Nextflow with AWS Batch

The content of this workshop is derived from a tutorial created by the nice folks at Seqera Labs, kudos to them! We won’t create or own pipelines and tweak code, but rather jump right in with a small proof-of-concept pipeline, which we will run locally in containers, submit locally to AWS Batch and run a batch job that submits to AWS Batch.


During this workshop you will implement a proof of concept of a RNA-seq pipeline. The goal of this workshop is not to become a Bioinformatician nor a Nextflow guru, but to get familiar with the concepts of nextflow and AWS Batch.

The estimated cost for running this 1.5 hour workshop will be less than $5.



Throughout this workshop, we provide commands for you to run in the terminal. These commands will look like this:


The command starts after $. Words that are UPPER_ITALIC_BOLD indicate a value that is unique to your environment. For example, the PRIVATE_KEY.PEM refers to the private key of an SSH key pair that you’ve created, and the EC2_PUBLIC_DNS_NAME is a value that is specific to an EC2 instance launched in your account.