Genomics workflow set made easy with AWS Genomics CLI

Brendan Bouffler
Date : March 25, 2022
Categories : AWS Batch ,AWS ParallelCluster ,Amazon NICE DCV ,Life Sciences
Tags : aws batch ,batch ,cpus ,covid 19 ,dcv ,ec2 ,gpus ,hpc ,high performance computing ,lustre ,parallel cluster ,schedulers ,storage ,wdl ,bioinformatics ,cloud ,cromwell ,genomics ,mini wdl ,nextflow ,pipelines ,snakemake ,virtualization ,vizualization ,techshorts

The AWS Genomics CLI (or AGC) seriously removes all the grunt work involved in setting up bioinformatics pipelines to run in the cloud. We know that Snakemake, Cromwell, NextFlow and miniWDL all work happily in the cloud on AWS Batch, but AGC means you don’t have to know to set all that stuff up - it does it for you.

You can have completely separate tool chains using completely different workflow languages all running at the same time, on the same infrastructure (if you like), sharing data and tooling.

Lee Pang from the dev team that built this came along to show us how it works, and - most importantly - how easy it is to get productive. Zero to hero in less than 30 mins - it’s really impressive.

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