Merge branch 'rename_gcms_workflow_cli' into 'lipid_dev'

Rename gcms workflow cli

See merge request mass-spectrometry/metams!4

.github/workflows/wdl_checker.yml

@@ -25,4 +25,4 @@ jobs:
     - name: Run MiniWDL
       run: |
         # Add the commands to run your MiniWDL workflow
-        miniwdl run wdl/metaMS.wdl -i wdl/metams_input.json --verbose --no-cache --copy-input-files
+        miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files

README.md

@@ -90,17 +90,17 @@ To be able to open chemstation files a installation of pythonnet is needed:
 ## Execution
 
 ```bash
-metaMS dump_toml_template metams.toml
+metaMS dump-gcms-toml-template gcms_metams.toml
 ```
 ```bash
-metaMS dump_corems_toml_template corems.toml
+metaMS dump-gcms-corems-toml-template gcms_corems.toml
 ```
 
- Modify the metams.toml and corems.toml accordingly to your dataset and workflow parameters
-make sure to include corems.json path inside the metams.toml: "corems_toml_path": "path_to_corems.toml" 
+ Modify the gcms_metams.toml and gcms_corems.toml accordingly to your dataset and workflow parameters
+make sure to include gcms_corems.json path inside the gcms_metams.toml: "corems_toml_path": "path_to_corems.toml" 
 
 ```bash
-metaMS run-gcms-workflow path_to_metams.toml
+metaMS run-gcms-workflow path_to_gcms_metams.toml
 ```
 
 ## MiniWDL 
@@ -109,9 +109,9 @@ Make sure you have python 3.9.13 installed before continue
 
 MiniWDL uses the microbiome/metaMS image so there is not need to install metaMS
 
-- Change wdl/metams_input.json to specify the data location
+- Change wdl/gcms_metams_input.json to specify the data location
 
-- Change data/corems.toml to specify the workflow parameters
+- Change data/gcms_corems.toml to specify the workflow parameters
 
 Install miniWDL:
 ```bash
@@ -120,7 +120,7 @@ pip3 install miniwdl
 
 Call:
 ```bash
-miniwdl run wdl/metaMS.wdl -i wdl/metams_input.json --verbose --no-cache --copy-input-files
+miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files
 ```
 ## MetaMS Docker Container
 

metaMS/cli.py

@@ -50,20 +50,20 @@ def run_gcms_workflow(gcms_workflow_paramaters_file, jobs, nmdc):
     else:
         run_gcms_metabolomics_workflow(gcms_workflow_paramaters_file, jobs)
 
-@cli.command()
+@cli.command(name='dump-gcms-toml-template')
 @click.argument('toml_file_name', required=True, type=str)
-def dump_toml_template(toml_file_name):
+def dump_gcms_toml_template(toml_file_name):
     '''Dumps a toml file template
-        to be used as the workflow parameters input 
+        to be used as the workflow parameters input for the GCMS workflow
     '''
     ref_lib_path = Path(toml_file_name).with_suffix('.toml')
     with open(ref_lib_path, 'w') as workflow_param:
 
         toml.dump(WorkflowParameters().__dict__, workflow_param)
 
-@cli.command()
+@cli.command(name='dump-gcms-corems-toml-template')
 @click.argument('toml_file_name', required=True, type=str)
-def dump_corems_toml_template(toml_file_name):
+def dump_gcms_corems_toml_template(toml_file_name):
     '''Dumps a CoreMS toml file template
         to be used as the workflow parameters input 
     '''

wdl/metaMS.wdl → wdl/metaMS_gcms.wdl

@@ -1,16 +1,16 @@
 version 1.0
 
 workflow gcmsMetabolomics {
-    call runMetaMS
+    call runMetaMSGCMS
 
     output {
-        String out = runMetaMS.out
-        File output_file = runMetaMS.output_file
-        File output_metafile = runMetaMS.output_metafile
+        String out = runMetaMSGCMS.out
+        File output_file = runMetaMSGCMS.output_file
+        File output_metafile = runMetaMSGCMS.output_metafile
     }
 }
 
-task runMetaMS {
+task runMetaMSGCMS {
     input {
         Array[File] file_paths
         File calibration_file_path

wdl/metams_input_gcms.json

@@ -0,0 +1,15 @@
+{
+        "gcmsMetabolomics.runMetaMSGCMS.file_paths": [
+        "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf",
+        "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf"
+    ],
+
+    "gcmsMetabolomics.runMetaMSGCMS.calibration_file_path": "./data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf",
+    "gcmsMetabolomics.runMetaMSGCMS.output_directory": "test_output",
+    "gcmsMetabolomics.runMetaMSGCMS.output_filename": "test_dataset",
+    "gcmsMetabolomics.runMetaMSGCMS.output_type": "csv",
+    "gcmsMetabolomics.runMetaMSGCMS.corems_toml_path": "./configuration/gcms_corems.toml",
+    "gcmsMetabolomics.runMetaMSGCMS.nmdc_metadata_path": "./configuration/nmdc_metadata.json",
+    "gcmsMetabolomics.runMetaMSGCMS.jobs_count": 4
+
+}