SGE.conf

include required(classpath("application"))
webservice {
  port = 8000
}
backend {
  default="SGE"
  providers {
    SGE {
      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
      config {
        concurrent-job-limit = 10000
        runtime-attributes= """
          Int? cpu=1
          Int? memory=4
        """
        submit = """
        qsub \
            -terse \
            -V \
            -b n \
            -wd ${cwd} \
            -N ${job_name} \
            ${'-pe BWA ' + cpu} \
            ${'-l h_vmem=' + memory + "G"} \
            -o ${out} \
            -e ${err} \
            ${script}
        """
        kill = "qdel ${job_id}"
        check-alive = "qstat -j ${job_id}"
        job-id-regex = "(\\d+)"

        filesystems {
          localization: [
            "soft-link", "copy", "hard-link"
          ]
          local {
            caching {
              duplication-strategy: [ "soft-link", "copy", "hard-link" ]
              hashing-strategy: "file"
            }
          }
        }
      }
    }
  }
}
system {
  abort-jobs-on-terminate = true
  io {
    number-of-requests = 10
    per = 10 seconds
    number-of-attempts = 180
  }
}
call-caching {
  enabled = true
  invalidate-bad-cache-results = true
}
database {
  db.url = "jdbc:mysql://ourdatabase/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
  db.user = "****"
  db.password = "****"
  db.driver = "com.mysql.jdbc.Driver"
  profile = "slick.jdbc.MySQLProfile$"
}
workflow-options {
  workflow-failure-mode = "ContinueWhilePossible"
}