etc/gatk-wdl/cromwell.conf

   1 # https://github.com/broadinstitute/cromwell/blob/develop/core/src/main/resources/reference.conf
   2
   3 # https://cromwell.readthedocs.io/en/develop/Configuring/#configuration-via-command-line
   4 # include the application.conf at the top
   5 include required(classpath("application"))
   6 # java -Dconfig.file=/path/to/yourOverrides.conf cromwell.jar
   7 # java -Dwebservice.port=8080 cromwell.jar
   8 #webservice.port = 58000
   9 webservice {
  10   port = 8000
  11   interface = 0.0.0.0
  12   binding-timeout = 5s
  13   instance.name = "reference"
  14 }
  15
  16 # JAVA_OPTS="-Dconfig.file=/share/FGI2017B/users/huxs/nsfcG/wgs/cromwell.conf" cromwell run mutect2.wdl -i mutect2.bgi.inputs.json > cromwell.mutect2.log &
  17 # JAVA_OPTS="-Dbackend.providers.Local.config.concurrent-job-limit=16" cromwell
  18 backend.providers.Local.config.concurrent-job-limit = 16
  19
  20 #backend {
  21 #  default = "Local"
  22 #  providers {
  23 #    Local {
  24 #      actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
  25 #      config {
  26 #        include required(classpath("reference_local_provider_config.inc.conf"))
  27 #        concurrent-job-limit = 16
  28 #      }
  29 #    }
  30 #  }
  31 #}