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Frits Sweijen authoredFrits Sweijen authored
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prep.cwl 8.99 KiB
class: Workflow
cwlVersion: v1.2
id: prep
label: prep
inputs:
- id: msin
type: Directory[]
- id: filter_baselines
type: string?
default: '*&'
- id: raw_data
type: boolean?
default: false
- id: propagatesolutions
type: boolean?
default: true
- id: flagunconverged
type: boolean?
default: false
- id: demix
type: boolean?
- id: max_dp3_threads
type: int?
default: 10
- id: memoryperc
type: int?
default: 20
- id: flag_baselines
type: string[]?
default: []
- id: avg_timeresolution
type: int?
default: 4
- id: avg_freqresolution
type: string?
default: '48.82kHz'
- id: process_baselines_cal
type: string?
default: '*&'
- id: demix_timeres
type: float?
default: 10
- id: demix_freqres
type: string?
default: '48.82kHz'
- id: demix_sources
type: string[]?
default: []
- id: min_separation
type: int?
default: 30
- id: do_smooth
type: boolean?
default: false
- id: max_separation_arcmin
type: float?
default: 1.0
- id: calibrator_path_skymodel
type:
- Directory?
- File?
- id: A-Team_skymodel
type: File?
- id: elevation
type: string?
default: 0deg..15deg
- id: amplmin
type: float?
default: 1.e-30
- id: rfistrategy type:
- File?
- string?
- id: lbfgs_historysize
type: int?
default: 10
- id: lbfgs_robustdof
type: float?
default: 200
- id: aoflag_reorder
type: boolean?
default: false
- id: aoflag_chunksize
type: int?
default: 2000
outputs:
- id: outh5parm
outputSource:
- h5parm_collector/outh5parm
type: File
- id: check_Ateam_separation.png
outputSource:
- check_ateam_separation/output_imag
type: File
- id: msout
outputSource:
- predict_calibrate/msout
type: Directory[]
- id: calibrator_name
outputSource:
- find_skymodel_cal/model_name
type: string
- id: outh5parm_logfile
outputSource:
- h5parm_collector/log
type: File[]
- id: check_Ateam_separation.json
outputSource:
- check_ateam_separation/output_json
type: File
- id: flagged_fraction_dict_refant
outputSource:
- predict_calibrate/flagged_fraction_dict
type: string[]
- id: flagged_fraction_dict
outputSource:
- dp3_prep_cal/flagged_fraction_dict
type: string[]
- id: logfiles
outputSource:
- concat_logfiles_calib/output
- concat_logfiles_predict/output
- concat_logfiles_blsmooth/output
- concat_logfiles_skymodels/output
- find_skymodel_cal/logfile
- concat_logfiles_prep_cal/output
- check_ateam_separation/logfile
- check_demix/logfile
- aoflag/logfile
type: File[]
linkMerge: merge_flattened
steps:
- id: select
in:
- id: input
source:
- msin
out:
- id: output
run: ../../steps/selectfirstdirectory.cwl label: select_only_first
- id: dp3_prep_cal
in:
- id: max_dp3_threads
source: max_dp3_threads
- 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
source: check_demix/out_demix
- id: msin
linkMerge: merge_flattened
source:
- msin
- id: msin_baseline
default: '*'
source: filter_baselines
- id: skymodel
source: merge_skymodels/skymodel_out
- id: timeresolution
default: 1
source: avg_timeresolution
- id: freqresolution
default: 12.21kHz
source: avg_freqresolution
- id: demix_timeres
source: demix_timeres
- id: demix_freqres
source: demix_freqres
- id: demix_baseline
default: '*'
source: process_baselines_cal
- id: target_source
source: find_skymodel_cal/model_name
- id: ntimechunk
default: 10
source: max_dp3_threads
- id: subtract_sources
source: check_demix/out_demix_sources
- id: lbfgs_historysize
source: lbfgs_historysize
- id: lbfgs_robustdof
source: lbfgs_robustdof
out:
- id: msout
- id: flagged_fraction_dict
- id: logfile
run: ./dp3_prep_cal.cwl
label: dp3_prep_cal
scatter:
- msin
- id: predict_calibrate
in:
- id: max_dp3_threads
source: max_dp3_threads
- id: msin
linkMerge: merge_flattened
source:
- aoflag/output_ms - id: do_smooth
source: do_smooth
- id: sourcedb
source: find_skymodel_cal/output_models
- id: flagunconverged
source: flagunconverged
- id: propagatesolutions
source: propagatesolutions
out:
- id: msout
- id: BLsmooth.log
- id: predict_cal.log
- id: calib_cal.log
- id: flagged_fraction_dict
- id: outh5parm
run: ./predict_calibrate.cwl
label: predict_calibrate
scatter:
- msin
- id: aoflag
in:
- id: msin
linkMerge: merge_flattened
source: dp3_prep_cal/msout
- id: verbose
default: true
- id: concatenate-frequency
default: true
- id: strategy
source: rfistrategy
- id: reorder
source: aoflag_reorder
- id: chunk-size
source: aoflag_chunksize
out:
- id: output_ms
- id: logfile
run: ../../steps/aoflag.cwl
label: aoflag
- id: check_ateam_separation
in:
- id: ms
source:
- select/output
- id: min_separation
source: min_separation
out:
- id: output_imag
- id: output_json
- id: logfile
run: ../../steps/check_ateam_separation.cwl
label: check_Ateam_separation
- id: check_demix
in:
- id: demix
source: demix
- id: skymodel
source: A-Team_skymodel
- id: demix_sources
source: demix_sources
- id: clip_sources
default: []
- id: Ateam_separation_file
source: check_ateam_separation/output_json
out:
- id: out_demix
- id: out_demix_sources
- id: logfile
run: ../../steps/check_demix.cwl
label: check_demix - id: find_skymodel_cal
in:
- id: msin
source:
- select/output
- 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
- id: merge_skymodels
in:
- id: inmodel1
source: find_skymodel_cal/output_models
- id: inmodel2
source: A-Team_skymodel
out:
- id: skymodel_out
- id: logfile
run: ../../steps/merge_skymodels.cwl
label: merge_skymodels
- id: concat_logfiles_prep_cal
in:
- id: file_list
linkMerge: merge_flattened
source:
- dp3_prep_cal/logfile
- id: file_prefix
default: dp3_prep_cal
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_prep_cal
- id: concat_logfiles_skymodels
in:
- id: file_list
linkMerge: merge_flattened
source:
- merge_skymodels/logfile
- id: file_prefix
default: merge_skymodels
out:
- id: output
run: ../../steps/concatenate_files.cwl
label: concat_logfiles_skymodels
- 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
- 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
- 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
- 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: ../../steps/H5ParmCollector.cwl
label: H5parm_collector
requirements:
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement