add tests for bruker updates

Author: bmeluch

.github/workflows/di_workflow_tests.yaml

@@ -32,6 +32,14 @@ jobs:
       run: |
         make docker-build-local
 
+    - name: Run Bruker di WDL with local Docker Image based on Dockerfile
+      run: |
+        miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_local_docker_bruker.json --verbose --no-cache --copy-input-files
+
+    - name: Run Bruker di WDL with pushed Docker Image
+      run: |
+        make wdl-run-di-bruker
+
     - name: Run di WDL with local Docker Image based on Dockerfile
       run: |
         miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files

Makefile

@@ -106,21 +106,21 @@ cascade-run:
 cli-run-di :
 	enviroMS run_di configuration/di_enviroms.toml --jobs 1 --replicas 1 --tasks 1
 
-wdl-run-di-thermo :
+wdl-run-di :
 
-	miniwdl run wdl/di_fticr_ms_thermo.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
+	miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
 
-wdl-run-di-thermo-local :
+wdl-run-di-local :
 	@make docker-build-local
-	miniwdl run wdl/di_fticr_ms_thermo.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
+	miniwdl run wdl/di_fticr_ms.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
 
 wdl-run-di-bruker :
 
-	miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input.json --verbose --no-cache --copy-input-files
+	miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_bruker.json --verbose --no-cache --copy-input-files
 
 wdl-run-di-bruker-local :
 	@make docker-build-local
-	miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_local_docker.json --verbose --no-cache --copy-input-files
+	miniwdl run wdl/di_fticr_ms_bruker.wdl -i wdl/di_fticr_wdl_input_local_docker_bruker.json --verbose --no-cache --copy-input-files
 
 wdl-run-lc :
 

wdl/di_fticr_ms_thermo.wdl wdl/di_fticr_ms.wdlwdl/di_fticr_ms_thermo.wdl renamed to wdl/di_fticr_ms.wdl

@@ -0,0 +1,29 @@
+{
+    
+    "fticrmsNOM.runDirectInfusion.file_paths": [
+        "data/raw_data/NEG_ESI_SRFA_Auto.d"
+    ],
+
+    "fticrmsNOM.runDirectInfusion.output_directory": "output",
+    "fticrmsNOM.runDirectInfusion.output_type": "csv",
+    "fticrmsNOM.runDirectInfusion.calibrate": true,
+    "fticrmsNOM.runDirectInfusion.batch_calibrate": true,
+    "fticrmsNOM.runDirectInfusion.calibration_ref_file_path": "./data/reference/SRFA.ref",
+    
+    "fticrmsNOM.runDirectInfusion.corems_toml_path": "./configuration/di_corems.toml",
+
+    "fticrmsNOM.runDirectInfusion.polarity": "negative",
+    "fticrmsNOM.runDirectInfusion.is_centroid": true,
+    "fticrmsNOM.runDirectInfusion.raw_file_start_scan": 1,
+    "fticrmsNOM.runDirectInfusion.raw_file_final_scan": 7,
+    
+    "fticrmsNOM.runDirectInfusion.plot_mz_error": false,
+    "fticrmsNOM.runDirectInfusion.plot_ms_assigned_unassigned": false,
+    "fticrmsNOM.runDirectInfusion.plot_c_dbe":  false,
+    "fticrmsNOM.runDirectInfusion.plot_van_krevelen": false,
+    "fticrmsNOM.runDirectInfusion.plot_ms_classes": false,
+    "fticrmsNOM.runDirectInfusion.plot_mz_error_classes": false,
+    "fticrmsNOM.runDirectInfusion.plot_qc": true
+
+}
+

wdl/di_fticr_wdl_input_bruker.json

@@ -0,0 +1,28 @@
+{
+    "fticrmsNOM.docker_image": "local-enviroms:latest",
+    
+    "fticrmsNOM.runDirectInfusion.file_paths": [
+        "data/raw_data/NEG_ESI_SRFA_Auto.d"
+    ],
+
+    "fticrmsNOM.runDirectInfusion.output_directory": "output",
+    "fticrmsNOM.runDirectInfusion.output_type": "csv",
+    "fticrmsNOM.runDirectInfusion.calibrate": true,
+    "fticrmsNOM.runDirectInfusion.batch_calibrate": true,
+    "fticrmsNOM.runDirectInfusion.calibration_ref_file_path": "./data/reference/SRFA.ref",
+    
+    "fticrmsNOM.runDirectInfusion.corems_toml_path": "./configuration/di_corems.toml",
+
+    "fticrmsNOM.runDirectInfusion.polarity": "negative",
+    "fticrmsNOM.runDirectInfusion.is_centroid": true,
+    "fticrmsNOM.runDirectInfusion.raw_file_start_scan": 1,
+    "fticrmsNOM.runDirectInfusion.raw_file_final_scan": 7,
+    
+    "fticrmsNOM.runDirectInfusion.plot_mz_error": false,
+    "fticrmsNOM.runDirectInfusion.plot_ms_assigned_unassigned": false,
+    "fticrmsNOM.runDirectInfusion.plot_c_dbe":  false,
+    "fticrmsNOM.runDirectInfusion.plot_van_krevelen": false,
+    "fticrmsNOM.runDirectInfusion.plot_ms_classes": false,
+    "fticrmsNOM.runDirectInfusion.plot_mz_error_classes": false,
+    "fticrmsNOM.runDirectInfusion.plot_qc": true
+}