class: Workflow
cwlVersion: v1.0
id: prep
label: prep
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: msin
type: 'Directory[]'
'sbg:x': -1000
'sbg:y': -900
- id: filter_baselines
type: string
'sbg:x': -1000
'sbg:y': -800
- id: raw_data
type: boolean
'sbg:x': -1000
'sbg:y': -700
- id: propagatesolutions
type: boolean
'sbg:x': -1000
'sbg:y': -600
- id: flagunconverged
type: boolean
'sbg:x': -1000
'sbg:y': -500
- id: demix
type: boolean
'sbg:x': -1000
'sbg:y': -400
- id: max_dppp_threads
type: int?
default: 10
'sbg:x': -1000
'sbg:y': -300
- id: memoryperc
type: int
'sbg:x': -1000
'sbg:y': -200
- id: flag_baselines
type: 'string[]'
'sbg:x': -1000
'sbg:y': -100
- id: avg_timeresolution
type: float
'sbg:x': -1000
'sbg:y': 0
- id: avg_freqresolution
type: string
'sbg:x': -1000
'sbg:y': 100
- id: process_baselines_cal
type: string
'sbg:x': -1000
'sbg:y': 200
- id: demix_timestep
type: int
'sbg:x': -1000
'sbg:y': 300
- id: demix_freqstep
type: int
'sbg:x': -1000
'sbg:y': 400
- id: demix_target
type: string
'sbg:x': -1000
'sbg:y': 500
- id: demix_sources
type: 'string[]'
'sbg:x': -1000
'sbg:y': 600
- id: min_length
type: int?
'sbg:x': -1000
'sbg:y': 700
- id: overhead
type: float?
'sbg:x': -1000
'sbg:y': 800
- id: min_separation
type: int?
'sbg:x': -1000
'sbg:y': 900
- id: do_smooth
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': 1000
- id: max_separation_arcmin
type: float?
'sbg:x': -1000
'sbg:y': 1100
- id: calibrator_path_skymodel
type: Directory?
'sbg:x': -1000
'sbg:y': 1200
- id: A-Team_skymodel
type: File?
'sbg:x': -1000
'sbg:y': 1300
- id: elevation
type: string
default: 0deg..20deg
'sbg:x': -1000
'sbg:y': 1400
- id: amplmin
type: float
default: 1.e-30
'sbg:x': -1000
'sbg:y': 1500
outputs:
- id: outh5parm
outputSource:
- h5parm_collector/outh5parm
type: File
'sbg:x': 1000
'sbg:y': -500
- id: check_Ateam_separation.png
outputSource:
- check_ateam_separation/output_imag
type: File
'sbg:x': 1000
'sbg:y': -300
- id: msout
outputSource:
- predict_calibrate/msout
type: 'Directory[]'
'sbg:x': 1000
'sbg:y': 0
- id: parset
outputSource:
- ndppp_prep_cal/parset
type: 'File[]'
'sbg:x': 1000
'sbg:y': 200
- id: calibrator_name
outputSource:
- find_skymodel_cal/model_name
type: string
'sbg:x': 1000
'sbg:y': 400
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
type: File[]
'sbg:x': 1000
'sbg:y': 650
- id: logfiles
linkMerge: merge_flattened
outputSource:
- concat_logfiles_calib/output
- concat_logfiles_predict/output
- concat_logfiles_blsmooth/output
- make_sourcedb/log
- find_skymodel_cal/logfile
- concat_logfiles_prep_cal/output
- make_sourcedb_ateam/log
- check_ateam_separation/logfile
type: 'File[]'
'sbg:x': 1000
'sbg:y': 800
steps:
- id: ndppp_prep_cal
in:
- id: baselines_to_flag
default: []
source:
- flag_baselines
- id: elevation_to_flag
source: elevation
- id: min_amplitude_to_flag
source: amplmin
- id: memoryperc
default: 20
source: memoryperc
- id: raw_data
default: false
source: raw_data
- id: demix
default: false
source: demix
- id: msin
linkMerge: merge_flattened
source:
- msin
- id: msin_baseline
default: '*'
source: filter_baselines
- id: skymodel
source: make_sourcedb_ateam/sourcedb
