---
pipeline:
  name: tempSpecificDepthLakes_level1_reshape
transform:
  cmd:
  - Rscript
  - ./flow.tsdl.comb.splt.R
  - DirIn=$DIR_IN
  - DirOut=/pfs/out
  - NameDirCombOut=/level1_reshape
  - NameVarTime=001|030
  - MrgeCols=startDateTime|endDateTime
  - FileSchmMapDepth=$FILE_SCHEMA_MAP_DEPTH
  - FileSchmMapCols=$FILE_SCHEMA_MAP_COLS
  - LocDir=location
  - StatDir=stats
  - QmDir=quality_metrics
  - NameFileSufxRm=basicStats|qualityMetrics
  image: quay.io/battelleecology/neon-is-tsdl-comb-splt-r:aa651ed4
  image_pull_secrets:
  - battelleecology-quay-read-all-pull-secret
  env:
    LOG_LEVEL: DEBUG
input:
  cross:
  - pfs:
      name: DIR_IN
      repo: tempSpecificDepthLakes_level1_group
      branch: master
      glob: "/tchain/*/*/*"
  - pfs:
      name: FILE_SCHEMA_MAP_COLS
      repo: avro_schemas_tempSpecificDepthLakes
      branch: master
      glob: "/tempSpecificDepthLakes/tempSpecificDepthLakes_dp01_column_term_substitutions.avsc"
  - pfs:
      name: FILE_SCHEMA_MAP_DEPTH
      repo: avro_schemas_tempSpecificDepthLakes
      branch: master
      glob: "/tempSpecificDepthLakes/tempSpecificDepthLakes_dp01_depth_term_map.avsc"
parallelism_spec:
  constant: 1
resource_requests:
  memory: 200M
  cpu: 0.5
autoscaling: true
scheduling_spec:
  node_selector:
    cloud.google.com/gke-ephemeral-storage-local-ssd: "true"
    nodepool.neonscience.org/pipeline: "yes"
    cloud.google.com/gke-spot: "true"
pod_spec: |-
  { "tolerations": [
    {
      "key": "nodepool.neonscience.org/pipeline",
      "operator": "Exists"
    },
    {
      "effect": "NoSchedule",
      "key": "cloud.google.com/gke-spot",
      "operator": "Exists"
    }  
  ] }
pod_patch: |-
  [
    { "op": "replace",
      "path":"/containers/1/resources/requests/memory",
      "value":"500M"
    },
    { "op": "replace",
      "path": "/containers/1/resources/requests/cpu",
      "value": ".2"
    }
  ]
