Merged A-team clipping with setup workflow.

workflows/clipAteam.cwl

-class: Workflow
-cwlVersion: v1.2
-id: clipAteam
-label: clipAteam
-
-inputs:
-  - id: msin
-    type: 'Directory[]'
-    doc: Input Measurement Set
- 
-steps:
-  - id: predictAteam
-    in:
-      - id: msin
-        linkMerge: merge_flattened
-        source: 
-          - msin
-    out:
-      - id: msout
-      - id: predict_logfile
-      - id: cliptar_logfile
-    run: ./subworkflows/predictAteam.cwl
-    scatter: msin
-    label: predictAteam
-  - id: concat_logfiles_predict
-    in:
-      - id: file_list
-        linkMerge: merge_flattened
-        source: predictAteam/predict_logfile
-      - id: file_prefix
-        default: predict
-    out:
-      - id: output
-    run: ../steps/concatenate_files.cwl
-    label: concat_logfiles_predict
-  - id: concat_logfiles_cliptar
-    in:
-      - id: file_list
-        linkMerge: merge_flattened
-        source: predictAteam/cliptar_logfile
-      - id: file_prefix
-        default: Ateamcliptar
-    out:
-      - id: output
-    run: ../steps/concatenate_files.cwl
-    label: concat_logfiles_cliptar
-  - id: save_logfiles
-    in:
-      - id: files
-        linkMerge: merge_flattened
-        source:
-          - concat_logfiles_predict/output
-          - concat_logfiles_cliptar/output
-      - id: sub_directory_name
-        default: clipAteam
-    out:
-      - id: dir
-    run: ../steps/collectfiles.cwl
-    label: save_logfiles
-
-outputs:
-  - id: logdir
-    outputSource: save_logfiles/dir
-    type: Directory
-  - id: msout
-    outputSource: predictAteam/msout
-    type: Directory[]
-
-requirements:
-  - class: MultipleInputFeatureRequirement
-  - class: SubworkflowFeatureRequirement
-  - class: ScatterFeatureRequirement

workflows/delay-calibration.cwl

@@ -55,16 +55,6 @@ steps:
         - id: msout
       run: ./setup.cwl
 
-    - id: clipAteam
-      in:
-        - id: msin
-          source: setup/msout
-      out:
-        - id: logdir
-        - id: msout
-      run: ./clipAteam.cwl
-      label: clipAteam
-
     - id: sort-concatenate-flag
       in:
         - id: msin
@@ -132,7 +122,6 @@ steps:
           linkMerge: merge_flattened
           source:
             - setup/logdir
-            - clipAteam/logdir
             - sort-concatenate-flag/logdir
             - phaseup/logdir
         - id: sub_directory_name

workflows/setup.cwl

@@ -60,7 +60,7 @@ steps:
       out:
         - id: parset
       run: ../steps/dp3_make_parset.cwl
-    - id: prep_target
+    - id: clip_A-team
       in:
         - id: parset
           source: dp3_make_parset/parset
@@ -73,18 +73,18 @@ steps:
       out:
         - id: logfiles
         - id: msout
-      run: ./subworkflows/prep_target.cwl
+      run: ./subworkflows/clip_A-team.cwl
       scatter: msin
-      label: prep_target
-    - id: concat_logfiles_prep_target
-      label: concat_logfiles_prep_target
+      label: clip_A-team.cwl
+    - id: concat_logfiles_clip_A-team
+      label: concat_logfiles_clip_A-team
       in:
         - id: file_list
           linkMerge: merge_flattened
           source:
-            - prep_target/logfiles
+            - clip_A-team/logfiles
         - id: file_prefix
-          default: dp3_prep_target
+          default: clip_A-team
       out:
         - id: output
       run: ../steps/concatenate_files.cwl
@@ -95,7 +95,7 @@ steps:
           source:
             - check_station_mismatch/logfile
             - download_cats/logfile 
-            - concat_logfiles_prep_target/output
+            - concat_logfiles_clip_A-team/output
         - id: sub_directory_name
           default: setup
       out:
@@ -114,5 +114,5 @@ outputs:
       outputSource: dp3_make_parset/parset
       type: File
     - id: msout
-      outputSource: prep_target/msout
+      outputSource: clip_A-team/msout
       type: Directory[]

