From 53d609cf1b9884cc25453cb1382987624e4f62f2 Mon Sep 17 00:00:00 2001
From: Katherine Heal <katherine.heal@pnnl.gov>
Date: Mon, 23 Sep 2024 16:31:39 -0700
Subject: [PATCH] Begin to specify wdl calls for gcms

---
 .github/workflows/wdl_checker.yml   |  2 +-
 README.md                           |  4 ++--
 metaMS/cli.py                       | 10 +++++-----
 wdl/{metaMS.wdl => metaMS_gcms.wdl} |  0
 4 files changed, 8 insertions(+), 8 deletions(-)
 rename wdl/{metaMS.wdl => metaMS_gcms.wdl} (100%)

diff --git a/.github/workflows/wdl_checker.yml b/.github/workflows/wdl_checker.yml
index f01f235..652aa5a 100644
--- a/.github/workflows/wdl_checker.yml
+++ b/.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
\ No newline at end of file
+        miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input.json --verbose --no-cache --copy-input-files
\ No newline at end of file
diff --git a/README.md b/README.md
index bbba6ab..bc3f332 100644
--- a/README.md
+++ b/README.md
@@ -90,10 +90,10 @@ 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 metams.toml
 ```
 ```bash
-metaMS dump-corems-toml-template corems.toml
+metaMS dump-gcms-corems-toml-template corems.toml
 ```
 
  Modify the metams.toml and corems.toml accordingly to your dataset and workflow parameters
diff --git a/metaMS/cli.py b/metaMS/cli.py
index 3107c92..5ef34a8 100644
--- a/metaMS/cli.py
+++ b/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-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 
     '''
diff --git a/wdl/metaMS.wdl b/wdl/metaMS_gcms.wdl
similarity index 100%
rename from wdl/metaMS.wdl
rename to wdl/metaMS_gcms.wdl