class: Workflow
cwlVersion: v1.0
id: finalize
label: finalize
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: msin
type: 'Directory[]'
'sbg:x': -1000
'sbg:y': -400
- id: input_h5parm
type: File
'sbg:x': -1000
'sbg:y': -300
- id: inh5parm_logfile
type: File
'sbg:x': -1000
'sbg:y': -200
- id: gsmcal_step
type: string
'sbg:x': -1000
'sbg:y': -100
- id: process_baselines_target
type: string
'sbg:x': -1000
'sbg:y': 0
- id: bad_antennas
type: string
'sbg:x': -1000
'sbg:y': 100
- id: insolutions
type: File
'sbg:x': -1000
'sbg:y': 200
- id: compression_bitrate
type: int
'sbg:x': -1000
'sbg:y': 300
- id: skymodel_source
type: string
'sbg:x': -1000
'sbg:y': 400
- id: total_bandwidth
type: int
'sbg:x': -1000
'sbg:y': 500
outputs:
- id: msout
outputSource:
- apply_gsmcal/msout
type: 'Directory[]'
'sbg:x': 1300
'sbg:y': 0
- id: solutions
outputSource:
- h5parm_pointingname/outh5parm
type: File
'sbg:x': 1300
'sbg:y': 200
- id: logfiles
outputSource:
- concat_logfiles_applygsm/output
- concat_logfiles_solutions/output
- concat_logfiles_structure/output
- concat_logfiles_wsclean/output
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1300
'sbg:y': 800
- id: inspection
outputSource:
- structure_function/structure_plot
- wsclean/image
type: 'File[]?'
linkMerge: merge_flattened
'sbg:x': 1300
'sbg:y': 500
steps:
- id: add_missing_stations
in:
- id: h5parm
source: input_h5parm
- id: refh5parm
source: insolutions
- id: solset
default: sol000
- id: refsolset
default: target
- id: soltab_in
source: gsmcal_step
valueFrom: $(self+'000')
- id: soltab_out
source:
- skymodel_source
- gsmcal_step
valueFrom: $(self.join(''))
- id: filter
source: process_baselines_target
- id: bad_antennas
source: bad_antennas
out:
- id: outh5parm
- id: log
run: ../../steps/add_missing_stations.cwl
label: add_missing_stations
'sbg:x': -200
'sbg:y': -300
- id: apply_gsmcal
in:
- id: msin
source: msin
- id: msout_name
linkMerge: merge_flattened
source:
- msin
valueFrom: $(self.nameroot+'_pre-cal.ms')
- id: msin_datacolumn
default: DATA
- id: parmdb
source: write_solutions/outh5parm
- id: msout_datacolumn
default: DATA
- id: correction
source:
- skymodel_source
- gsmcal_step
valueFrom: $(self.join(''))
- id: solset
default: target
- id: storagemanager
default: Dysco
- id: databitrate
source: compression_bitrate
out:
- id: msout
- id: logfile
run: ../../lofar-cwl/steps/applytarget.cwl
label: apply_gsmcal
scatter:
- msin
- msout_name
scatterMethod: dotproduct
'sbg:x': 400
'sbg:y': 0
- id: average
in:
- id: msin
source: apply_gsmcal/msout
- id: msout_name
linkMerge: merge_flattened
source:
- apply_gsmcal/msout
valueFrom: $(self.nameroot+'_wsclean.ms')
- id: msin_datacolumn
default: DATA
- id: msout_datacolumn
default: DATA
- id: overwrite
default: false
- id: storagemanager
default: Dysco
- id: avg_timestep
default: 2
- id: avg_freqstep
default: 2
out:
- id: msout
- id: logfile
run: ../../lofar-cwl/steps/average.cwl
label: average
scatter:
- msin
- msout_name
scatterMethod: dotproduct
'sbg:x': 600
'sbg:y': -200
- id: wsclean
in:
- id: msin
source:
- average/msout
- id: image_scale
default: 15asec
- id: niter
default: 1000000
- id: nmiter
default: 5
- id: multiscale
default: true
- id: mgain
default: 0.8
- id: ncpu
default: 4
- id: parallel-gridding
default: 1
- id: parallel-deconvolution
default: 1500
- id: parallel-reordering
default: 4
- id: channels-out
source: total_bandwidth
valueFrom: $(Math.round(self/1000000))
- id: join-channels
default: true
- id: taper-gaussian
default: 40asec
- id: weighting
default: briggs -0.5
- id: maxuvw-m
default: 20000
- id: image_name
source: get_targetname/targetname
out:
- id: dirty_image
- id: image
- id: logfile
run: ../../lofar-cwl/steps/wsclean.cwl
label: wsclean
'sbg:x': 800
'sbg:y': -200
- id: merge_array_files
in:
- id: input
source:
- apply_gsmcal/logfile
out:
- id: output
run: ../../steps/merge_array_files.cwl
label: merge_array_files
'sbg:x': 600
'sbg:y': 0
- id: write_solutions
in:
- id: h5parmFile
source: add_missing_stations/outh5parm
- id: outsolset
default: target
- id: insoltab
source:
- skymodel_source
- gsmcal_step
valueFrom: $(self.join(''))
- id: input_file
source: insolutions
- id: squeeze
default: true
- id: verbose
default: true
- id: history
default: true
out:
- id: outh5parm
- id: log
run: ../../steps/h5parmcat.cwl
label: write_solutions
'sbg:x': 200
'sbg:y': 500
- id: h5parm_pointingname
in:
- id: h5parmFile
source: write_solutions/outh5parm
- id: solsetName
default: target
- id: pointing
source: get_targetname/targetname
out:
- id: outh5parm
- id: log
run: ../../steps/h5parm_pointingname.cwl
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
source:
- merge_array_files/output
- id: file_prefix
default: apply_gsmcal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_applygsm
'sbg:x': 750
'sbg:y': 500
- id: concat_logfiles_solutions
in:
- id: file_list
linkMerge: merge_flattened
source:
- inh5parm_logfile
- add_missing_stations/log
- write_solutions/log
- get_targetname/logfile
- h5parm_pointingname/log
- id: file_prefix
default: losoto_gsmcal
out:
- id: output
run: ../../steps/concatenate_files.cwl
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: concat_logfiles_wsclean
in:
- id: file_list
linkMerge: merge_flattened
source:
- wsclean/logfile
- id: file_prefix
default: wsclean
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_wsclean
'sbg:x': 1100
'sbg:y': 500
- id: get_targetname
in:
- id: msin
linkMerge: merge_flattened
source:
- msin
out:
- id: targetname
- id: logfile
run: ../../steps/get_targetname.cwl
label: get_targetname
'sbg:x': 200
'sbg:y': 200
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement