CWLtool

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

1. python 3.6+
2. Docker
3. (Optional) cURL
4. (Optional) git

Getting Started

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

1. cwltool
2. 02_download_collection_files.cdl

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

1. Clone with Git

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

2. 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.

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cd dnastack-client-library-worked-examples/

Download and install cwltool by one of the following methods.

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

   1	sudo apt-get install cwltool

2. Or pip

   1	pip3 install cwlref-runner cwltool

Running the workflow

To run the workflow:

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cwltool ./examples/cwl/02_download_collection_files.cwl

Output files can be found in the current directory.