Merge branch 'shallow_listing' into 'master'

Shallow listing

See merge request eosc/prefactor3-cwl!35

Former-commit-id: 1ba6f2fa

steps/identify_bad_antennas.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: identify_bad_antennas
@@ -38,7 +38,7 @@ outputs:
         glob: 'out.json'
         outputEval: $(JSON.parse(self[0].contents).flaggedants)
   - id: logfile
-    type: File?
+    type: File
     outputBinding:
       glob: identifyBadAntennas.log    
         

steps/identify_bad_antennas_join.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: identify_bad_antennas_join
@@ -47,7 +47,7 @@ outputs:
         glob: 'out.json'
         outputEval: $(JSON.parse(self[0].contents).filter)
   - id: logfile
-    type: File?
+    type: File
     outputBinding:
       glob: identifyBadAntennas.log
 

steps/merge_array.cwl

@@ -2,7 +2,7 @@ id: merge_array
 label: merge_array
 class: ExpressionTool
 
-cwlVersion: v1.0
+cwlVersion: v1.1
 inputs: 
     - id: input
       type:

steps/merge_array_files.cwl

@@ -2,7 +2,7 @@ id: merge_array_files
 label: merge_array_files
 class: ExpressionTool
 
-cwlVersion: v1.0
+cwlVersion: v1.1
 inputs: 
     - id: input
       type:

steps/plot_Ateamclipper.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: plot_Ateamclipper

steps/plot_unflagged.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: plot_unflagged
@@ -38,7 +38,7 @@ outputs:
     outputBinding:
       glob: 'unflagged_fraction.png'
   - id: logfile
-    type: File[]?
+    type: File[]
     outputBinding:
       glob: 'plot_unflagged_fraction*.log'
 

steps/read_surl_list.cwl

 class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: read_surl_file
 inputs:
   - id: surl_list

steps/selectfirstdirectory.cwl

@@ -2,7 +2,7 @@ id: selectfirstdirectory
 label: selectfirstdirectory
 class: ExpressionTool
 
-cwlVersion: v1.0
+cwlVersion: v1.1
 inputs: 
     - id: input
       type: Directory[]
@@ -22,4 +22,3 @@ expression: |
   ${
     return {'output': inputs.input[0]}
   }
-

steps/selectfirstfile.cwl

 class: ExpressionTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: select_first_file
 inputs:
   - id: inputs

steps/separate_results_directory.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: separate_results_directory

steps/sort_times_into_freqGroups.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: sort_times_into_freqGroups
@@ -89,7 +89,7 @@ outputs:
         glob: 'out.json'
         outputEval: $(JSON.parse(self[0].contents).total_bandwidth)
   - id: logfile
-    type: File?
+    type: File
     outputBinding:
       glob: sort_times_into_freqGroups.log    
         
@@ -99,4 +99,5 @@ requirements:
 hints:
   - class: DockerRequirement
     dockerPull: lofareosc/prefactor3-cwl
-stdout: sort_times_into_freqGroups.log
\ No newline at end of file
+stdout: sort_times_into_freqGroups.log
+stderr: sort_times_into_freqGroups_err.log
\ No newline at end of file

steps/stage.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: stage

steps/structure_function.cwl

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

steps/summary.cwl

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

steps/surl_copy.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: surl_copy

steps/transfer_solutions.cwl

 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: transfer_solutions

steps/untar.cwl

 id: untar
 label: untar
 class: CommandLineTool
-cwlVersion: v1.0
+cwlVersion: v1.1
 inputs: 
   - id: tar_file
     type: File

steps/uvplot.cwl

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

subworkflow/apply_calibrate_bp.cwl

 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: apply_calibrate
 label: apply_calibrate
 $namespaces:
@@ -10,15 +10,18 @@ inputs:
     'sbg:x': -1000
     'sbg:y': -200
   - id: do_smooth
-    type: boolean
+    type: boolean?
+    default: false
     'sbg:x': -1000
     'sbg:y': -100
   - id: flagunconverged
-    type: boolean
+    type: boolean?
+    default: false
     'sbg:x': -1000
     'sbg:y': 100
   - id: propagatesolutions
-    type: boolean
+    type: boolean?
+    default: true
     'sbg:x': -1000
     'sbg:y': 200
   - id: input_h5parm

subworkflow/apply_calibrate_fr.cwl

 class: Workflow
-cwlVersion: v1.0
+cwlVersion: v1.1
 id: apply_calibrate
 label: apply_calibrate
 $namespaces:
@@ -10,15 +10,18 @@ inputs:
     'sbg:x': -1000
     'sbg:y': -200
   - id: do_smooth
-    type: boolean
+    type: boolean?
+    default: false
     'sbg:x': -1000
     'sbg:y': -100
   - id: flagunconverged
-    type: boolean
+    type: boolean?
+    default: false
     'sbg:x': -1000
     'sbg:y': 100
   - id: propagatesolutions
-    type: boolean
+    type: boolean?
+    default: true
     'sbg:x': -1000
     'sbg:y': 200
   - id: input_h5parm