Merge branch 'patch_flag_statistics' into 'master'

Corrected handling of intermediate output.

See merge request !16

steps/dp3_prep_target.cwl

@@ -90,11 +90,13 @@ outputs:
     - id: flag_statistics_before
       type: string
       outputBinding:
+        loadContents: true
         glob: $(inputs.flag_statistics_filename_before)
         outputEval: $(JSON.parse(self[0].contents).flagged_fraction_dict)
     - id: flag_statistics_after
       type: string
       outputBinding:
+        loadContents: true
         glob: $(inputs.flag_statistics_filename_after)
         outputEval: $(JSON.parse(self[0].contents).flagged_fraction_dict)
 

steps/predict.cwl

@@ -90,6 +90,7 @@ arguments:
   - steps=[filter,predict]
   - predict.usechannelfreq=False
   - predict.operation=replace
+  - predict.beamproximitylimit=2000
   - filter.baseline=[CR]S*&
   - filter.remove=False
   - msout=.

workflows/setup.cwl

@@ -143,8 +143,6 @@ steps:
             - download_cats/logfile 
             - concat_logfiles_clip_A-team/output
             - check_ateam_separation/logfile
-            - initial_flags_join/logfile
-            - prep_target_flags_join/logfile
         - id: sub_directory_name
           default: setup
       out: