From f13ef04e593c28e01e825637fcb083389c357cd8 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Fri, 25 Oct 2019 12:24:50 +0200
Subject: [PATCH] Add demo imaging pipeline
---
prefactor_calibrator_image.cwl | 90 ++++++++++++++++++++++++++++++++++
test_jobs/demo_prefactor.json | 17 +++++++
2 files changed, 107 insertions(+)
create mode 100644 prefactor_calibrator_image.cwl
create mode 100644 test_jobs/demo_prefactor.json
diff --git a/prefactor_calibrator_image.cwl b/prefactor_calibrator_image.cwl
new file mode 100644
index 00000000..fc5c16d2
--- /dev/null
+++ b/prefactor_calibrator_image.cwl
@@ -0,0 +1,90 @@
+class: Workflow
+cwlVersion: v1.0
+id: prefactor_calibrator_image
+label: prefactor_calibrator_image
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -549
+ 'sbg:y': -168
+outputs:
+ - id: image
+ outputSource:
+ - wsclean/image
+ type: 'File[]'
+ 'sbg:x': 206
+ 'sbg:y': -189
+ - id: dirty_image
+ outputSource:
+ - wsclean/dirty_image
+ type: 'File[]'
+ 'sbg:x': 271
+ 'sbg:y': -87
+ - id: image_1
+ outputSource:
+ - wsclean_1/image
+ type: 'File[]'
+ 'sbg:x': -133
+ 'sbg:y': -405
+ - id: dirty_image_1
+ outputSource:
+ - wsclean_1/dirty_image
+ type: 'File[]'
+ 'sbg:x': -26
+ 'sbg:y': -292
+steps:
+ - id: prefactor_calibrator
+ in:
+ - id: msin
+ source:
+ - msin
+ - id: raw_data
+ default: true
+ - id: demix
+ default: false
+ out:
+ - id: demix_parmdb
+ - id: output_ms
+ run: ./prefactor_calibrator.cwl
+ label: prefactor_calibrator
+ 'sbg:x': -234
+ 'sbg:y': -94
+ - id: wsclean
+ in:
+ - id: image_name
+ source: msin
+ valueFrom: $(inputs.msin.basename)
+ - id: msin
+ source: prefactor_calibrator/output_ms
+ out:
+ - id: dirty_image
+ - id: image
+ run: steps/wsclean.cwl
+ label: WSClean
+ scatter:
+ - msin
+ 'sbg:x': 6
+ 'sbg:y': -102
+ - id: wsclean_1
+ in:
+ - id: image_name
+ source: msin
+ valueFrom: flagged_$(inputs.msin.basename)
+ - id: msin
+ source: msin
+ out:
+ - id: dirty_image
+ - id: image
+ run: steps/wsclean.cwl
+ label: WSClean
+ scatter:
+ - msin
+ 'sbg:x': -317
+ 'sbg:y': -302
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement
+ - class: StepInputExpressionRequirement
+ - class: InlineJavascriptRequirement
diff --git a/test_jobs/demo_prefactor.json b/test_jobs/demo_prefactor.json
new file mode 100644
index 00000000..d51872d1
--- /dev/null
+++ b/test_jobs/demo_prefactor.json
@@ -0,0 +1,17 @@
+{
+ "msin": [
+ {
+ "class": "Directory",
+ "path": "/home/mmancini/git/prefactor3-cwl/test_data/L570745_SB003_uv_first10.MS"
+ },
+ {
+ "class": "Directory",
+ "path": "/home/mmancini/git/prefactor3-cwl/test_data/L570745_SB005_uv_first10.MS"
+ },
+ {
+ "class": "Directory",
+ "path": "/home/mmancini/git/prefactor3-cwl/test_data/L570745_SB008_uv_first10.MS"
+ }
+ ]
+}
+
--
GitLab