Revert lipid changes - MetabRef not ready

Author: kheal

metaMS/cli.py

@@ -169,9 +169,9 @@ def run_lipidomics_workflow(
     file_paths, 
     output_directory, 
     corems_params, 
+    db_location, 
     scan_translator_path, 
-    cores,
-    db_location=None
+    cores
     ):
     """Run the lipidomics workflow
 
@@ -185,13 +185,12 @@ def run_lipidomics_workflow(
         The directory where the output files will be stored
     corems_params : str
         The path corems parameters toml file
+    db_location : str
+        The path to the sqlite database for lipid spectra searching
     scan_translator_path : str
         The path to the scan translator file
     cores : int
         The number of cores to use for processing
-    db_location : str | None
-        The path to the sqlite database for lipid spectra searching
-        No longer used, only present for compatibility
     """
     if paramaters_file is not None:
         if cores is not None or file_paths is not None:
@@ -214,10 +213,14 @@ def run_lipidomics_workflow(
                 "Must provide an output directory if not using a parameters file"
             )
             return
+        if db_location is None:
+            click.echo("No database path provided")
+            return
         run_lcms_lipidomics_workflow(
             file_paths=file_paths,
             output_directory=output_directory,
             corems_toml_path=corems_params,
+            db_location=db_location,
             scan_translator_path=scan_translator_path,
             cores=cores,
         )
@@ -342,4 +345,4 @@ def run_lcmsmetab_workflow(
             msp_file_path=msp_file_path,
             scan_translator_path=scan_translator_path,
             cores=cores,
-        )
+        )

wdl/metaMS_lcmslipidomics.wdl

@@ -21,6 +21,7 @@ task runMetaMSLCMSLipidomics {
         Array[File] file_paths
         String output_directory
         File corems_toml_path
+        File db_location
         File scan_translator_path
         Int cores
         String? docker_image
@@ -31,6 +32,7 @@ task runMetaMSLCMSLipidomics {
             -i ${sep=',' file_paths} \
             -o ${output_directory} \
             -c ${corems_toml_path} \
+            -d ${db_location} \
             -s ${scan_translator_path} \
             -j ${cores}
         EXIT_CODE=$?

wdl/metams_input_lipidomics.json

@@ -5,6 +5,7 @@
     ],
     "lcmsLipidomics.runMetaMSLCMSLipidomics.output_directory": "output",
     "lcmsLipidomics.runMetaMSLCMSLipidomics.corems_toml_path": "./test_data/test_lipid_data/emsl_lipidomics_corems_params_test.toml",
+    "lcmsLipidomics.runMetaMSLCMSLipidomics.db_location": "./test_data/test_lipid_data/lipid_ref.sqlite",
     "lcmsLipidomics.runMetaMSLCMSLipidomics.scan_translator_path": "./test_data/test_lipid_data/emsl_lipidomics_scan_translator.toml",
     "lcmsLipidomics.runMetaMSLCMSLipidomics.cores": 1
 }

wdl/metams_input_lipidomics_local_docker.json

@@ -6,6 +6,7 @@
     ],
     "lcmsLipidomics.runMetaMSLCMSLipidomics.output_directory": "output",
     "lcmsLipidomics.runMetaMSLCMSLipidomics.corems_toml_path": "./test_data/test_lipid_data/emsl_lipidomics_corems_params_test.toml",
+    "lcmsLipidomics.runMetaMSLCMSLipidomics.db_location": "./test_data/test_lipid_data/lipid_ref.sqlite",
     "lcmsLipidomics.runMetaMSLCMSLipidomics.scan_translator_path": "./test_data/test_lipid_data/emsl_lipidomics_scan_translator.toml",
     "lcmsLipidomics.runMetaMSLCMSLipidomics.cores": 1
 }