rules.yaml

rulez:
  version: 1

parser:
  type: $graph
  driver: cwl

onstage:
  driver: cwl

  stage_in:
    connection_node: node_stage_in
    if_scatter:
      scatterMethod: dotproduct
    input:
      template:
        overwrite: True

  on_stage:
    connection_node: on_stage

  stage_out:
    connection_node: node_stage_out
    scatter: False
    if_scatter:
      scatterMethod: dotproduct
    follow_node: node_metrics_out


output:
  driver: cwl
  name: '-'
  type: $graph


cwl:
  GlobalInput:
    Directory: string
    Directory[]: string[]

  OptionalInput:
    Directory: string?
    Directory[]: string[]?

  stage_in:
    Directory?:
      type: string?

    Directory:
      type: string?

    Directory[]:
      type: string[]

  stage_out:
    Directory:
      type: Directory

    Directory[]:
      type: Directory[]

  outputBindingResult:
    command:
      Directory:
        outputBinding:
          glob: .
        type: Directory
      Directory[]:
        outputBinding:
          glob: .
        type: Directory[]
      Directory?:
        outputBinding:
          glob: ${ if (inputs.input == null) {return null } else {return ".";} }
        type: Directory?
    stepOut:
      type:
        items: Directory
        type: array