Select Git revision
Code owners
Assign users and groups as approvers for specific file changes. Learn more.
prep.cwl 10.92 KiB
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': -1700
- id: cal_solutions
type: File
'sbg:x': -1000
'sbg:y': -1600
- id: flag_baselines
type: 'string[]?'
default: []
'sbg:x': -1000
'sbg:y': -1500
- id: process_baselines_target
type: string?
default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': -1400
- id: filter_baselines
type: string?
default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': -1300
- id: rfistrategy
type: string?
default: HBAdefault.rfis
'sbg:x': -1000
'sbg:y': -1200
- id: raw_data
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -1100
- id: propagatesolutions
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': -1000
- id: demix_sources
type: 'string[]?'
default:
- CasA
- CygA
'sbg:x': -1000
'sbg:y': -900
- id: demix_target
type: string?
default: ''
'sbg:x': -1000
'sbg:y': -800
- id: demix_freqstep
type: int?
default: 16
'sbg:x': -1000
'sbg:y': -700
- id: demix_timestep
type: int?
default: 10
'sbg:x': -1000
'sbg:y': -600
- id: demix
type: boolean?
default: false 'sbg:x': -1000
'sbg:y': -500
- id: apply_tec
type: boolean
default: false
'sbg:x': -1000
'sbg:y': -400
- id: apply_clock
type: boolean
default: true
'sbg:x': -1000
'sbg:y': -300
- id: apply_phase
type: boolean
default: false
'sbg:x': -1000
'sbg:y': -200
- id: apply_RM
type: boolean
default: true
'sbg:x': -1000
'sbg:y': -100
- id: apply_beam
type: boolean
default: true
'sbg:x': -1000
'sbg:y': 0
- id: clipATeam
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 100
- id: updateweights
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 200
- id: max_dppp_threads
type: int?
default: 10
'sbg:x': -1000
'sbg:y': 300
- id: memoryperc
type: int?
default: 20
'sbg:x': -1000
'sbg:y': 400
- id: min_separation
type: int?
default: 30
'sbg:x': -1000
'sbg:y': 500
- id: A-Team_skymodel
type: File?
'sbg:x': -1000
'sbg:y': 600
- id: avg_timeresolution
type: float?
default: 4
'sbg:x': -1000
'sbg:y': 700
- id: avg_freqresolution
type: string?
default: 48.82kHz
'sbg:x': -1000
'sbg:y': 800
- id: ionex_server
type: string?
default: 'ftp://ftp.aiub.unibe.ch/CODE/'
'sbg:x': -1000 'sbg:y': 900
- id: ionex_prefix
type: string?
default: CODG
'sbg:x': -1000
'sbg:y': 1000
- id: proxy_server
type: string?
default: null
'sbg:x': -1000
'sbg:y': 1100
- id: proxy_port
type: int?
default: null
'sbg:x': -1000
'sbg:y': 1200
- id: proxy_type
type: string?
default: null
'sbg:x': -1000
'sbg:y': 1300
- id: proxy_user
type: string?
default: null
'sbg:x': -1000
'sbg:y': 1400
- id: proxy_pass
type: string?
