Merge branch 'copyST_gains' into 'master'

Added the copyST_gains step.

See merge request !10

steps/copyST_gains.cwl

+cwlVersion: v1.2
+class: CommandLineTool
+id: copyST_gains
+label: copyST_gains
+
+baseCommand:
+    - python3
+    - run_h5merger.py
+
+inputs:
+    - id: msin
+      type: Directory
+      doc: Input measurement set.
+    - id: selfcal_solution
+      type: File
+      doc: Self-calibration solution h5 file.
+    - id: h5merger
+      type: Directory
+      doc: Path to a copy of the LOFAR_helper scripts.
+
+outputs:
+    - id: h5parm
+      type: File
+      doc: |
+        Selfcal_solution with linear polarization and 
+        addition of ST001 solutions for core stations.
+      outputBinding:
+        glob: '*_toapply.h5'
+    - id: logfile
+      type: File[]
+      outputBinding:
+        glob: copyST_gains*.log
+
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entry: $(inputs.selfcal_solution)
+        writable: true
+      - entryname: run_h5merger.py
+        entry: |
+            import subprocess
+            import json
+
+            inputs = json.loads(r"""$(inputs)""")
+            msin = inputs['msin']['path']
+            h5parm = inputs['selfcal_solution']
+            # ensure that the path points at the actual script
+            h5_merger = inputs['h5merger']['path'] + '/h5_merger.py'
+
+            h5parm_in = h5parm['basename']
+            h5parm_out = h5parm['basename'].replace('.h5','_toapply.h5')
+
+            ## run on the h5parm using a measurement set for the core station info
+            h5_modify = subprocess.run(['python3', f'{h5_merger}',
+                                        '--ms', f'{msin}',
+                                        '--h5_tables', f'{h5parm_in}',
+                                        '--h5_out', f'{h5parm_out}',
+                                        '--circ2lin', '--add_cs',
+                                        '--h5_time', f'{h5parm_in}'],
+                                        capture_output=True, text=True)
+            
+            print("run_h5merger stdout:", h5_modify.stdout)
+            print("run_h5merger stderr:", h5_modify.stderr)
+
+hints:
+  - class: DockerRequirement
+    dockerPull: vlbi-cwl
+
+stdout: copyST_gains.log
+stderr: copyST_gains_err.log