diff --git a/steps/structure_function.cwl b/steps/structure_function.cwl new file mode 100644 index 0000000000000000000000000000000000000000..434d75f0513a3a4b421f9624bb0c4078382728e3 --- /dev/null +++ b/steps/structure_function.cwl @@ -0,0 +1,62 @@ +class: CommandLineTool +cwlVersion: v1.0 +$namespaces: + lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl' + sbg: 'https://www.sevenbridges.com/' +id: structure_function +baseCommand: + - python3 + - /usr/local/bin/getStructure_from_phases.py +inputs: + - format: 'lofar:#H5Parm' + id: h5parmFile + type: File + inputBinding: + position: 0 + doc: List of h5parm files + - default: 'target' + id: solset + type: string? + inputBinding: + position: 0 + prefix: '--solset' + doc: Input solset name + - default: 'phase000' + id: soltab + type: string? + inputBinding: + position: 0 + prefix: '--soltab' + doc: Name of the soltab + - default: 'POINTING' + id: outbasename + type: string? + inputBinding: + position: 0 + prefix: '--outbasename' + doc: Namebase of the output files +outputs: + - id: structure_plot + doc: Output plot + type: File + outputBinding: + glob: $(inputs.outbasename+'_structure.png') + - id: structure_txt + doc: Output text + type: File + outputBinding: + glob: $(inputs.outbasename+'_structure.txt') + - id: log + type: File[] + outputBinding: + glob: 'structure_function*.log' +label: structure_function +requirements: + - class: InlineJavascriptRequirement +hints: + - class: DockerRequirement + dockerPull: lofareosc/prefactor:HBAcalibrator +stdout: structure_function.log +stderr: structure_function_err.log +$schema: + - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl' diff --git a/workflows/prefactor_target.cwl b/workflows/prefactor_target.cwl index b1ab44771de0d879150e593ff54262623c766282..f2082880e94595b2ae42814022a8af0cabe0d7b0 100644 --- a/workflows/prefactor_target.cwl +++ b/workflows/prefactor_target.cwl @@ -242,6 +242,7 @@ outputs: - id: inspection outputSource: - prep/inspection + - finalize/inspection type: 'File[]' linkMerge: merge_flattened 'sbg:x': 2000 @@ -404,6 +405,7 @@ steps: out: - id: msout - id: solutions + - id: inspection - id: logfiles run: ./prefactor_target/finalize.cwl label: finalize diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl index f4949a3706604404023ef2dbee393b1da7ab5c0d..1b3ab90517337f3c404cb666c4b49f7b80190226 100644 --- a/workflows/prefactor_target/finalize.cwl +++ b/workflows/prefactor_target/finalize.cwl @@ -46,22 +46,30 @@ outputs: outputSource: - apply_gsmcal/msout type: 'Directory[]' - 'sbg:x': 1000 + 'sbg:x': 1300 'sbg:y': 0 - id: solutions outputSource: - h5parm_pointingname/outh5parm type: File - 'sbg:x': 1000 + 'sbg:x': 1300 'sbg:y': 200 - id: logfiles outputSource: - concat_logfiles_applygsm/output - concat_logfiles_solutions/output + - concat_logfiles_structure/output type: 'File[]' linkMerge: merge_flattened - 'sbg:x': 1000 + 'sbg:x': 1300 'sbg:y': 800 + - id: inspection + outputSource: + - structure_function/structure_plot + type: 'File[]?' + linkMerge: merge_flattened + 'sbg:x': 1300 + 'sbg:y': 500 steps: - id: add_missing_stations in: @@ -169,6 +177,27 @@ steps: label: h5parm_pointingname 'sbg:x': 400 'sbg:y': 200 + - id: structure_function + in: + - id: h5parmFile + source: write_solutions/outh5parm + - id: solset + default: 'target' + - id: soltab + source: + - skymodel_source + - gsmcal_step + valueFrom: $(self.join('')) + - id: outbasename + source: get_targetname/targetname + out: + - id: structure_plot + - id: structure_txt + - id: log + run: ../../steps/structure_function.cwl + label: structure_function + 'sbg:x': 500 + 'sbg:y': 300 - id: concat_logfiles_applygsm in: - id: file_list @@ -200,6 +229,22 @@ steps: label: concat_logfiles_solutions 'sbg:x': 500 'sbg:y': 500 + - id: concat_logfiles_structure + in: + - id: file_list + linkMerge: merge_flattened + source: + - structure_function/log + - structure_function/structure_txt + - id: file_prefix + source: get_targetname/targetname + valueFrom: $(self+'_structure') + out: + - id: output + run: ../../steps/concatenate_files.cwl + label: concat_logfiles_structure + 'sbg:x': 950 + 'sbg:y': 500 - id: get_targetname in: - id: msin