cwlVersion: v1.2

$namespaces:
  s: https://schema.org/
  cwltool: http://commonwl.org/cwltool#

s:softwareVersion: 1.0.0

$graph:

- class: Workflow
  id: pipeline-tree
  doc: ...
  inputs:
    dir:
      type: Directory
      doc: Directory to list files
  steps:
    step_1:
      run: '#tree'
      in:
        dir: dir
      out:
      - file_tree
      - metadata
    step_2:
      run: '#2stac2'
      in:
        file1: step_1/file_tree
        metadata: step_1/metadata
      out:
      - results
    
  outputs:
  - id: wf_outputs
    outputSource:
    - step_2/results
    type:
      Directory

- class: CommandLineTool
  baseCommand: tree
  id: tree

  arguments:
  - --dir
  - valueFrom: $( inputs.dir )

  inputs:
    dir:
      type: Directory
      doc: directory
      
  outputs:
    file_tree:
      type: File
      outputBinding:
        glob: "result/file_tree.txt"
      doc: tree list
      s:fileFormat: "application/text"
    metadata:
      type: File
      outputBinding:
        glob: "result/metadata.json"
      doc: tree list
      s:fileFormat: "application/json"
      
  requirements:
    NetworkAccess:
      networkAccess: true

    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/tree:1.0.0

- class: CommandLineTool
  baseCommand: 2stac
  id: 2stac2

  arguments:
  - valueFrom: $(
      function () {
        var files_array = [];

        Object.keys(inputs).forEach(element => {
          if(element != 'metadata') {
            files_array.push('--files');
            files_array.push(inputs[element]);
          } else {
            files_array.push('--metadata');
            files_array.push(inputs[element]);
          }
        });

        return files_array;
      }())
  
  inputs:
    file1:
      type: File
      doc: List directory tree
    metadata:
      type: File
      doc: The resulting metadata of the previous model to insert in STAC 
      s:name: Input metadata file
      s:description: The resulting metadata of the previous model to insert in STAC 
      s:keywords:
        - metadata
        - File
      s:fileFormat: "application/json"

  outputs:
    results:
      outputBinding:
        glob: .
      type: Directory
      doc: STAC output

  requirements:
    EnvVarRequirement:
      envDef:
        PATH: /srv/conda/envs/model-env/bin:/srv/conda/bin:/srv/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
    ResourceRequirement: {}
    InlineJavascriptRequirement: {}
    DockerRequirement:
      dockerPull: iliad-repository.inesctec.pt/2stac2:1.0.0