Add test workflow

.gitlab-ci.yml

@@ -21,7 +21,7 @@ before_script:
   - source venv/bin/activate
   - pip install cwltool cwl-runner
   - cd test_data
-  - tar -xvf ${TEST_DATASET_NAME}
+  - tar -xf ${TEST_DATASET_NAME}
   - cd $CI_PROJECT_DIR
 
 after_script:
@@ -39,3 +39,4 @@ test_DPPP_step:
     - cwl-runner steps/DP3.AveragerStepGenerator.cwl test_jobs/averager_step_generator.json
     - cwl-runner steps/DP3.AOFlaggerStepGenerator.cwl test_jobs/aoflagger_step_generator.json
     - ! cwl-runner steps/DP3.AveragerStepGenerator.cwl test_jobs/averager_step_generator_error.json
+    - cwltool test_workflow/flag_average.cwl msin=test_data/L570745_SB001_uv_first10.MS

test_workflow/test.cwl

-class: Workflow
-cwlVersion: v1.0
-id: test
-label: test
-$namespaces:
-  sbg: 'https://www.sevenbridges.com'
-inputs:
-  - id: msin
-    type: Directory
-    'sbg:x': -1111
-    'sbg:y': -277
-outputs:
-  - id: msout
-    outputSource:
-      - dppp/msout
-    type: Directory
-    'sbg:x': -772.234375
-    'sbg:y': -472.50433349609375
-steps:
-  - id: aoflagger_step_generator
-    in: []
-    out:
-      - id: parameters_out
-    run: ../steps/DP3.AOFlaggerStepGenerator.cwl
-    'sbg:x': -1357.640625
-    'sbg:y': -729.5
-  - id: average_step_generator
-    in:
-      - id: input_parset
-        source:
-          - aoflagger_step_generator/parameters_out
-    out:
-      - id: parameters_out
-    run: ../steps/DP3.AveragerStepGenerator.cwl
-    'sbg:x': -1125
-    'sbg:y': -729
-  - id: generic_step
-    in:
-      - id: parameters_input
-        source:
-          - average_step_generator/parameters_out
-    out:
-      - id: output_parset
-      - id: input_files
-      - id: input_directories
-    run: ../steps/DP3.ParsetGenerator.cwl
-    'sbg:x': -1174
-    'sbg:y': -525
-  - id: dppp
-    in:
-      - id: parset
-        source: generic_step/output_parset
-      - id: msin
-        source: msin
-      - id: secondary_files
-        source:
-          - generic_step/input_files
-    out:
-      - id: msout
-    run: ../steps/DPPP.cwl
-    'sbg:x': -957
-    'sbg:y': -530
-requirements:
-  - class: SubworkflowFeatureRequirement