Reconfigure lcms metab test data makefile commands

Author: kheal

.github/workflows/workflow_tests.yml

@@ -28,9 +28,13 @@ jobs:
         python -m pip install --upgrade pip
         pip install miniwdl
     
-    - name: Download LCMS metabolomics test data
+    - name: Download LCMS metabolomics database
       run: |
-        make get-lcms-metab-test-data
+        make get-lcms-database
+    
+    - name: Download lipidomics test data
+      run: |
+        make get-lipid-test-data
     
     - name: Run Lipidomics WDL with lipidomics test data
       run: |

Makefile

@@ -119,6 +119,12 @@ wdl-run-gcms-local:
 	@make docker-build-local
 	@miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms_local_docker.json --verbose --no-cache --copy-input-files
 
+get-lcms-database:
+	@echo "Downloading LC-MS database"
+	@mkdir -p test_data/test_lcms_metab_data
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lcms_metab_data/database.msp https://nmdcdemo.emsl.pnnl.gov/metabolomics/databases/20250407_gnps_curated.msp
+	@echo "LC-MS database downloaded"
+
 get-lipid-test-data:
 	@echo "Downloading test data for lipidomics"
 	@mkdir -p test_data

metaMS/lcms_metabolomics_workflow.py

@@ -363,7 +363,7 @@ def process_complete_workflow(args):
 
         # MS2 processing and export
         process_ms2(lcms_obj, metadata, scan_translator)
-        export_results(lcms_obj, output_path, metadata["molecular_metadata"], final=True)
+        export_results(lcms_obj, str(output_path), metadata["molecular_metadata"], final=True)
 
         return f"Completed: {output_path}"
     except Exception as e:
@@ -446,6 +446,7 @@ def run_lcms_metabolomics_workflow(
     if cores == 1 or len(files_list) == 1:
         for file_in, output_path in zip(files_list, out_paths_list):
             args = (file_in, output_path, params_toml, scan_translator, metadata)
+            process_complete_workflow(args)
 
     elif cores > 1:
         with Pool(cores) as pool:

wdl/metams_input_lcms_metabolomics_local_docker.json

@@ -1,12 +1,12 @@
 {
     "lcmsMetabolomics.docker_image": "local-metams:latest",
     "lcmsMetabolomics.runMetaMSLCMSMetabolomics.file_paths": [
-        "./test_data/test_lcms_metab_data/Blanch_Nat_Lip_C_4_AB_M_08_NEG_25Jan18_Brandi-WCSH5801.raw",
-        "./test_data/test_lcms_metab_data/Blanch_Nat_Lip_C_4_AB_M_08_POS_23Jan18_Brandi-WCSH5801.raw"
+        "./test_data/test_lipid_data/Blanch_Nat_Lip_C_4_AB_M_08_NEG_25Jan18_Brandi-WCSH5801.raw",
+        "./test_data/test_lipid_data/Blanch_Nat_Lip_C_4_AB_M_08_POS_23Jan18_Brandi-WCSH5801.raw"
     ],
     "lcmsMetabolomics.runMetaMSLCMSMetabolomics.output_directory": "output",
-    "lcmsMetabolomics.runMetaMSLCMSMetabolomics.corems_toml_path": "./test_data/test_lcms_metab_data/emsl_lcmetab_corems_params_test.toml",
-    "lcmsMetabolomics.runMetaMSLCMSMetabolomics.msp_file_path": "./test_data/test_lcms_metab_data/20250407_gnps_curated.msp",
-    "lcmsMetabolomics.runMetaMSLCMSMetabolomics.scan_translator_path": "./test_data/test_lcms_metab_data/emsl_lcmetab_scan_translator.toml",
+    "lcmsMetabolomics.runMetaMSLCMSMetabolomics.corems_toml_path": "./configuration/lcms_metab_configs/emsl_lcms_metab_corems_params.toml",
+    "lcmsMetabolomics.runMetaMSLCMSMetabolomics.msp_file_path": "./test_data/test_lcms_metab_data/database.msp",
+    "lcmsMetabolomics.runMetaMSLCMSMetabolomics.scan_translator_path": "./configuration/lcms_metab_configs/emsl_lcms_metab_scan_translator.toml",
     "lcmsMetabolomics.runMetaMSLCMSMetabolomics.cores": 1
 }