application.conf

webservice {
  port = 8000
  interface = 0.0.0.0
  instance.name = "reference"
}

akka {
  loggers = ["akka.event.slf4j.Slf4jLogger"]
  actor {
    default-dispatcher {
      fork-join-executor {
        # Number of threads = min(parallelism-factor * cpus, parallelism-max)
        # Below are the default values set by Akka, uncomment to tune these

        #parallelism-factor = 3.0
        #parallelism-max = 64
      }
    }
  }

  dispatchers {
    # A dispatcher for actors performing blocking io operations
    # Prevents the whole system from being slowed down when waiting for responses from external resources for instance
    io-dispatcher {
      type = Dispatcher
      executor = "fork-join-executor"
      # Using the forkjoin defaults, this can be tuned if we wish
    }

    # A dispatcher for actors handling API operations
    # Keeps the API responsive regardless of the load of workflows being run
    api-dispatcher {
      type = Dispatcher
      executor = "fork-join-executor"
    }

    # A dispatcher for engine actors
    # Because backends behaviour is unpredictable (potentially blocking, slow) the engine runs
    # on its own dispatcher to prevent backends from affecting its performance.
    engine-dispatcher {
      type = Dispatcher
      executor = "fork-join-executor"
    }

    # A dispatcher used by supported backend actors
    backend-dispatcher {
      type = Dispatcher
      executor = "fork-join-executor"
    }

    # Note that without further configuration, all other actors run on the default dispatcher
  }
}

spray.can {
  server {
    request-timeout = 40s
  }
  client {
    request-timeout = 40s
    connecting-timeout = 40s
  }
}

system {
  // If 'true', a SIGINT will trigger Cromwell to attempt to abort all currently running jobs before exiting
  abort-jobs-on-terminate = false

  // Max number of retries per job that the engine will attempt in case of a retryable failure received from the backend
  max-retries = 10

  // If 'true' then when Cromwell starts up, it tries to restart incomplete workflows
  workflow-restart = true

  // Cromwell will cap the number of running workflows at N
  max-concurrent-workflows = 5000

  // Cromwell will launch up to N submitted workflows at a time, regardless of how many open workflow slots exist
  max-workflow-launch-count = 50

  // Number of seconds between workflow launches
  new-workflow-poll-rate = 20

  // Since the WorkflowLogCopyRouter is initialized in code, this is the number of workers
  number-of-workflow-log-copy-workers = 10
}

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: "/scratch1/fs1/gtac-mgi/CLE/myeloseq/cromwell-workflow-logs"

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

  // 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"
}

// Optional call-caching configuration.
call-caching {
  enabled = false
  invalidate-bad-cache-results = false
}

backend {
  default = "LSF"
  providers {
    Local {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
        run-in-background = true
        runtime-attributes = "String? docker"
        submit = "/bin/bash ${script}"
        submit-docker = "docker run --rm -v ${cwd}:${docker_cwd} -i ${docker} /bin/bash < ${script}"

        root: "/scratch1/fs1/gtac-mgi/CLE/myeloseq/cromwell-executions"

        filesystems {
          local {
            localization: [
              "hard-link", "soft-link", "copy"
            ]
          }
        }
      }
    }

    LSF {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
        runtime-attributes = """
        Int cpu = 1
        Int memory_gb = 8
        String? queue
        String? dragen_env
        String? docker_image
        String? resource
        String? job_group
        """

        submit = """
        ${dragen_env} \
        bsub \
        -J ${job_name} \
        -cwd ${cwd} \
        -o ${out} \
        -e ${err} \
        -G 'compute-gtac-mgi' \
        -a "${docker_image}" \
        -q ${queue} \
        -g ${job_group} \
        -M ${memory_gb}G \
        -n ${cpu} \
        -R "span[hosts=1] select[mem>${memory_gb}G] rusage[mem=${memory_gb}G]" \
        /bin/bash ${script}
        """

        submit-docker = """
        ${dragen_env} \
        bsub \
        -J ${job_name} \
        -cwd ${cwd} \
        -o ${out} \
        -e ${err} \
        -G 'compute-gtac-mgi' \
        -a "${docker_image}" \
        -q ${queue} \
        -g ${job_group} \
        -M ${memory_gb}G \
        -n ${cpu} \
        -R "span[hosts=1] select[mem>${memory_gb}G] rusage[mem=${memory_gb}G]" \
        /bin/bash ${script}
        """
        kill = "bkill ${job_id}"
        check-alive = "bjobs -noheader -o \"stat\" ${job_id} | /bin/grep 'PEND\\|RUN'"
        job-id-regex = "Job <(\\d+)>.*"
        root: "/scratch1/fs1/gtac-mgi/CLE/myeloseq/cromwell-executions"
      }
    }
  }
}

services {
  KeyValue {
    class = "cromwell.services.keyvalue.impl.SqlKeyValueServiceActor"
  }
  MetadataService {
    class = "cromwell.services.metadata.impl.MetadataServiceActor"
  }
}