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Version: 23.3.0

Custom AWS Batch launch container

You can customize your Seqera instance's Nextflow launch container, e.g., to include private CA certificates or compliance software in your Nextflow environment.

Seqera recommends using the default Nextflow launch container wherever possible. Custom launch containers can complicate your Seqera configuration and upgrade process.

Specify the path to your custom launch container image with an environment variable:

Use an AWS Batch job definition as a Seqera custom launch container

Seqera Platform automatically registers an AWS Batch job definition to launch pipelines with the required Nextflow runtime.

If you need to manage this manually, create a job definition in your AWS Batch environment with the following settings:

  • name: any of your choice
  • image: a custom image based on the Seqera nf-launcher image
  • vcpus: at least 1
  • memory: at least 1000
  • command: true

After the job definition is registered, update your Seqera Enterprise configuration with the following (replace <YOUR_JOB_DEFINITION_NAME> with the name of the job definition):

The custom launch container is set at the root level, so all executions in your Seqera instance will use this container. If you set an AWS Batch job definition as your custom launch container, launching workflow executions in other cloud provider compute environments will fail.


The repository where your launch container resides must be accessible to the Batch cluster's ECS Agent.