DSL2

• Ports NF encryption pipeline to dsl2
• Uses an egapass file instead of --ega_password - addresses #1
• Moves ega-cryptor JAR to moduleDir, removing the need to specify --ega_cryptor

conf/eddie.config

-/*
- * ----------------------------------------------------
- *  University of Edinburgh eddie config file
- * ----------------------------------------------------
- */
-
-executor = "local"
-
-process {
-
-  beforeScript = """
-  . /etc/profile.d/modules.sh
-  sleep 2;
-  """
-
-  penv = "sharedmem"
-
-  cpus = 2
-  memory = 4.GB
-  time = 4.h
-  clusterOptions = "-l h_vmem=${memory.toString().replaceAll(/[\sB]/,'')}"
-
-  errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'terminate' }
-  maxRetries = 1
-  maxErrors = '-1'
-
-  withName: encrypt {
-    cpus = { check_max( 8, 'cpus' ) }
-    memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-    time = { check_max( 4.h * task.attempt, 'time' ) }
-  }
-
-}
-
-params {
-  // Defaults only, expecting to be overwritten
-  max_memory = 256.GB
-  max_cpus = 16
-  max_time = 240.h
-}