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prefactor_target.cwl 10.02 KiB
class: Workflow
cwlVersion: v1.0
id: prefactor_target
label: prefactor_target
$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: refant
type: string?
default: CS00.*
'sbg:x': -1000
'sbg:y': -1500
- id: flag_baselines
type: 'string[]?'
default: []
'sbg:x': -1000
'sbg:y': -1400
- id: process_baselines_target
type: string?
default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': -1300
- id: filter_baselines
type: string?
default: '[CR]S*&'
'sbg:x': -1000
'sbg:y': -1200
- id: do_smooth
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -1100
- id: rfistrategy
type: string?
default: HBAdefault.rfis
'sbg:x': -1000
'sbg:y': -1000
- id: min_unflagged_fraction
type: float?
default: 0.5
'sbg:x': -1000
'sbg:y': -900
- id: compression_bitrate
type: int?
default: 16
'sbg:x': -1000
'sbg:y': -800
- id: raw_data
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -700
- id: propagatesolutions
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': -600
- id: demix_sources
type: 'string[]?'
default:
- CasA
- CygA 'sbg:x': -1000
'sbg:y': -500
- id: demix_target
type: string?
default: ''
'sbg:x': -1000
'sbg:y': -400
- id: demix_freqstep
type: int?
default: 16
'sbg:x': -1000
'sbg:y': -300
- id: demix_timestep
type: int?
default: 10
'sbg:x': -1000
'sbg:y': -200
- id: demix
type: boolean?
default: false
'sbg:x': -1000
'sbg:y': -100
- id: apply_tec
type: boolean
default: false
'sbg:x': -1000
'sbg:y': 0
- id: apply_clock
type: boolean
default: true
'sbg:x': -1000
'sbg:y': 100
- 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': 300
- id: apply_beam
type: boolean
default: true
'sbg:x': -1000
'sbg:y': 400
- id: clipATeam
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 500
- id: gsmcal_step
type: string?
default: phase
'sbg:x': -1000
'sbg:y': 600
- id: updateweights
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 700
- id: max_dppp_threads
type: int?
default: 10
'sbg:x': -1000
'sbg:y': 800
- id: memoryperc
type: int?
default: 20 'sbg:x': -1000
'sbg:y': 900
- id: min_length
type: int?
default: 5
'sbg:x': -1000
'sbg:y': 1000
- id: overhead
type: float?
default: 0.7
'sbg:x': -1000
'sbg:y': 1100
- id: min_separation
type: int?
default: 30
'sbg:x': -1000
'sbg:y': 1200
- id: A-Team_skymodel
type: File?
'sbg:x': -1000
'sbg:y': 1300
- id: target_skymodel
type: File?
'sbg:x': -1000
'sbg:y': 1400
- id: use_target
type: boolean?
default: true
'sbg:x': -1000
'sbg:y': 1500
- id: skymodel_source
type: string?
default: TGSS
'sbg:x': -1000
'sbg:y': 1600
- id: avg_timeresolution
type: float?
default: 4
'sbg:x': -1000
'sbg:y': 1700
- id: avg_freqresolution
type: string?
default: 48.82kHz
'sbg:x': -1000
'sbg:y': 1800
- id: avg_timeresolution_concat
type: int?
default: 8
'sbg:x': -1000
'sbg:y': 1900
- id: avg_freqresolution_concat
type: string?
default: 97.64kHz
'sbg:x': -1000
'sbg:y': 2000
- id: num_SBs_per_group
type: int?
default: 10
'sbg:x': -1000
'sbg:y': 2100
- id: reference_stationSB
type: int?
default: null
'sbg:x': -1000
'sbg:y': 2200
- id: ionex_server
type: string?
default: 'ftp://ftp.aiub.unibe.ch/CODE/'
'sbg:x': -1000
'sbg:y': 2300 - id: ionex_prefix
type: string?
default: CODG
'sbg:x': -1000
'sbg:y': 2400
- id: proxy_server
type: string?
default: null
'sbg:x': -1000
'sbg:y': 2500
- id: proxy_port
type: string?
default: null
'sbg:x': -1000
'sbg:y': 2600
- id: proxy_type
type: string?
default: null
'sbg:x': -1000
'sbg:y': 2700
- id: proxy_user
type: string?
default: null
'sbg:x': -1000
'sbg:y': 2800
- id: proxy_pass
type: string?