default: null
'sbg:x': -1000
'sbg:y': 1500
- id: elevation
type: string
default: 0deg..20deg
'sbg:x': -1000
'sbg:y': 1600
- id: amplmin
type: float
default: 1.e-30
'sbg:x': -1000
'sbg:y': 1700
outputs:
- id: outh5parm
outputSource:
- createRMh5parm/h5parmout
type: File
'sbg:x': 1000
'sbg:y': -500
- id: inspection
outputSource:
- check_ateam_separation/output_imag
- losoto_plot_RM/output_plots
- plot_Ateamclipper/output_imag
type: 'File[]?'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': -300
- id: msout
outputSource:
- dppp_prep_target/msout
type: 'Directory[]'
'sbg:x': 1000
'sbg:y': 0
- id: logfiles
outputSource:
- make_sourcedb_ateam/log
- check_ateam_separation/logfile
- concat_logfiles_stationlist/output
- concat_logfiles_RMextract/output
- concat_logfiles_prep_targ/output - concat_logfiles_predict_targ/output
- concat_logfiles_clipper_targ/output
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 1000
'sbg:y': 800
steps:
- 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': -500
'sbg:y': -300
- id: compare_station_list
in:
- id: msin
source:
- msin
- id: h5parmdb
source: cal_solutions
- id: solset_name
default: 'calibrator'
- id: filter
source: filter_baselines
out:
- id: filter_out
- id: logfile
run: ../../steps/compare_station_list.cwl
label: compare_station_list
'sbg:x': -500
'sbg:y': -500
- 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: createRMh5parm
in:
- id: msin
source:
- msin
- id: h5parm
source: cal_solutions
- id: ionex_server
source: ionex_server
- id: ionex_prefix
source: ionex_prefix
- id: solset
default: target
- id: proxyserver
source: proxy_server
- id: proxyport
source: proxy_port
- id: proxytype source: proxy_type
- id: proxyuser
source: proxy_user
- id: proxypass
source: proxy_pass
out:
- id: h5parmout
- id: logfile
run: ../../steps/createRMh5parm.cwl
label: createRMh5parm
'sbg:x': -500
'sbg:y': 0
- id: losoto_plot_RM
in:
- id: input_h5parm
source: createRMh5parm/h5parmout
- id: soltab
default: target/RMextract
- id: axesInPlot
default:
- time
- id: axisInTable
default: ant
- id: prefix
default: RMextract
out:
- id: output_plots
- id: logfile
- id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_RM
'sbg:x': 0
'sbg:y': -300
- id: dppp_prep_target
in:
- id: msin
linkMerge: merge_flattened
source:
- msin
- id: msin_baseline
default: '*'
source: compare_station_list/filter_out
- id: baselines_to_flag
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: 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: process_baselines_target
default: '*'
source: process_baselines_target
- id: target_source
source: demix_target
- id: ntimechunk
default: 10
source: max_dppp_threads
- id: subtract_sources
source:
- demix_sources
- id: parmdb
source: createRMh5parm/h5parmout
- id: apply_tec_correction
source: apply_tec
default: false
- id: apply_rm_correction
source: apply_RM
default: true
- id: apply_phase_correction
source: apply_phase
default: false
- id: apply_clock_correction
source: apply_clock
default: true
- id: apply_beam_correction
source: apply_beam
default: true
- id: filter_baselines
source: compare_station_list/filter_out
- id: updateweights
source: updateweights
out:
- id: msout
- id: prep_logfile
- id: predict_logfile
- id: clipper_logfile
- id: clipper_output
- id: parset
run: ../../subworkflow/ndppp_prep_targ.cwl
label: ndppp_prep_target
scatter:
- msin
'sbg:x': 0
'sbg:y': 0
- id: plot_Ateamclipper
in:
- id: clipper_output
source: concat_logfiles_clipper_output/output
out:
- id: output_imag
run: ../../steps/plot_Ateamclipper.cwl
label: concat_logfiles_clipper_output
'sbg:x': 600
'sbg:y': 200
- id: concat_logfiles_clipper_output
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/clipper_output
- id: file_prefix
default: Ateamclipper
- id: file_suffix
default: txt
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_clipper_output
'sbg:x': 400 'sbg:y': 200
- id: concat_logfiles_prep_targ
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/prep_logfile
- id: file_prefix
default: ndppp_prep_targ
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_prep_target
'sbg:x': 400
'sbg:y': 300
- id: concat_logfiles_predict_targ
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/predict_logfile
- id: file_prefix
default: predict_targ
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_predict_targ
'sbg:x': 400
'sbg:y': 400
- id: concat_logfiles_clipper_targ
in:
- id: file_list
linkMerge: merge_flattened
source: dppp_prep_target/clipper_logfile
- id: file_prefix
default: Ateamclipper
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_clipper_targ
'sbg:x': 400
'sbg:y': 500
- id: concat_logfiles_RMextract
in:
- id: file_list
linkMerge: merge_flattened
source:
- createRMh5parm/logfile
- losoto_plot_RM/logfile
- id: file_prefix
default: RMextract
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_RMextract
'sbg:x': 400
'sbg:y': 600
- id: concat_logfiles_stationlist
in:
- id: file_list
linkMerge: merge_flattened
source:
- compare_station_list/logfile
- id: file_prefix
default: compareStationList
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_stationlist
'sbg:x': 400
'sbg:y': 700
requirements: - class: ScatterFeatureRequirement