Merge branch 'shallow_listing' into 'master'

Shallow listing See merge request eosc/prefactor3-cwl!35 Former-commit-id: c8ac0b00 [formerly 1ba6f2fa] Former-commit-id: 7c8ff63f Former-commit-id: 89ffab29

Merge branch 'shallow_listing' into 'master'
bae94184 · alex · 996d266e · 5cf7ea36 · bae94184 · bae94184
Commit bae94184 authored 3 years ago by alex
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -65,6 +65,6 @@ run_hba_full:
  script:
    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/HBA_calibrator.cwl test_jobs/HBA_calibrator.json
    - test_jobs/check_workflow_results.py results /builds/eosc/prefactor3-cwl/data/results_calibrator
-#    - rm -rf results
+    - rm -rf results
-#    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/HBA_target.cwl test_jobs/HBA_target.json
+    - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH workflows/HBA_target.cwl test_jobs/HBA_target.json
-#    - test_jobs/check_workflow_results.py results /builds/eosc/prefactor3-cwl/data/results_target
+    - test_jobs/check_workflow_results.py results /builds/eosc/prefactor3-cwl/data/results_target
--- a/lofar-cwl/steps/AOFlagger.cwl
+++ b/lofar-cwl/steps/AOFlagger.cwl
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: aoflagger
 requirements:

--- a/lofar-cwl/steps/Ateamclipper.cwl
+++ b/lofar-cwl/steps/Ateamclipper.cwl
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
  sbg: 'https://www.sevenbridges.com/'
 id: check_ateam_separation
@@ -21,7 +21,7 @@ outputs:
    outputBinding:
      glob: $(inputs.msin.basename)
  - id: logfile
-    type: 'File[]'
+    type: File[]
    outputBinding:
      glob: Ateamclipper.log
  - id: output

--- a/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.AOFlaggerStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: aoflagger_step_generator
 inputs:

--- a/lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ApplyBeamStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: applybeam_step_generator
 inputs:

--- a/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ApplyCalStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: applycal_step_generator
 inputs:

--- a/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.AveragerStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: average_step_generator
 inputs:

--- a/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.DemixerStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
  sbg: 'https://www.sevenbridges.com/'
 id: demix_step_generator

--- a/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl
+++ b/lofar-cwl/steps/DP3.EmptyParsetGenerator.cwl
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
 class: CommandLineTool
 id: empty_parset_generator
 baseCommand: [echo, 'steps=[]']

--- a/lofar-cwl/steps/DP3.Execute.cwl
+++ b/lofar-cwl/steps/DP3.Execute.cwl
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: dp3_execute
 label: DP3.Execute
 $namespaces:

--- a/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.FilterStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
  sbg: 'https://www.sevenbridges.com/'
 id: dp3-filter-step-generator

--- a/lofar-cwl/steps/DP3.GenericStep.cwl
+++ b/lofar-cwl/steps/DP3.GenericStep.cwl
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
 class: ExpressionTool
 id: generic_step

--- a/lofar-cwl/steps/DP3.ParsetGenerator.cwl
+++ b/lofar-cwl/steps/DP3.ParsetGenerator.cwl
 #!/usr/bin/env cwl-runner
-cwlVersion: v1.0
+cwlVersion: v1.1
 class: CommandLineTool
 id: generic_step

--- a/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
+++ b/lofar-cwl/steps/DP3.PreflaggerStepGenerator.cwl
 #!/usr/bin/env cwl-runner
 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: preflag_step_generator
 inputs:

--- a/lofar-cwl/steps/DP3.Selector.cwl
+++ b/lofar-cwl/steps/DP3.Selector.cwl
 class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: selector
 inputs:
  - id: select_a

--- a/lofar-cwl/steps/DPPP.cwl
+++ b/lofar-cwl/steps/DPPP.cwl
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
  sbg: 'https://www.sevenbridges.com/'
 id: dppp

--- a/lofar-cwl/steps/DirSelector.cwl
+++ b/lofar-cwl/steps/DirSelector.cwl
 class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: dirselector
 inputs:
  - id: inputs

--- a/lofar-cwl/steps/FileSelector.cwl
+++ b/lofar-cwl/steps/FileSelector.cwl
 class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: fileselector
 inputs:
  - id: inputs

--- a/lofar-cwl/steps/H5ParmCollector.cwl
+++ b/lofar-cwl/steps/H5ParmCollector.cwl
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
  sbg: 'https://www.sevenbridges.com/'
  lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl

--- a/lofar-cwl/steps/LoSoTo.Abs.cwl
+++ b/lofar-cwl/steps/LoSoTo.Abs.cwl
 #!/usr/bin/env cwl-runner
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: losoto_abs
 $namespaces: