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Register now to book your onboarding and training for Genomics England CloudOS.

This course will provide a comprehensive overview of running Nextflow with AWS Batch in CloudOS. Follow the journey of linking a repository, setting up configurations, running and monitoring jobs. It is intended for users who run their own or their collaborator’s already built pipelines. Running WDL workflows will also be introduced. As an optional add-on, this course includes how to launch jobs using CloudOS CLI.


  1. Bringing public and private tools into CloudOS with GitHub, GitLab and Docker
  2. Setting up Batch configurations and parameters
  3. Running, monitoring and troubleshooting pipelines
  4. Introduction to cost optimisations for running pipelines in CloudOS

Intended Audience

This course is intended for technical users who tend to test and develop code within a command line interface.

Attendees should be comfortable with command line tools and writing code in bash and Python or R. Familiarity with SQL is useful but not required.


Basic knowledge of running Nextflow or Cromwell workflows

Registrations are now closed.