Merge branch 'lcms_metab_bjm' into 'lcms_metab'

Add LC metabolomics workflow

See merge request mass-spectrometry/metams!22

Author: kheal

.github/workflows/workflow_tests.yml

@@ -28,14 +28,19 @@ jobs:
         python -m pip install --upgrade pip
         pip install miniwdl
     
-    - name: Download test data for lipidomics
+    - name: Download LCMS metabolomics database and test data
       run: |
-        make get-lipid-test-data
-    
-    - name: Run Lipidomics WDL with lipidomics test data
+        make get-test-data
+
+    - name: Run Lipidomics WDL with lipidomics test data and pushed Docker Image
       run: |
         miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
-    
+
+    # This will fail until the new Docker image is pushed to Docker Hub
+    #- name: Run LCMS metabolomics WDL with test data and pushed Docker Image
+    #  run: |
+    #    make wdl-run-lcms-metab
+
     - name: Run GCMS WDL with pushed Docker Image
       run: |
         miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files
@@ -52,6 +57,10 @@ jobs:
       run: |
         miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics_local_docker.json --verbose --no-cache --copy-input-files
     
-    - name: Remove lipidomics test data
+    - name: Run LCMS metabolomics WDL with local Docker Image based on Dockerfile
+      run: |
+        miniwdl run wdl/metaMS_lcms_metabolomics.wdl -i wdl/metams_input_lcms_metabolomics_local_docker.json --verbose --no-cache --copy-input-files
+    
+    - name: Remove test data
       run: |
         rm -rf test_data

Dockerfile

@@ -21,7 +21,7 @@ COPY metaMS/ /metams/metaMS/
 COPY README.md disclaimer.txt Makefile requirements.txt setup.py /metams/
 
 # Install the correct version of CoreMS from github
-RUN pip install git+https://github.com/EMSL-Computing/CoreMS.git@v3.3.0
+RUN pip install git+https://github.com/EMSL-Computing/CoreMS.git@v3.6.0
 
 # Install the MetaMS package in editable mode
 RUN pip3 install --editable .

Makefile

@@ -119,11 +119,18 @@ 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
-	@curl -L -o test_data/test_lipid_data.zip https://nmdcdemo.emsl.pnnl.gov/lipidomics/test_data/metams_lipid_test_data/test_lipid_data.zip
-	@unzip test_data/test_lipid_data.zip -d test_data/
+	@mkdir -p test_data/test_lipid_data
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lipid_data.zip https://nmdcdemo.emsl.pnnl.gov/lipidomics/test_data/metams_lipid_test_data/test_lipid_data.zip
+	@unzip test_data/test_lipid_data.zip -d test_data/test_lipid_data/
 	@rm test_data/test_lipid_data.zip
 	@echo "Test data downloaded and unzipped"
 
@@ -134,6 +141,17 @@ wdl-run-lipid-local:
 	@make docker-build-local
 	miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics_local_docker.json --verbose --no-cache --copy-input-files
 
+get-test-data:
+	@make get-lipid-test-data
+	@make get-lcms-database
+
+wdl-run-lcms-metab :
+	miniwdl run wdl/metaMS_lcms_metabolomics.wdl -i wdl/metams_input_lcms_metabolomics.json --verbose --no-cache --copy-input-files
+
+wdl-run-lcms-metab-local:
+	@make docker-build-local
+	miniwdl run wdl/metaMS_lcms_metabolomics.wdl -i wdl/metams_input_lcms_metabolomics_local_docker.json --verbose --no-cache --copy-input-files
+
 convert_lipid_rst_to_md:
     # convert the lipid documentation from rst to md and render it into html
 	pandoc -f rst -t markdown -o docs/lcms_lipidomics/README_LCMS_LIPID.md docs/lcms_lipidomics/index.rst