diff --git a/lofar-cwl/steps/ms_concat.cwl b/lofar-cwl/steps/ms_concat.cwl index c374f67951bfc9d73f0e8049636bf29541edc8c6..e52cb633efc76310b182afbf2abbb44416f8ef36 100644 --- a/lofar-cwl/steps/ms_concat.cwl +++ b/lofar-cwl/steps/ms_concat.cwl @@ -3,14 +3,13 @@ cwlVersion: v1.0 $namespaces: sbg: 'https://www.sevenbridges.com/' id: ms_concat - - baseCommand: - - concat_MS.py + - python3 + - /usr/local/bin/concat_MS_CWL.py inputs: - - id: min_length + - default: 50 + id: min_length type: int? - default: 50 inputBinding: position: 0 prefix: '--min_length' @@ -35,25 +34,25 @@ inputs: position: 2 outputs: - id: concat_meta_ms - type: Directory[] + type: 'Directory[]' outputBinding: - glob: > + glob: | $(inputs.msout)_[0-9*] - id: concat_additional_ms - type: Directory[] + type: 'Directory[]' outputBinding: glob: $(inputs.msout)_*_CONCAT - id: ms_outs - type: Directory[] + type: 'Directory[]' outputBinding: outputEval: $(inputs.msin) label: ms_concat requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: lofareosc/lofar-pipeline-ci:latest - - class: InlineJavascriptRequirement + dockerPull: 'lofareosc/prefactor:HBAcalibrator' - class: InitialWorkDirRequirement listing: - entry: $(inputs.msin) writable: true + - class: InlineJavascriptRequirement diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl index 6900feb7fdc08730ad0357bdb15cb31e33dc300e..d13e6dfc90f66a6240beecdadfb95893559f509a 100644 --- a/workflows/prefactor_calibrator.cwl +++ b/workflows/prefactor_calibrator.cwl @@ -266,6 +266,10 @@ steps: source: do_smooth - id: max_separation_arcmin source: max_separation_arcmin + - id: min_length + source: min_length + - id: overhead + source: overhead - id: min_separation source: min_separation - id: A-Team_skymodel diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl index 015ecc8ced357248bb9ff920b51e7ae2989e3529..19c83157c9bdee00aed2f515bbfe4736a1bf0706 100644 --- a/workflows/prefactor_calibrator/prep.cwl +++ b/workflows/prefactor_calibrator/prep.cwl @@ -66,32 +66,40 @@ inputs: type: boolean 'sbg:x': -1000 'sbg:y': 500 - - id: min_separation + - id: min_length type: int? 'sbg:x': -1000 'sbg:y': 600 - - id: max_separation_arcmin + - id: overhead type: float? 'sbg:x': -1000 'sbg:y': 700 + - id: min_separation + type: int? + 'sbg:x': -1000 + 'sbg:y': 800 + - id: max_separation_arcmin + type: float? + 'sbg:x': -1000 + 'sbg:y': 900 - id: calibrator_path_skymodel type: Directory? 'sbg:x': -1000 - 'sbg:y': 800 + 'sbg:y': 1000 - id: A-Team_skymodel type: File? 'sbg:x': -1000 - 'sbg:y': 900 + 'sbg:y': 1100 - id: elevation type: string default: 0deg..20deg 'sbg:x': -1000 - 'sbg:y': 1000 + 'sbg:y': 1200 - id: amplmin type: float default: 1.e-30 'sbg:x': -1000 - 'sbg:y': 1100 + 'sbg:y': 1300 outputs: - id: check_Ateam_separation.png outputSource: @@ -113,7 +121,7 @@ outputs: 'sbg:y': -100 - id: msout outputSource: - - ndppp_prep_cal/msout + - ms_concat/ms_outs type: 'Directory[]' 'sbg:x': 1000 'sbg:y': 0 @@ -225,18 +233,37 @@ steps: - id: find_skymodel_cal in: - id: msin - source: msin + source: + - msin - id: skymodels source: calibrator_path_skymodel - id: max_separation_arcmin source: max_separation_arcmin out: - id: output_models + - id: model_name - id: logfile run: ../../steps/find_skymodel_cal.cwl label: find_skymodel_cal 'sbg:x': -500 'sbg:y': 500 + - id: ms_concat + in: + - id: min_length + source: min_length + - id: overhead + source: overhead + - id: msin + source: + - ndppp_prep_cal/msout + out: + - id: concat_meta_ms + - id: concat_additional_ms + - id: ms_outs + run: ../../lofar-cwl/steps/ms_concat.cwl + label: ms_concat + 'sbg:x': 300 + 'sbg:y': 0 requirements: - class: SubworkflowFeatureRequirement - class: ScatterFeatureRequirement