EFS Workflow Filesystem

Amazon EFS Workflow Filesystem

Workflow engines that support it may use Amazon EFS as a shared “scratch” space for hosting workflow intermediates and outputs. Initial inputs are localized once from S3 and final outputs are written back to S3 when the workflow is complete. All intermediate I/O is performed against the EFS filesystem.


  1. Compared with the S3 Filesystem there is no redundant I/O of inputs from S3.
  2. Each tasks individual I/O operations tend to be smaller than the copy from S3 so there is less network congestion on the container host.
  3. Option to use provisioned IOPs to provide high sustained throughput.
  4. The volume is elastic and will expand and contract as needed.
  5. It is simple to start an Amazon EC2 instance from the AWS console and connect it to the EFS volume to view outputs as they are created. This can be useful for debugging a workflow.


  1. Amazon EFS volumes are more expensive than storing intermediates and output in S3, especially when the volume uses provisioned IOPs.
  2. The volume exists for the lifetime of the context and will incur costs based on its size for the lifetime of the context. If you no longer need the context we recommend destroying it.
  3. Call caching is only possible for as long as the volume exists, i.e. the lifetime of the context.

Provisioned IOPs

Amazon EFS volumes deployed by the Amazon Genomics CLI use “bursting” throughput by default. For workflows that have high I/O throughput or in scenarios where you may have many workflows running in the same context at the same time, you may exhaust the burst credits of the volume. This might cause a workflow to slow down or even fail. Available volume credits can be monitored in the Amazon EFS console, and/ or Amazon CloudWatch. If you observe the exhaustion of burst credits you may want to consider deploying a context with provisioned throughput IOPs.

The following fragment of an agc-project.yaml file is an example of how to configure provisioned throughput for the Amazon EFS volume used by miniwdl in an Amazon Genomics CLI context.

      - type: wdl
        engine: miniwdl
          fsType: EFS
            provisionedThroughput: 1024

Supporting Engines

The use of Amazon EFS as a shared file system is supported by the miniwdl and Snakemake engines. Both use EFS with bursting throughput by default and both support provisioned IOPs.