Reorganise steps

workflows/linc_target/gsmcal.cwl

@@ -318,49 +318,7 @@ steps:
     label: concat
     scatter:
       - group_id
-  - id: aoflag
-    in:
-      - id: msin
-        source: merge_array_concat/output
-      - id: verbose
-        default: true
-      - id: concatenate-frequency
-        source: aoflag_freqconcat
-      - id: strategy
-        source: rfistrategy
-      - id: reorder
-        source: aoflag_reorder
-      - id: chunk-size
-        source: aoflag_chunksize
-    out:
-      - id: output_ms
-      - id: logfile
-    run: ../../steps/aoflag.cwl
-    label: aoflag
-  - id: check_unflagged_fraction
-    in:
-      - id: msin
-        source: aoflag/output_ms
-      - id: min_fraction
-        source: min_unflagged_fraction
-    out:
-      - id: msout
-      - id: frequency
-      - id: unflagged_fraction
-      - id: filenames
-      - id: logfile
-    run: ../../steps/check_unflagged_fraction.cwl
-    label: check_unflagged_fraction
-    scatter:
-      - msin
-  - id: merge_array
-    in:
-      - id: input
-        source: check_unflagged_fraction/msout
-    out:
-      - id: output
-    run: ../../steps/merge_array.cwl
-    label: merge_array
+
   - id: merge_array_concat
     in:
       - id: input
@@ -369,28 +327,12 @@ steps:
       - id: output
     run: ../../steps/merge_array.cwl
     label: merge_array_concat
-  - id: merge_array_files
-    in:
-      - id: input
-        source: check_unflagged_fraction/logfile
-    out:
-      - id: output
-    run: ../../steps/merge_array_files.cwl
-    label: merge_array_files
-  - id: check_filtered_MS_array
-    in:
-      - id: input
-        source: merge_array/output
-    out:
-      - id: output
-    run: ../../steps/check_filtered_MS_array.cwl
-    label: check_filtered_MS_array
 
   - id: sort_times_into_freqGroups_full
     in:
       - id: msin
         source:
-          - aoflag/output_ms
+          - merge_array_concat/output
       - id: numbands
         valueFrom: $(-1)
       - id: DP3fill
@@ -439,7 +381,7 @@ steps:
     scatter: group_id
     when: $(inputs.execute && inputs.selfcal_strategy == 'HBA') 
   
-  - id: merge_array_full
+  - id: merge_array_concat_full
     in:
       - id: input
         source: concat2/msout
@@ -447,25 +389,77 @@ steps:
       - id: output
     run: ../../steps/merge_array.cwl
     label: merge_array_full
-  - id: check_filtered_MS_array_full
+
+  - id: aoflag
     in:
-      - id: input
-        source: merge_array_full/output
+      - id: msin
+        source: merge_array_concat/output
+      - id: verbose
+        default: true
+      - id: concatenate-frequency
+        source: aoflag_freqconcat
+      - id: strategy
+        source: rfistrategy
+      - id: reorder
+        source: aoflag_reorder
+      - id: chunk-size
+        source: aoflag_chunksize
     out:
-      - id: output
-    run: ../../steps/check_filtered_MS_array.cwl
-    label: check_filtered_MS_array_full
-
+      - id: output_ms
+      - id: logfile
+    run: ../../steps/aoflag.cwl
+    label: aoflag
 
+  - id: check_unflagged_fraction
+    in:
+      - id: msin
+        source: aoflag/output_ms
+      - id: min_fraction
+        source: min_unflagged_fraction
+    out:
+      - id: msout
+      - id: frequency
+      - id: unflagged_fraction
+      - id: filenames
+      - id: logfile
+    run: ../../steps/check_unflagged_fraction.cwl
+    label: check_unflagged_fraction
+    scatter:
+      - msin
 
+  - id: merge_array_files
+    in:
+      - id: input
+        source: check_unflagged_fraction/logfile
+    out:
+      - id: output
+    run: ../../steps/merge_array_files.cwl
+    label: merge_array_files
 
+  - id: check_filtered_MS_array
+    in:
+      - id: input
+        source: merge_array/output
+    out:
+      - id: output
+    run: ../../steps/check_filtered_MS_array.cwl
+    label: check_filtered_MS_array
+  
+  - id: merge_array
+    in:
+      - id: input
+        source: check_unflagged_fraction/msout
+    out:
+      - id: output
+    run: ../../steps/merge_array.cwl
+    label: merge_array
 
   - id: calibrate_target
     in:
       - id: max_dp3_threads
         source: max_dp3_threads
       - id: msin
-        source: check_filtered_MS_array_full/output
+        source: check_filtered_MS_array/output
       - id: skymodel
         source: target_skymodel
       - id: do_smooth