workflows/subworkflows/prep_target.cwl → workflows/subworkflows/clip_A-team.cwl

 class: Workflow
 cwlVersion: v1.2
-id: prep_target
-label: prep_target
+id: clip_A-team
+label: clip_A-team
 
 requirements:
     - class: InlineJavascriptRequirement
-    - class: SubworkflowFeatureRequirement
     - class: StepInputExpressionRequirement
-    - class: MultipleInputFeatureRequirement
-    - class: InitialWorkDirRequirement
-      listing:
-        - entry: $(inputs.msin)
-          writable: true
 
 inputs:
     - id: parset
+      doc: DP3 parset.
       type: File
     - id: msin
+      doc: input measurement set.
       type: Directory
     - id: solset
+      doc: H5 solutions file.
       type: File
 
 steps:
@@ -38,6 +35,25 @@ steps:
         - id: logfile
         - id: msout
       run: ../../steps/dp3_prep_target.cwl
+    - id: predict
+      in:
+        - id: msin
+          source: dp3_prep_target/msout
+      out:
+        - id: msout
+        - id: logfile
+      run: ../../steps/predict.cwl
+      label: predict
+    - id: Ateamcliptar
+      in:
+        - id: msin
+          source: predict/msout
+      out:
+        - id: msout
+        - id: logfile
+        - id: output
+      run: ../../steps/Ateamclipper.cwl
+      label: Ateamcliptar
     - id: concat_logfiles_prep_targ
       label: concat_logfiles_prep_target
       in:
@@ -50,13 +66,49 @@ steps:
       out:
         - id: output
       run: ../../steps/concatenate_files.cwl
+    - id: concat_logfiles_predict
+      in:
+        - id: file_list
+          linkMerge: merge_flattened
+          source: predict/logfile
+        - id: file_prefix
+          default: predict
+      out:
+        - id: output
+      run: ../../steps/concatenate_files.cwl
+      label: concat_logfiles_predict
+    - id: concat_logfiles_cliptar
+      in:
+        - id: file_list
+          linkMerge: merge_flattened
+          source: Ateamcliptar/logfile
+        - id: file_prefix
+          default: Ateamcliptar
+      out:
+        - id: output
+      run: ../../steps/concatenate_files.cwl
+      label: concat_logfiles_cliptar
+    - id: concat_logfiles_clip_A-team
+      in:
+        - id: file_list
+          linkMerge: merge_flattened
+          source:
+            - concat_logfiles_prep_targ/output
+            - concat_logfiles_predict/output
+            - concat_logfiles_cliptar/output
+        - id: file_prefix
+          default: Ateamcliptar
+      out:
+        - id: output
+      run: ../../steps/concatenate_files.cwl
+      label: concat_logfiles_clip_A-team
 
 outputs:
     - id: logfiles
-      outputSource: 
-        - concat_logfiles_prep_targ/output
+      outputSource:
+        - concat_logfiles_clip_A-team/output
       type: File
     - id: msout
       outputSource:
-        - dp3_prep_target/msout
+        - Ateamcliptar/msout
       type: Directory

workflows/subworkflows/predictAteam.cwl

@@ -7,8 +7,28 @@ inputs:
   - id: msin
     type: Directory
     doc: Input Measurement Set
+  - id: solset
+    type: File
+    doc: LINC target solutions file.
  
 steps:
+    - id: prep_target
+      in:
+        - id: parset
+          source: dp3_make_parset/parset
+        - id: msin
+          linkMerge: merge_flattened
+          source: 
+            - msin
+        - id: solset
+          source: solset
+      out:
+        - id: logfiles
+        - id: msout
+      run: ./subworkflows/prep_target.cwl
+      scatter: msin
+      label: prep_target
+
   - id: predict
     in:
       - id: msin