A backend is a way to run the commands of your workflow. Cromwell allows for backends conforming to the Cromwell backend specification to be plugged into the Cromwell engine. Additionally, backends are included with the Cromwell distribution:

  • Local
  • HPC, including Sun Grid Engine, LSF, HTCondor & SLURM
    • Run jobs as subprocesses or via a dispatcher.
    • Supports launching in Docker containers.
    • Use bash, qsub, and bsub to run scripts.
  • Google Cloud
    • Launch jobs on Google Compute Engine through the Google Genomics Pipelines API.
    • Launch jobs on servers that support the GA4GH Task Execution Schema (TES).
  • AWS Batch (beta)
    • Use Job Queues on AWS Batch

HPC backends are put under the same umbrella because they all use the same generic configuration that can be specialized to fit the need of a particular technology.

Backends are specified in the backend.providers configuration. Each backend has a configuration that looks like:

BackendName {
  actor-factory = "FQN of BackendLifecycleActorFactory class"
  config {

The structure within the config block will vary from one backend to another; it is the backend implementation's responsibility to be able to interpret its configuration.

The providers section can contain multiple backends which will all be available to Cromwell.

Backend Job Limits

All backends support limiting the number of concurrent jobs by specifying the following option in the backend's configuration stanza:

backend {
  providers {
    BackendName {
      actor-factory = ...
      config {
        concurrent-job-limit = 5

Backend Filesystems

Each backend will utilize a filesystem to store the directory structure and results of an executed workflow. The backend/filesystem pairings are as follows:

Additional filesystems capabilities can be added depending on the backend. For instance, an HPC backend can be configured to work with files on Google Cloud Storage. See the HPC documentation for more details.