local.conf

backend {
  # Override the default backend.
  #default = "LocalExample"

  # The list of providers.
  providers {
    # Copy paste the contents of a backend provider in this section
    # Examples in cromwell.example.backends include:
    # LocalExample: What you should use if you want to define a new backend provider
    # AWS: Amazon Web Services
    # BCS: Alibaba Cloud Batch Compute
    # TES: protocol defined by GA4GH
    # TESK: the same, with kubernetes support
    # Google Pipelines, v2 (PAPIv2)
    # Docker
    # Singularity: a container safe for HPC
    # Singularity+Slurm: and an example on Slurm
    # udocker: another rootless container solution
    # udocker+slurm: also exemplified on slurm
    # HtCondor: workload manager at UW-Madison
    # LSF: the Platform Load Sharing Facility backend
    # SGE: Sun Grid Engine
    # SLURM: workload manager

    # Note that these other backend examples will need tweaking and configuration.
    # Please open an issue https://www.github.com/broadinstitute/cromwell if you have any questions

    # The local provider is included by default. This is an example.
    # Define a new backend provider.
    Local {
      # The actor that runs the backend. In this case, it's the Shared File System (SFS) ConfigBackend.
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"

      # The backend custom configuration.
      config {

        # Optional limits on the number of concurrent jobs
        #concurrent-job-limit = 5

        # If true submits scripts to the bash background using "&". Only usefull for dispatchers that do NOT submit
        # the job and then immediately return a scheduled job id.
        # run-in-background = true

        # `temporary-directory` creates the temporary directory for commands.
        #
        # If this value is not set explicitly, the default value creates a unique temporary directory, equivalent to:
        # temporary-directory = "$(mktemp -d \"$PWD\"/tmp.XXXXXX)"
        #
        # The expression is run from the execution directory for the script. The expression must create the directory
        # if it does not exist, and then return the full path to the directory.
        #
        # To create and return a non-random temporary directory, use something like:
        # temporary-directory = "$(mkdir -p /tmp/mydir && echo /tmp/mydir)"

        # `script-epilogue` configures a shell command to run after the execution of every command block.
        #
        # If this value is not set explicitly, the default value is `sync`, equivalent to:
        # script-epilogue = "sync"
        #
        # To turn off the default `sync` behavior set this value to an empty string:
        # script-epilogue = ""

	# `glob-link-command` specifies command used to link glob outputs, by default using hard-links.
	# If filesystem doesn't allow hard-links (e.g., beeGFS), change to soft-links as follows:
	# glob-link-command = "ln -sL GLOB_PATTERN GLOB_DIRECTORY"

	# The list of possible runtime custom attributes.
        runtime-attributes = """
        String? docker
        String? docker_user
        """

        # Submit string when there is no "docker" runtime attribute.
        submit = "/usr/bin/env bash ${script}"

        # Submit string when there is a "docker" runtime attribute.
        submit-docker = """
        docker run \
          --rm -i \
          ${"--user " + docker_user} \
          --entrypoint ${job_shell} \
          -v ${cwd}:${docker_cwd} \
          -v /tmp/data:/data \
          ${docker} ${docker_script}
        """

        # Root directory where Cromwell writes job results.  This directory must be
        # visible and writeable by the Cromwell process as well as the jobs that Cromwell
        # launches.
        root = "cromwell-executions"

        # Root directory where Cromwell writes job results in the container. This value
        # can be used to specify where the execution folder is mounted in the container.
        # it is used for the construction of the docker_cwd string in the submit-docker
        # value above.
        dockerRoot = "/cromwell-executions"

        # File system configuration.
        filesystems {

          # For SFS backends, the "local" configuration specifies how files are handled.
          local {

            # Try to hard link (ln), then soft-link (ln -s), and if both fail, then copy the files.
            localization: [
              "hard-link", "soft-link", "copy"
            ]
            # An experimental localization strategy called "cached-copy" is also available for SFS backends.
            # This will copy a file to a cache and then hard-link from the cache. It will copy the file to the cache again
            # when the maximum number of hardlinks for a file is reached. The maximum number of hardlinks can be set with:
            # max-hardlinks: 950

            # Call caching strategies
            caching {
              # When copying a cached result, what type of file duplication should occur. Attempted in the order listed below:
              duplication-strategy: [
                "hard-link", "soft-link", "copy"
              ]

              # Possible values: file, path, path+modtime
              # "file" will compute an md5 hash of the file content.
              # "path" will compute an md5 hash of the file path. This strategy will only be effective if the duplication-strategy (above) is set to "soft-link",
              # in order to allow for the original file path to be hashed.
              # "path+modtime" will compute an md5 hash of the file path and the last modified time. The same conditions as for "path" apply here.
              # Default: file
              hashing-strategy: "file"

              # When true, will check if a sibling file with the same name and the .md5 extension exists, and if it does, use the content of this file as a hash.
              # If false or the md5 does not exist, will proceed with the above-defined hashing strategy.
              check-sibling-md5: false
            }
          }
        }
      }
    }
  }
}