diff --git a/Dockerfile b/Dockerfile
index c1b6c21..1315b11 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,7 +4,14 @@ WORKDIR /metams
 COPY metaMS/ /metams/metaMS/
 COPY README.md disclaimer.txt Makefile requirements.txt setup.py /metams/
 COPY db/ /metams/db/
-RUN pip3 install --editable .
 
+# Install the specific version of corems
+RUN pip3 install corems==2.2.1
+
+# Install other dependencies from requirements.txt
+RUN pip3 install -r requirements.txt
+
+# Install the MetaMS package in editable mode
+RUN pip3 install --editable .
 
 
diff --git a/metaMS/cli.py b/metaMS/cli.py
index 2610733..7d41b3a 100644
--- a/metaMS/cli.py
+++ b/metaMS/cli.py
@@ -198,3 +198,6 @@ def run_lipidomics_workflow(paramaters_file, directory, output_directory, token_
             directory=directory, output_directory=output_directory, cores=cores
         )
     click.echo("Running lipidomics workflow")
+    # test call:
+    # MetaMS run-lipidomics-workflow -p configuration/lipidomics_metams.toml
+    # miniwdl run wdl/metaMS_lipidomics.wdl -i wdl/metams_input_lipidomics.json
diff --git a/metaMS/lcms_lipidomics_workflow.py b/metaMS/lcms_lipidomics_workflow.py
index 12ed00a..323738b 100644
--- a/metaMS/lcms_lipidomics_workflow.py
+++ b/metaMS/lcms_lipidomics_workflow.py
@@ -4,8 +4,8 @@
 import datetime
 from multiprocessing import Pool
 
-from corems.mass_spectra.input.mzml import MZMLSpectraParser
-from corems.mass_spectra.input.rawFileReader import ImportMassSpectraThermoMSFileReader
+#from corems.mass_spectra.input.mzml import MZMLSpectraParser
+#from corems.mass_spectra.input.rawFileReader import ImportMassSpectraThermoMSFileReader
 
 @dataclass
 class LipidomicsWorkflowParameters:
@@ -58,10 +58,12 @@ def instantiate_lcms_obj(file_in):
         #parser = ImportMassSpectraThermoMSFileReader(file_in)
 
     if ".mzML" in str(file_in):
-        parser = MZMLSpectraParser(file_in)
+        #parser = MZMLSpectraParser(file_in)
+        pass
 
     # Instantiate lc-ms data object using parser and pull in ms1 spectra into dataframe (without storing as MassSpectrum objects to save memory)
-    myLCMSobj = parser.get_lcms_obj(spectra="ms1")
+    #myLCMSobj = parser.get_lcms_obj(spectra="ms1")
+    myLCMSobj = None
 
     return myLCMSobj
 
@@ -129,5 +131,6 @@ def run_lcms_lipidomics_workflow(
         mz_dicts = pool.starmap(run_lipid_sp_ms1, args)
         pool.close()
         pool.join()
+    print("Finished processing all files")
 
     # TODO KRH: Add full lipidomics workflow here
diff --git a/requirements.txt b/requirements.txt
index c02842b..2eb2860 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-corems>=2.0.0
+corems==2.2.1
 Click>=7.1.1
 requests
 nmdc-schema>=7.0.0
diff --git a/wdl/metaMS_gcms.wdl b/wdl/metaMS_gcms.wdl
deleted file mode 100644
index 2c812f9..0000000
--- a/wdl/metaMS_gcms.wdl
+++ /dev/null
@@ -1,46 +0,0 @@
-version 1.0
-
-workflow gcmsMetabolomics {
-    call runMetaMSGCMS
-
-    output {
-        String out = runMetaMSGCMS.out
-        File output_file = runMetaMSGCMS.output_file
-        File output_metafile = runMetaMSGCMS.output_metafile
-    }
-}
-
-task runMetaMSGCMS {
-    input {
-        Array[File] file_paths
-        File calibration_file_path
-        String output_directory
-        String output_filename
-        String output_type
-        File corems_toml_path
-        File nmdc_metadata_path
-        Int jobs_count
-    }
-
-    command {
-        metaMS run-gcms-wdl-workflow \
-            ${sep=',' file_paths} \
-            ${calibration_file_path} \
-            ${output_directory} \
-            ${output_filename} \
-            ${output_type} \
-            ${corems_toml_path} \
-            ${nmdc_metadata_path} \
-            --jobs ${jobs_count}
-    }
-
-    output {
-        String out = read_string(stdout())
-        File output_file = "${output_directory}/${output_filename}.${output_type}"
-        File output_metafile = "${output_directory}/${output_filename}.json"
-    }
-
-    runtime {
-        docker: "microbiomedata/metams:2.2.2"
-    }
-}
\ No newline at end of file
diff --git a/wdl/metaMS_lipidomics.wdl b/wdl/metaMS_lipidomics.wdl
index 296ef23..dea4d11 100644
--- a/wdl/metaMS_lipidomics.wdl
+++ b/wdl/metaMS_lipidomics.wdl
@@ -17,5 +17,4 @@ task runLipidomicsMetaMS {
         docker: "local-metams:latest"
         #TODO KRH: Change to dockerhub version after we've pushed the updated image
     }
-}
-
+}
\ No newline at end of file
diff --git a/wdl/metams_input_lipidomics.json b/wdl/metams_input_lipidomics.json
index e113869..056f702 100644
--- a/wdl/metams_input_lipidomics.json
+++ b/wdl/metams_input_lipidomics.json
@@ -1,3 +1,3 @@
 {
-    "lcmsLipidomics.runLipidomicsMetaMS.config_file": "lipidomics_metams.toml"
+    "lcmsLipidomics.runLipidomicsMetaMS.config_file": "./configuration/lipidomics_metams.toml"
 }
\ No newline at end of file