Merge branch 'cwl-v12' into 'master'

Bump CWL Version to v1.2

See merge request eosc/prefactor3-cwl!57

Former-commit-id: 9ce49282 [formerly fae42eb2]
Former-commit-id: af1d6e51
Former-commit-id: b38cd200

steps/bulk_rename.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: bulk_rename
@@ -33,7 +33,7 @@ requirements:
           FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)
           mkdir tmp
           for i in "\${!FILE_LIST[@]}"; do 
-            cp "\${FILE_LIST[\$i]}" "tmp/\${FILE_PREFIX}_\${i}\${FILE_SUFFIX}"
+            cp "\${FILE_LIST[\${i}]}" "tmp/\${FILE_PREFIX}_\${i}\${FILE_SUFFIX}"
           done
         writable: false
   - class: InlineJavascriptRequirement

steps/check_ateam_separation.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 id: check_ateam_separation
 baseCommand:
   - check_Ateam_separation.py

steps/check_filtered_MS_array.cwl

@@ -2,7 +2,7 @@ id: check_filtered_MS_array
 label: check_filtered_MS_array
 class: ExpressionTool
 
-cwlVersion: v1.1
+cwlVersion: v1.2
 inputs:
     - id: input
       type: Directory[]

steps/check_unflagged_fraction.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: check_unflagged_fraction

steps/collectlog.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: collectlog

steps/compare_station_list.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: compare_station_list

steps/concatenate_files.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: concatfiles

steps/createRMh5parm.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 id: createRMh5parm
 label: createRMh5parm
 baseCommand:

steps/create_workflow_input.cwl

@@ -3,7 +3,7 @@ $namespaces:
 id: create_workflow_input
 label: create_workflow_input
 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 inputs: 
   - id: msin
     type: Directory[]

steps/directory_listing.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: directory_listing

steps/dppp_make_parset_cal.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 id: make_parset
 label: define_parset
 $namespaces:

steps/dppp_make_parset_target.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 id: make_parset
 label: define_parset
 $namespaces:

steps/dppp_prep_cal.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: dppp

steps/dppp_prep_target.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: dppp

steps/filter_ms_group.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 id: filter_ms_group
 baseCommand:
   - python3

steps/findRefAnt.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: dppp

steps/findRefAnt_join.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: findRefAnt_join

steps/find_skymodel_cal.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: find_skymodel_cal_py

steps/find_skymodel_target.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   sbg: 'https://www.sevenbridges.com/'
 id: find_skymodel_target_py

steps/get_targetname.cwl

 class: CommandLineTool
-cwlVersion: v1.1
+cwlVersion: v1.2
 $namespaces:
   lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
   sbg: 'https://www.sevenbridges.com/'