DNAnexus
DNAnexus supports WDL workflows through their dx-toolkit
and dxCompiler
tools. This guide demonstrates running the 02_download_collection_files.wdl
workflow, which typically takes 5-10 minutes to complete.
Prerequisites
Before beginning, ensure you have the following:
Java 8 or higher
Python 3.5 or higher
Optional: cURL, git
Getting Started
The following software and workflows are required and will be installed and used as part of this tutorial:
Getting the Example Workflow
Clone with 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:
Installing Required Tools
Download dxCompiler:
Download the latest version of dxCompiler
by one of the following methods. This allows direct conversion and uploading of WDL workflows to DNAnexus.
Using cURL
Or download from the releases page to the current directory and rename the file to dxCompiler.jar
.
Install and initialize dx-toolkit
Download and initialize dx-toolkit
. You will be prompted to log into your DNAnexus account.
Running a Workflow
Create a project on DNAnexus where the workflow and associated files will be stored.
Once your project has been setup, import the WDL workflow
02_download_collection_files.wdl
to the DNAnexus platform using dxCompiler.
To run the newly created workflow on the DNAnexus platform, select the project folder and Workflow item, and click "Run" as Analysis.
To view the progress of the workflow at any time, select the "Monitor" tab.
Inputs or parameters of the workflow can be modified. For example, to download from a different collection.
The output files can be found in and downloaded from the folder specified in the Run dialog. In this case, the root of the DNAnexus project.
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