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Local execution

With Fusion, you can run Nextflow pipelines using the local executor and a cloud storage bucket as the pipeline scratch directory. This is useful to scale your pipeline execution vertically with a large compute instance, without the need to allocate a large storage volume for temporary pipeline data.

Nextflow CLI

tip

This configuration requires Docker or a similar container engine to run pipeline tasks.

  1. Set AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY environment variables to grant Nextflow and Fusion access to your storage credentials. See Credentials for more information.

  2. Add the following to your nextflow.config file:

    wave.enabled = true
    docker.enabled = true
    fusion.enabled = true
    fusion.exportStorageCredentials = true
  3. Run the pipeline with the Nextflow run command:

    nextflow run <PIPELINE_SCRIPT> -w s3://<S3_BUCKET>/work

    Replace the following:

    • PIPELINE_SCRIPT: your pipeline Git repository URI
    • S3_BUCKET: your S3 bucket name
tip

To achieve optimal performance, set up an SSD volume as the temporary directory.

warning

The option fusion.exportStorageCredentials leaks credentials on the task launcher script created by Nextflow. This option should only be used for testing and development purposes.