pipeline/script/cromwell.examples.conf

# This is an example of how you can use the LocalExample backend to define
# a new backend provider. *This is not a complete configuration file!* The
# content here should be copy pasted into the backend -> providers section
# of cromwell.example.backends/cromwell.examples.conf in the root of the repository.
# You should uncomment lines that you want to define, and read carefully to customize
# the file. If you have any questions, please open an issue at
# https://www.github.com/broadinstitute/cromwell/issues

# Documentation
# https://cromwell.readthedocs.io/en/stable/backends/Local/

# Define a new backend provider.

LocalExample {

  # 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} \
          ${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"
        ]

        # Call caching strategies
        caching {
          # When copying a cached result, what type of file duplication should occur.
          # For more information check: https://cromwell.readthedocs.io/en/stable/backends/HPC/#shared-filesystem
          duplication-strategy: [
            "hard-link", "soft-link", "copy"
          ]

          # Strategy to determine if a file has been used before.
          # For extended explanation and alternative strategies check: https://cromwell.readthedocs.io/en/stable/Configuring/#call-caching
          hashing-strategy: "md5"

          # 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
        }
      }
    }

    # The defaults for runtime attributes if not provided.
    default-runtime-attributes {
      failOnStderr: false
      continueOnReturnCode: 0
    }
  }
}

workflow-options {
  # These workflow options will be encrypted when stored in the database
  #encrypted-fields: []

  # AES-256 key to use to encrypt the values in `encrypted-fields`
  #base64-encryption-key: "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA="

  # Directory where to write per workflow logs
  workflow-log-dir: "logs"

  # When true, per workflow logs will be deleted after copying
  workflow-log-temporary: false

  # Workflow-failure-mode determines what happens to other calls when a call fails. Can be either ContinueWhilePossible or NoNewCalls.
  # Can also be overridden in workflow options. Defaults to NoNewCalls. Uncomment to change:
  workflow-failure-mode: "ContinueWhilePossible"

  default {
    # When a workflow type is not provided on workflow submission, this specifies the default type.
    #workflow-type: WDL

    # When a workflow type version is not provided on workflow submission, this specifies the default type version.
    #workflow-type-version: "draft-2"

    # To set a default hog group rather than defaulting to workflow ID:
    # hogGroup: "static"
  }
}