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SNAP Graph inline

CWL allows creating files using the InitialWorkDirRequirement:

      InitialWorkDirRequirement:
        listing:
          - entryname: graph.xml
            entry: |-

The file graph.xml is created before executing the CommandLineTool. This approach is thus used to create the SNAP Graph with the content provided in the CWL document.

This approach removes the File parameter used in the previous section and provides a self-standing CWL document:

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class: CommandLineTool
id: sar-calibration

requirements:
  DockerRequirement:
    dockerPull: snap-gpt
  EnvVarRequirement:
    envDef:
      PATH: /srv/conda/envs/env_snap/snap/bin:/usr/share/java/maven/bin:/usr/share/java/maven/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
  ResourceRequirement: {}
  InitialWorkDirRequirement:
    listing:
      - entryname: calibration.xml
        entry: |-
          <graph id="Graph">
            <version>1.0</version>
            <node id="Read">
              <operator>Read</operator>
              <sources/>
              <parameters class="com.bc.ceres.binding.dom.XppDomElement">
                <file>${inFile}</file>
                <formatName>SENTINEL-1</formatName>
              </parameters>
            </node>
            <node id="Calibration">
              <operator>Calibration</operator>
              <sources>
                <sourceProduct refid="Read"/>
              </sources>
              <parameters class="com.bc.ceres.binding.dom.XppDomElement">
                <sourceBands/>
                <auxFile>Product Auxiliary File</auxFile>
                <externalAuxFile/>
                <outputImageInComplex>false</outputImageInComplex>
                <outputImageScaleInDb>false</outputImageScaleInDb>
                <createGammaBand>false</createGammaBand>
                <createBetaBand>false</createBetaBand>
                <selectedPolarisations>${selPol}</selectedPolarisations>
                <outputSigmaBand>true</outputSigmaBand>
                <outputGammaBand>false</outputGammaBand>
                <outputBetaBand>false</outputBetaBand>
              </parameters>
            </node>
            <node id="Write">
              <operator>Write</operator>
              <sources>
                <sourceProduct refid="Calibration"/>
              </sources>
              <parameters class="com.bc.ceres.binding.dom.XppDomElement">
                <file>./cal.dim</file>
                <formatName>BEAM-DIMAP</formatName>
              </parameters>
            </node>
          </graph>

baseCommand: [gpt, calibration.xml]

inputs:

  polarization:
    inputBinding:
      position: 1
      prefix: -PselPol=
      separate: false
    type: string

  safe:
    inputBinding:
      position: 2
      prefix: -PinFile=
      separate: false
    type: Directory

outputs:
  results:
    outputBinding:
      glob: .
    type: Directory

stderr: std.err
stdout: std.out

cwlVersion: v1.0

The baseCommand is updated to add the calibration.xml argument:

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   </graph>

baseCommand: [gpt, calibration.xml]

inputs:

The Workflow is updated accordingly: 

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$graph:
- class: Workflow
  id: main
  doc: SNAP Sentinel-1 GRD Calibration
  label: SNAP Sentinel-1 GRD Calibration

  inputs:

    polarization:
      doc: Polarization channel 
      label: Polarization channel 
      type: string

    safe:
      doc: Sentinel-1 GRD product SAFE Directory
      label: Sentinel-1 GRD product SAFE Directory
      type: Directory

  outputs:
  - id: wf_outputs
    outputSource:
    - node_1/results
    type: Directory

  requirements:
    SubworkflowFeatureRequirement: {}

  steps:

    node_1:
      in:
        snap_graph: snap_graph
        polarization: polarization
      out:
      - results
      run: '#sar-calibration'

- class: CommandLineTool
  id: sar-calibration

  requirements:
    DockerRequirement:
      dockerPull: snap-gpt
    EnvVarRequirement:
      envDef:
        PATH: /srv/conda/envs/env_snap/snap/bin:/usr/share/java/maven/bin:/usr/share/java/maven/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
    ResourceRequirement: {}
    InitialWorkDirRequirement:
      listing:
        - entryname: calibration.xml
          entry: |-
            <graph id="Graph">
              <version>1.0</version>
              <node id="Read">
                <operator>Read</operator>
                <sources/>
                <parameters class="com.bc.ceres.binding.dom.XppDomElement">
                  <file>${inFile}</file>
                  <formatName>SENTINEL-1</formatName>
                </parameters>
              </node>
              <node id="Calibration">
                <operator>Calibration</operator>
                <sources>
                  <sourceProduct refid="Read"/>
                </sources>
                <parameters class="com.bc.ceres.binding.dom.XppDomElement">
                  <sourceBands/>
                  <auxFile>Product Auxiliary File</auxFile>
                  <externalAuxFile/>
                  <outputImageInComplex>false</outputImageInComplex>
                  <outputImageScaleInDb>false</outputImageScaleInDb>
                  <createGammaBand>false</createGammaBand>
                  <createBetaBand>false</createBetaBand>
                  <selectedPolarisations>${selPol}</selectedPolarisations>
                  <outputSigmaBand>true</outputSigmaBand>
                  <outputGammaBand>false</outputGammaBand>
                  <outputBetaBand>false</outputBetaBand>
                </parameters>
              </node>
              <node id="Write">
                <operator>Write</operator>
                <sources>
                  <sourceProduct refid="Calibration"/>
                </sources>
                <parameters class="com.bc.ceres.binding.dom.XppDomElement">
                  <file>./cal.dim</file>
                  <formatName>BEAM-DIMAP</formatName>
                </parameters>
              </node>
            </graph>

  baseCommand: [gpt, calibration.xml]

  inputs:

    polarization:
      inputBinding:
        position: 2
        prefix: -PselPol=
        separate: false
      type: string
    safe:
      inputBinding:
        position: 2
        prefix: -PinFile=
        separate: false
      type: Directory

  outputs:
    results:
      outputBinding:
        glob: .
      type: Directory

  stderr: std.err
  stdout: std.out

cwlVersion: v1.0