Merge branch 'lcms_metab' into 'master'

Update to CoreMS 3.8.1

See merge request mass-spectrometry/metams!25

Author: kheal

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.2.1
+current_version = 3.2.2
 commit = False
 tag = False
 

.bumpversion_lcmsmetab.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.1
+current_version = 1.0.2
 commit = False
 tag = False
 

.bumpversion_lipid.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.1
+current_version = 1.2.2
 commit = False
 tag = False
 

.github/workflows/workflow_tests.yml

@@ -32,33 +32,33 @@ jobs:
       run: |
         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
-
-    - 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
-
     - name: Build Docker Image
       run: |
         docker build -t local-metams:latest .
     
     - name: Run GCMS WDL with local Docker Image based on Dockerfile
       run: |
         miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms_local_docker.json --verbose --no-cache --copy-input-files
-    
+        
+    - 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: Run Lipidomics WDL with local Docker Image based on Dockerfile
       run: |
         miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics_local_docker.json --verbose --no-cache --copy-input-files
-    
-    - name: Run LCMS metabolomics WDL with local Docker Image based on Dockerfile
+
+    - name: Run Lipidomics WDL with lipidomics test data and pushed Docker Image
       run: |
-        miniwdl run wdl/metaMS_lcms_metabolomics.wdl -i wdl/metams_input_lcms_metabolomics_local_docker.json --verbose --no-cache --copy-input-files
+        miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
+
+    - 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
     
     - name: Remove test data
       run: |

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@v3.8.0
+RUN pip install git+https://github.com/EMSL-Computing/CoreMS.git@v3.8.1
 
 # Install the MetaMS package in editable mode
 RUN pip3 install --editable .

MAINTAINERS.md

@@ -45,9 +45,9 @@ To test a workflow before an associated docker image is pushed, you can run the
 The following steps should be followed in order
 
 ### Bump Version Numbers
-The versioning of the repo, docker image and the GC/MS workflow are currently 3.2.1.
-The version of the lipid workflow is currently 1.2.1.
-The version of the LCMS metabolomics workflow is currently 1.0.1.
+The versioning of the repo, docker image and the GC/MS workflow are currently 3.2.2.
+The version of the lipid workflow is currently 1.2.2.
+The version of the LCMS metabolomics workflow is currently 1.0.2.
 
 To bump the repo *and all workflows*, run one of the following commands.  This will update the runtime version of all of the workflows, the version of the repo and the version of the docker image.
 

Makefile

@@ -134,6 +134,15 @@ get-lipid-test-data:
 	@rm test_data/test_lipid_data.zip
 	@echo "Test data downloaded and unzipped"
 
+get-lcms-metab-test-data:
+	@echo "Downloading test data for LC-MS metabolomics"
+	@mkdir -p test_data
+	@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/lcms_test_data1.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data1.mzML
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lcms_metab_data/lcms_test_data2.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data2.mzML
+	@curl --retry 3 --retry-delay 5 --connect-timeout 30 --max-time 300 -L -o test_data/test_lcms_metab_data/lcms_test_data3.mzML https://nmdcdemo.emsl.pnnl.gov/metabolomics/test_data/metams_lcms_metab_test_data/lcms_test_data3.mzML
+	@echo "LCMS test data downloaded"
+
 wdl-run-lipid :
 	miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files
 
@@ -144,6 +153,7 @@ wdl-run-lipid-local:
 get-test-data:
 	@make get-lipid-test-data
 	@make get-lcms-database
+	@make get-lcms-metab-test-data
 
 wdl-run-lcms-metab :
 	miniwdl run wdl/metaMS_lcms_metabolomics.wdl -i wdl/metams_input_lcms_metabolomics.json --verbose --no-cache --copy-input-files

README.md

@@ -10,7 +10,7 @@
 
 ## Current Version
 
-### `3.2.1`
+### `3.2.2`
 
 ## Available Workflows
 

configuration/lcms_metab_configs/mzml_centroid_scan_translator.toml

@@ -0,0 +1,3 @@
+[ms2]
+scan_filter = "hcd"
+resolution = "high"

docs/gcms_metabolomics/README_GCMS.md

@@ -20,7 +20,7 @@
 
 ## Current Version
 
-### `3.2.1`
+### `3.2.2`
 
 ### Data input formats