default: null
'sbg:x': -1000
'sbg:y': 2900
outputs:
- id: inspection
outputSource:
- prep/inspection
- gsmcal/inspection
- finalize/inspection
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 2000
'sbg:y': -600
- id: solutions
outputSource:
- finalize/solutions
type: File
'sbg:x': 2000
'sbg:y': -500
- id: msout
outputSource:
- finalize/msout
type: 'Directory[]'
'sbg:x': 2000
'sbg:y': 0
- id: logfiles
outputSource:
- prep/logfiles
- concat_logfiles_RefAnt/output
- gsmcal/logfiles
- finalize/logfiles
type: 'File[]'
linkMerge: merge_flattened
'sbg:x': 2000
'sbg:y': 600
steps:
- id: prep
in:
- id: msin
source:
- msin
- id: cal_solutions
source: cal_solutions - id: flag_baselines
source:
- flag_baselines
- id: process_baselines_target
source: process_baselines_target
- id: filter_baselines
source: filter_baselines
- id: raw_data
source: raw_data
- id: propagatesolutions
source: propagatesolutions
- id: demix_sources
source:
- demix_sources
- id: demix_target
source: demix_target
- id: demix_freqstep
source: demix_freqstep
- id: demix_timestep
source: demix_timestep
- id: demix
source: demix
- id: apply_tec
source: apply_tec
- id: apply_clock
source: apply_clock
- id: apply_phase
source: apply_phase
- id: apply_RM
source: apply_RM
- id: apply_beam
source: apply_beam
- id: clipATeam
source: clipATeam
- id: updateweights
source: updateweights
- id: max_dppp_threads
source: max_dppp_threads
- id: memoryperc
source: memoryperc
- id: min_separation
source: min_separation
- id: A-Team_skymodel
source: A-Team_skymodel
- id: avg_timeresolution
source: avg_timeresolution
- id: avg_freqresolution
source: avg_freqresolution
- id: ionex_server
source: ionex_server
- id: ionex_prefix
source: ionex_prefix
- id: proxy_server
source: proxy_server
- id: proxy_port
source: proxy_port
- id: proxy_type
source: proxy_type
- id: proxy_user
source: proxy_user
- id: proxy_pass
source: proxy_pass
out:
- id: outh5parm
- id: inspection
- id: msout
- id: logfiles
run: ./prefactor_target/prep.cwl
label: prep
'sbg:x': 0 'sbg:y': 0
- id: findRefAnt
in:
- id: msin
source: prep/msout
out:
- id: flagged_fraction_dict
- id: logfile
run: ./../steps/findRefAnt.cwl
label: findRefAnt
scatter:
- msin
'sbg:x': 400
'sbg:y': 0
- id: findRefAnt_join
in:
- id: flagged_fraction_dict
source:
- findRefAnt/flagged_fraction_dict
- id: filter_station
source: refant
out:
- id: refant
- id: logfile
run: ./../steps/findRefAnt_join.cwl
label: findRefAnt_join
'sbg:x': 600
'sbg:y': 0
- id: concat_logfiles_RefAnt
in:
- id: file_list
linkMerge: merge_flattened
source:
- findRefAnt/logfile
- findRefAnt_join/logfile
- id: file_prefix
default: findRefAnt
out:
- id: output
run: ./../steps/concatenate_files.cwl
label: concat_logfiles_RefAnt
'sbg:x': 800
'sbg:y': 300
- id: gsmcal
in:
- id: msin
source:
- prep/msout
- id: filter_baselines
source: process_baselines_target
- id: num_SBs_per_group
source: num_SBs_per_group
- id: reference_stationSB
source: reference_stationSB
- id: use_target
source: use_target
- id: target_skymodel
source: target_skymodel
- id: skymodel_source
source: skymodel_source
- id: do_smooth
source: do_smooth
- id: propagatesolutions
source: propagatesolutions
- id: avg_timeresolution_concat
source: avg_timeresolution_concat
- id: avg_freqresolution_concat
source: avg_freqresolution_concat
- id: min_unflagged_fraction
source: min_unflagged_fraction - id: refant
source: findRefAnt_join/refant
- id: overhead
source: overhead
- id: min_length
source: min_length
out:
- id: msout
- id: outh5parm
- id: bad_antennas
- id: outh5parm_logfile
- id: inspection
- id: logfiles
run: ./prefactor_target/gsmcal.cwl
label: gsmcal
'sbg:x': 900
'sbg:y': 0
- id: finalize
in:
- id: msin
source:
- gsmcal/msout
- id: input_h5parm
source: gsmcal/outh5parm
- id: inh5parm_logfile
source: gsmcal/outh5parm_logfile
- id: gsmcal_step
source: gsmcal_step
- id: process_baselines_target
source: process_baselines_target
- id: bad_antennas
source: gsmcal/bad_antennas
- id: insolutions
source: prep/outh5parm
- id: compression_bitrate
source: compression_bitrate
- id: skymodel_source
source: skymodel_source
out:
- id: msout
- id: solutions
- id: logfiles
- id: inspection
run: ./prefactor_target/finalize.cwl
label: finalize
'sbg:x': 1200
'sbg:y': 0
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement