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class: Workflow
cwlVersion: v1.2
id: delay-calibration
label: delay-calibration
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
- id: msin
type: 'Directory[]'
- id: solset
type: File
doc: The solution set from the prefactor pipeline.
- id: filter_baselines
type: string?
default: "*&"
- id: flag_baselines
type: string?
default: "[]"
- id: phasesol
type: string?
default: TGSSphase
- id: configfile
type: File
doc: Settings for the delay calibration in delay_solve.
- id: selfcal
type: Directory
doc: Path of external calibration scripts.
- id: h5merger
type: Directory
doc: External LOFAR helper scripts for mergin h5 files.
steps:
- id: setup
label: setup
in:
- id: msin
source: msin
- id: solset
source: solset
- id: filter_baselines
source: filter_baselines
- id: flag_baselines
source: flag_baselines
- id: phasesol
source: phasesol
out:
- id: parset
- id: delay_calibrators
- id: logdir
- id: msout

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- id: initial_flags
- id: prep_target_flags
- id: check_Ateam_separation_file
run: ./setup.cwl

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source: setup/msout

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- id: concat_flags
run: ./concatenate-flag.cwl
label: sort-concatenate-flag
# - id: apply-ddf
# in:
# - id: input1
# source: input1
# - id: input2
# source: input2
# out:
# - id: output1
# run: ../steps/step1.cwl
# label: step1
- id: phaseup
in:
- id: msin
source: sort-concatenate-flag/msout
- id: delay_calibrator
source: setup/delay_calibrators
- id: configfile
source: configfile
- id: selfcal
source: selfcal
- id: h5merger
source: h5merger

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- id: flags
source:
- setup/initial_flags
- setup/prep_target_flags
- sort-concatenate-flag/concat_flags
- id: check_Ateam_separation.json
source: setup/check_Ateam_separation_file
out:
- id: msout

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- id: solutions
- id: pictures

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- id: phaseup_flags
- id: logdir

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# - id: summary_file
run: ./phaseup-concat.cwl
label: phaseup
- id: store_logs
in:
- id: files
linkMerge: merge_flattened
source:
- setup/logdir
- sort-concatenate-flag/logdir
- phaseup/logdir
- id: sub_directory_name
default: logs
out:
- id: dir
run: ../steps/collectfiles.cwl
label: store_logs
outputs:
- id: msout
outputSource: sort-concatenate-flag/msout
type: Directory[]

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- id: delay_cat
outputSource: setup/delay_calibrators
type: File

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- id: logs
outputSource: store_logs/dir
type: Directory

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- id: pictures
outputSource: phaseup/pictures
type: File[]
- id: solutions
outputSource: phaseup/solutions
type: File[]

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committed
# - id: summary_file
# outputSource: phaseup-concat.cwl
# type: File