Posted On: May 27, 2022

Today, we are excited to announce that the Amazon Genomics CLI v1.5.0 has added support for workflows written in the Common Workflow Language (CWL) using the Toil workflow engine. In addition to CWL, the Amazon Genomics CLI supports workflows written with Workflow Definition Language (WDL), Nextflow, and Snakemake enabling customers to run a wide variety of genomics data analyses like joint calling of genome variants and single-cell RNAseq.

The Amazon Genomics CLI simplifies and automates the deployment of cloud resources like workflow engines and compute clusters, providing genomics and life science customers with an easy-to-use command line to quickly setup and run genomics workflows on Amazon Web Services (AWS).

The Common Workflow Language is an open standard for describing how to run command line tools and connect them to create workflows. Tools and workflows described using CWL are portable across a variety of platforms, making it easy to scale complex data analysis and machine learning workflows from a single laptop to cloud computing environments. Toil is a scalable, efficient, cross platform pipeline management system developed by the University of California Santa Cruz Genomics Institute (UCSC-GI), and provides full support for CWL v1.2. Thanks to an open source contribution from the Toil team at UCSC-GI, you can now quickly deploy Toil into your AWS account as an Amazon Genomics CLI context to run CWL workflows. Like other contexts used by the Amazon Genomics CLI, Toil will use AWS Batch for compute, leveraging optimal job placement and utilization of either Amazon EC2 On-Demand or Spot instances.

This release also includes the ability to configure specific VPC subnets to use when providing your own VPC during account activation, as well as specifying a custom AMI to use in contexts. These enhancements will help customers use Amazon Genomics CLI in AWS environments that require the use of hardened AMIs and have unique networking topologies.

Amazon Genomics CLI is available for use in all commercial AWS regions except Amazon Web Services China (Beijing) Region, operated by Sinnet and Amazon Web Services China (Ningxia) Region, operated by NWCD, AWS GovCloud (US), and air-gapped regions.

To learn more and get started with Amazon Genomics CLI visit: