From 1df2b26449ceb6bb2dd947754ef5273eaba7f296 Mon Sep 17 00:00:00 2001
From: Alexander Drabent <drabent@lof009.control.lofar>
Date: Wed, 27 Nov 2019 17:00:48 +0000
Subject: [PATCH] first workflow structure design
---
workflows/HBA.cwl | 96 ++++++++++++++++++++++++++++++
workflows/prefactor.cwl | 42 +++++++++++++
workflows/prefactor_calibrator.cwl | 18 ++----
workflows/prefactor_target.cwl | 21 +++++++
4 files changed, 163 insertions(+), 14 deletions(-)
create mode 100644 workflows/HBA.cwl
create mode 100644 workflows/prefactor.cwl
create mode 100644 workflows/prefactor_target.cwl
diff --git a/workflows/HBA.cwl b/workflows/HBA.cwl
new file mode 100644
index 00000000..b5fba088
--- /dev/null
+++ b/workflows/HBA.cwl
@@ -0,0 +1,96 @@
+class: Workflow
+cwlVersion: v1.0
+id: HBA
+label: HBA.cwl
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin_calibrator
+ type: 'Directory[]'
+ 'sbg:x': -245
+ 'sbg:y': -44
+ - id: min_separation_Ateam
+ type: float
+ default: 30
+ 'sbg:x': -265
+ 'sbg:y': -153
+ - id: filter_baseline
+ type: string
+ default: '*&'
+ 'sbg:x': 145
+ 'sbg:y': 85
+ - id: flag_baselines
+ type: string
+ default: '[]'
+ 'sbg:x': 9
+ 'sbg:y': 232
+ - id: process_baselines_cal
+ type: string
+ default: '*&'
+ 'sbg:x': -320
+ 'sbg:y': 220
+ - id: raw_data
+ type: boolean
+ default: false
+ 'sbg:x': 258
+ 'sbg:y': -49
+ - id: memoryperc
+ type: int
+ default: 90
+ 'sbg:x': 206
+ 'sbg:y': 212
+ - id: avg_timeresolution
+ type: float
+ default: 4.0
+ 'sbg:x': -534
+ 'sbg:y': 175
+ - id: avg_freqresolution
+ type: string
+ default: '48.82kHz'
+ 'sbg:x': -459
+ 'sbg:y': -47
+ - id: demix
+ type: boolean
+ 'sbg:x': 255
+ 'sbg:y': 96
+ - id: demix_timestep
+ type: int
+ default: 16
+ 'sbg:x': 92
+ 'sbg:y': 158
+ - id: demix_freqstep
+ type: boolean
+ default: 16
+ 'sbg:x': -387
+ 'sbg:y': 103
+ - id: demix_target
+ type: string
+ default: ''
+ 'sbg:x': -70
+ 'sbg:y': 157
+ - id: demix_sources
+ type: string
+ default: '[CasA,CygA]'
+ 'sbg:x': -182
+ 'sbg:y': 135
+outputs:
+ - id: solutions
+ outputSource:
+ - prefactor/solutions
+ type: File
+ 'sbg:x': 99
+ 'sbg:y': -44
+steps:
+ - id: prefactor
+ in:
+ - id: msin
+ source:
+ - msin_calibrator
+ out:
+ - id: solutions
+ run: ./prefactor.cwl
+ label: prefactor.cwl
+ 'sbg:x': -72.39886474609375
+ 'sbg:y': -44.5
+requirements:
+ - class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor.cwl b/workflows/prefactor.cwl
new file mode 100644
index 00000000..c9fdcecd
--- /dev/null
+++ b/workflows/prefactor.cwl
@@ -0,0 +1,42 @@
+class: Workflow
+cwlVersion: v1.0
+id: prefactor
+label: prefactor.cwl
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -708.0858764648438
+ 'sbg:y': -306
+outputs:
+ - id: solutions
+ outputSource:
+ - prefactor_target/solutions
+ type: File
+ 'sbg:x': -169.21875
+ 'sbg:y': -319.5
+steps:
+ - id: prefactor_target
+ in:
+ - id: cal_solutions
+ source: prefactor_calibrator/outh5parm
+ out:
+ - id: solutions
+ run: ./prefactor_target.cwl
+ label: prefactor_target
+ 'sbg:x': -345
+ 'sbg:y': -321
+ - id: prefactor_calibrator
+ in:
+ - id: msin
+ source:
+ - msin
+ out:
+ - id: outh5parm
+ run: ./prefactor_calibrator.cwl
+ label: prefactor_calibrator
+ 'sbg:x': -520
+ 'sbg:y': -324
+requirements:
+ - class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 895265e5..084e4c9f 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -22,16 +22,6 @@ inputs:
'sbg:x': -175.89886474609375
'sbg:y': -724.5
outputs:
- - id: demix_parmdb
- outputSource:
- - ndppp_prep_cal/demix_parmdb
- type:
- - 'null'
- - Directory
- - type: array
- items: Directory
- 'sbg:x': -67.85011291503906
- 'sbg:y': -356.76287841796875
- id: outh5parm
outputSource:
- h5parm_collector/outh5parm
@@ -60,7 +50,7 @@ steps:
out:
- id: msout
- id: demix_parmdb
- run: subworkflow/ndppp_prep_cal.cwl
+ run: ../subworkflow/ndppp_prep_cal.cwl
label: ndppp_prep_cal
scatter:
- msin
@@ -73,7 +63,7 @@ steps:
- ndppp_prep_cal/msout
out:
- id: output_ms
- run: steps/AOFlagger.cwl
+ run: ../steps/AOFlagger.cwl
label: AOFlagger
scatterMethod: flat_crossproduct
'sbg:x': -164
@@ -87,7 +77,7 @@ steps:
out:
- id: h5parm
- id: msout
- run: subworkflow/calib_cal.cwl
+ run: ../subworkflow/calib_cal.cwl
label: calib_cal
scatter:
- msin
@@ -100,7 +90,7 @@ steps:
- calib_cal/h5parm
out:
- id: outh5parm
- run: steps/H5ParmCollector.cwl
+ run: ../steps/H5ParmCollector.cwl
label: H5parm_collector
'sbg:x': 292.1979675292969
'sbg:y': -543.7208251953125
diff --git a/workflows/prefactor_target.cwl b/workflows/prefactor_target.cwl
new file mode 100644
index 00000000..7986942f
--- /dev/null
+++ b/workflows/prefactor_target.cwl
@@ -0,0 +1,21 @@
+class: Workflow
+cwlVersion: v1.0
+id: prefactor_target
+label: prefactor_target
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: cal_solutions
+ type: File
+ 'sbg:x': -327
+ 'sbg:y': -42
+outputs:
+ - id: solutions
+ outputSource:
+ - cal_solutions
+ type: File
+ 'sbg:x': -58
+ 'sbg:y': -43
+ source: input.cal_solutions
+steps: []
+requirements: []
--
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