWL Tool

Common Workflow Language (CWL) provides an alternative workflow specification to WDL. This guide demonstrates running the 02_download_collection_files workflow in CWL format using CWLtool and Docker.

Prerequisites

• Python 3.6 or higher

• Docker

• Optional: cURL and git

Setup Instructions

You'll need to download:

• cwltool

• 02_download_collection_files.wdl

Getting the Example Workflow

Download the worked examples repository using either method:

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.

cd dnastack-client-library-worked-examples/

Installing CWL Tool

Install cwltool using either method:

Download and install cwltool by one of the following methods.

Using apt for Debian, Ubuntu, and similar Linux distributions

sudo apt-get install cwltool

Or use pip

pip3 install cwlref-runner cwltool

Running the workflow

To run the workflow:

cwltool ./examples/cwl/02_download_collection_files.cwl

Output files can be found in the current directory.