CWL Tool

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.

Prerequisites

• python 3.6+

• Docker

• (Optional) cURL

• (Optional) git

Getting Started

The following software and workflow are required and will be downloaded, installed, and used as part of this tutorial:

• cwltool

• 02_download_collection_files.wdl

Download the worked examples repository by one of the following methods.

1. Clone with Git

git clone https://github.com/DNAstack/dnastack-client-library-worked-examples.git

or

1. 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/

[block:image] { "images": [ { "image": [] } ] } [/block]

Download and install cwltool by one of the following methods.

1. Using apt for Debian, Ubuntu, and similar Linux distributions

sudo apt-get install cwltool

or

1. 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.