- id: timeresolution
default: 1
source: avg_timeresolution
- id: freqresolution
default: 12.21kHz
source: avg_freqresolution
- id: demix_timestep
default: 1
source: demix_timestep
- id: demix_freqstep
default: 1
source: demix_freqstep
- id: demix_baseline
default: '*'
source: process_baselines_cal
- id: target_source
source: demix_target
- id: ntimechunk
default: 10
source: max_dppp_threads
- id: subtract_sources
source:
- demix_sources
out:
- id: msout
- id: logfile
- id: parset
run: ../../subworkflow/ndppp_prep_cal.cwl
label: ndppp_prep_cal
scatter:
- msin
'sbg:x': 0
'sbg:y': 0
- id: predict_calibrate
in:
- id: msin
linkMerge: merge_flattened
source:
- ndppp_prep_cal/msout
- id: do_smooth
source: do_smooth
- id: sourcedb
source: make_sourcedb/sourcedb
- id: flagunconverged
source: flagunconverged
- id: propagatesolutions
source: propagatesolutions
out:
- id: msout
- id: BLsmooth.log
- id: predict_cal.log
- id: calib_cal.log
- id: outh5parm
run: ../../subworkflow/predict_calibrate.cwl
label: predict_calibrate
scatter:
- msin
'sbg:x': 500
'sbg:y': 0
- id: check_ateam_separation
in:
- id: ms
source:
- msin
- id: min_separation
source: min_separation
out:
- id: output_imag
- id: logfile
run: ../../lofar-cwl/steps/check_ateam_separation.cwl
label: check_Ateam_separation
'sbg:x': 0
'sbg:y': -300
- id: make_sourcedb_ateam
in:
- id: sky_model
source: A-Team_skymodel
- id: logname
default: make_sourcedb_ateam.log
out:
- id: sourcedb
- id: log
run: ../../lofar-cwl/steps/makesourcedb.cwl
label: make_sourcedb_ateam
'sbg:x': -500
'sbg:y': 300
- id: find_skymodel_cal
in:
- id: 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: make_sourcedb
in:
- id: sky_model
source: find_skymodel_cal/output_models
- id: output_file_name
default: calibrator.sourcedb
out:
- id: sourcedb
- id: log
run: ../../lofar-cwl/steps/makesourcedb.cwl
label: make_sourcedb
'sbg:x': 0
'sbg:y': 500
- id: concat_logfiles_prep_cal
in:
- id: file_list
linkMerge: merge_flattened
source: ndppp_prep_cal/logfile
- id: file_prefix
default: ndppp_prep_cal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_prep_cal
'sbg:x': 250
'sbg:y': 300
- id: concat_logfiles_blsmooth
in:
- id: file_list
source:
- predict_calibrate/BLsmooth.log
- id: file_prefix
default: blsmooth_prep
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_blsmooth
'sbg:x': 750
'sbg:y': 300
- id: concat_logfiles_predict
in:
- id: file_list
linkMerge: merge_flattened
source:
- predict_calibrate/predict_cal.log
- id: file_prefix
default: predict_cal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_predict
'sbg:x': 750
'sbg:y': 500
- id: concat_logfiles_calib
in:
- id: file_list
source:
- predict_calibrate/calib_cal.log
- id: file_prefix
default: calib_cal_prep
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_calib
'sbg:x': 750
'sbg:y': 800
- id: h5parm_collector
in:
- id: h5parmFiles
source:
- predict_calibrate/outh5parm
- id: squeeze
default: true
- id: verbose
default: true
- id: clobber
default: true
out:
- id: outh5parm
- id: log
run: ../../lofar-cwl/steps/H5ParmCollector.cwl
label: H5parm_collector
'sbg:x': 750
'sbg:y': -300
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement