bcbio-cromwell-gcp.conf

include required(classpath("application"))

system {
  workflow-restart = true
}
call-caching {
  enabled = true
}
load-control {
  # Avoid watching memory, since the load-controller stops jobs on local runs
  memory-threshold-in-mb = 1
}

cwltool-runner {
  # Use external cwltool to avoid slow runtimes with java embedded pre-processing
  class = "cwl.CwltoolProcess"
}


database {
  profile = "slick.jdbc.HsqldbProfile$"
  db {
    driver = "org.hsqldb.jdbcDriver"
    url = "jdbc:hsqldb:file:/home/chapmanb/drive/work/cwl/test_bcbio_cwl/gcp/cromwell_work/persist/metadata;shutdown=false;hsqldb.tx=mvcc"
    connectionTimeout = 200000
  }
}



google {
  application-name = "cromwell"
  auths = [
    {
      name = "gcp-auth"
      scheme = "service_account"
      json-file = ${?GOOGLE_APPLICATION_CREDENTIALS}
    }
  ]
}
engine {
  filesystems {
    gcs {
      auth = "gcp-auth"
      project = "somatic-validation"
    }
  }
}


backend {
  providers {
    Local {
      config {
        concurrent-job-limit = 1
        runtime-attributes = """
        Int? cpu
        Int? memory_mb
        String? docker
        String? docker_user
        Int? cpuMin
        Int? cpuMax
        Int? memoryMin
        Int? memoryMax
        String? outDirMin
        String? outDirMax
        String? tmpDirMin
        String? tmpDirMax
        """
        
             filesystems {

        gcs {
          auth = "gcp-auth"
          caching {
            duplication-strategy = "copy"
          }
        }
        }

      }
    }


    PAPI {
      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
      config {
        project = "somatic-validation"
        root = "gs://bcbiotest/gcp/work_cromwell"

        genomics {
          auth = "gcp-auth"
          endpoint-url = "https://genomics.googleapis.com/"
        }

        filesystems {
          gcs {
            auth = "gcp-auth"
            project = "somatic-validation"
          }
        }
      }
    }

  }
}