erisone-ml.conf

# This line is required. It pulls in default overrides from the embedded cromwell `application.conf` needed for proper
# performance of cromwell.
#include required("application")
include required(classpath("application"))
workflow-options  { 
	workflow-log-temporary = true
}

database {
  profile = "slick.jdbc.MySQLProfile$"
  db {
    driver = "com.mysql.cj.jdbc.Driver"
    url = "[URL]"
    user = "cromwell"
    password = "[PASSWORD]"
    connectionTimeout = 5000
  }
}

call-caching {
  enabled = true
  invalidate-bad-cache-results = true
}

docker {
  hash-lookup {
    # Set this to match your available quota against the Google Container Engine API
    #gcr-api-queries-per-100-seconds = 1000

    # Time in minutes before an entry expires from the docker hashes cache and needs to be fetched again
    #cache-entry-ttl = "20 minutes"

    # Maximum number of elements to be kept in the cache. If the limit is reached, old elements will be removed from the cache
    #cache-size = 200

    # How should docker hashes be looked up. Possible values are "local" and "remote"
    # "local": Lookup hashes on the local docker daemon using the cli
    # "remote": Lookup hashes on docker hub and gcr
    #method = "remote"
  }
}

engine {
  # This instructs the engine which filesystems are at its disposal to perform any IO operation that it might need.
  # For instance, WDL variables declared at the Workflow level will be evaluated using the filesystems declared here.
  # If you intend to be able to run workflows with this kind of declarations:
  # workflow {
  #    String str = read_string("gs://bucket/my-file.txt")
  # }
  # You will need to provide the engine with a gcs filesystem
  # Note that the default filesystem (local) is always available.
  filesystems {
    #  gcs {
    #    auth = "application-default"
    #  }
    local {
      #enabled: true
    }
  }
}

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

  # The list of providers.
  providers {
    LSF_singularity {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
	run-in-background = true
        runtime-attributes = """
        String simg
        """
	root = "cromwell-executions"
        submit = "bsub -q big-multi singularity exec ${simg} ${script}"
        kill = "bkill ${job_id}"
        check-alive = "bjobs ${job_id}"
        job-id-regex = "Job <(\\d+)>.*"
      }
    }
    singularity {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
        run-in-background = true
        runtime-attributes = """
	String simg
        """
        root = "cromwell-executions"
        submit = "chmod 755 ${script} && /opt/singularity/2.5.2/bin/singularity exec --cleanenv --bind ${cwd}:${cwd} --nv /data/aryee/simg/${simg} ${script}"
      }
    }

    Local { 
            actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
            config {
                run-in-background = true
                submit = "bash ${script}"
            }
        }

  }
}