Merge branch 'master' of https://git.astron.nl/eosc/prefactor3-cwl

.gitlab-ci.yml

@@ -173,12 +173,12 @@ predict:
 prefactor_calibrator:
   stage: integration_test
   script:
-    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json
+    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json
 
 toil:
   stage: integration_test
   script:
-    - toil-cwl-runner --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH --jobStore jobstore --writeLogs logs --workDir workdir prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json
+    - toil-cwl-runner --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH --jobStore jobstore --writeLogs logs --workDir workdir workflows/prefactor_calibrator.cwl test_jobs/integration_test_prefactor_calibrator.json
 
 flag_average:
   stage: integration_test

prefactor_calibrator_image.cwl

-class: Workflow
-cwlVersion: v1.0
-id: prefactor_calibrator_image
-label: prefactor_calibrator_image
-$namespaces:
-  sbg: 'https://www.sevenbridges.com/'
-inputs:
-  - id: msin
-    type: 'Directory[]'
-    'sbg:x': -549
-    'sbg:y': -168
-outputs:
-  - id: image
-    outputSource:
-      - wsclean/image
-    type: 'File[]'
-    'sbg:x': 206
-    'sbg:y': -189
-  - id: dirty_image
-    outputSource:
-      - wsclean/dirty_image
-    type: 'File[]'
-    'sbg:x': 271
-    'sbg:y': -87
-  - id: image_1
-    outputSource:
-      - wsclean_1/image
-    type: 'File[]'
-    'sbg:x': -133
-    'sbg:y': -405
-  - id: dirty_image_1
-    outputSource:
-      - wsclean_1/dirty_image
-    type: 'File[]'
-    'sbg:x': -26
-    'sbg:y': -292
-steps:
-  - id: prefactor_calibrator
-    in:
-      - id: msin
-        source:
-          - msin
-      - id: raw_data
-        default: true
-      - id: demix
-        default: false
-    out:
-      - id: demix_parmdb
-      - id: output_ms
-    run: ./prefactor_calibrator.cwl
-    label: prefactor_calibrator
-    'sbg:x': -234
-    'sbg:y': -94
-  - id: wsclean
-    in:
-      - id: image_name
-        source: msin
-        valueFrom: $(inputs.msin.basename)
-      - id: msin
-        source: prefactor_calibrator/output_ms
-    out:
-      - id: dirty_image
-      - id: image
-    run: steps/wsclean.cwl
-    label: WSClean
-    scatter:
-      - msin
-    'sbg:x': 6
-    'sbg:y': -102
-  - id: wsclean_1
-    in:
-      - id: image_name
-        source: msin
-        valueFrom: flagged_$(inputs.msin.basename)
-      - id: msin
-        source: msin
-    out:
-      - id: dirty_image
-      - id: image
-    run: steps/wsclean.cwl
-    label: WSClean
-    scatter:
-      - msin
-    'sbg:x': -317
-    'sbg:y': -302
-requirements:
-  - class: SubworkflowFeatureRequirement
-  - class: ScatterFeatureRequirement
-  - class: StepInputExpressionRequirement
-  - class: InlineJavascriptRequirement