Edit

CBICA · Sep 11, 2024 · dfaca17 · dfaca17
1 parent 1cd3922
commit dfaca17
Show file tree

Hide file tree

Showing 6 changed files with 340 additions and 276 deletions.
diff --git a/run.py b/run.py
@@ -4,62 +4,32 @@
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
-    parser.add_argument("--dir_input", help="Provide input folder", required=True)
-    parser.add_argument("--dir_output", help="Provide output folder", required=True)
-    parser.add_argument("--studies", type=int, help="Provide total studies", required=True)
-    parser.add_argument("--cores", help="Select number of cores that the workflow will use to run", required=True)
-    parser.add_argument("--dry_run", help="Select dry run", default=0)
-    parser.add_argument("--version", type=str, default="test", help="Provide version")
-    parser.add_argument("--conda", type=int, help="Run workflows without initializing a coda environment again", default=0)
+    parser.add_argument("--input_rois", help="Provide input csv name with ROIs", required=True)
+    parser.add_argument("--input_demog", help="Provide input csv name with demographic info", required=True)
+    parser.add_argument("--input_config", help="Provide input config file name", required=True)
+    parser.add_argument("--dir_output", help="Provide output folder name", required=True)
 
     options = parser.parse_args()
 
-    if int(options.cores) < 1:
-        print("Please select a valid number of cores(>=1)")
-        exit(0)
+    # Read default config file
+    with open(options.input_config, 'r') as f:
+        config = json.load(f)
 
-    if int(options.conda) == 1:
-        os.system("pip install -r requirements.txt")
-        os.system("conda install -n base -c conda-forge mamba")
-        os.system("mamba init")
-        os.system("mamba create -c conda-forge -c bioconda -n NiChart_Workflows python=3.8")
-        os.system("conda activate NiChart_Workflows")
-        os.system("mamba install -c conda-forge -c bioconda snakemake")
 
-    # generate info.json file for configuration
-    if not os.path.exists("info.json"):
-        os.system("touch info.json")
+    # Update the default config using the input args
+    config['input_rois'] = options.input_rois
+    config['input_demog'] = options.input_demog
+    config['dir_output'] = options.dir_output
 
-    config = {
-        "version": options.version,
-        "dir_input": options.dir_input,
-        "dir_output": options.dir_output,
-        "studies": options.studies,
-        "list_ROIs_all": "MUSE/list_MUSE_all.csv",
-        "list_ROIs_single": "MUSE/list_MUSE_single.csv",
-        "list_ROIs_primary": "MUSE/list_MUSE_primary.csv",
-        "list_derived_ROIs": "MUSE/list_MUSE_mapping_derived.csv",
-        "corr_type": "normICV",
-        "model_combat": "models/vISTAG1/COMBAT/combined_DLMUSE_raw_COMBATModel.pkl.gz",
-        "model_SPARE-AD": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-AD_Model.pkl.gz",
-        "model_SPARE-Age": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-Age_Model.pkl.gz",
-        "model_SPARE-Diabetes": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-Diabetes_Model.pkl.gz",
-        "model_SPARE-Hyperlipidemia": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-Hyperlipidemia_Model.pkl.gz",
-        "model_SPARE-Hypertension": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-Hypertension_Model.pkl.gz",
-        "model_SPARE-Obesity": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-Obesity_Model.pkl.gz",
-        "model_SPARE-Smoking": "models/vISTAG1/SPARE/combined_DLMUSE_raw_COMBAT_SPARE-Smoking_Model.pkl.gz",
-        "studies": [f"Study{i + 1}" for i in range(options.studies)],
-        "SPARE_types": ["AD", "Age", "Diabetes", "Hyperlipidemia", "Hypertension", "Obesity", "Smoking"],
-        "seg_types": ["DLMUSE"]
-    }
+    # Create out dir
+    if not os.path.exists(options.dir_output):
+        os.makedirs(options.dir_output)    
 
+    # Write config file
     json_config = json.dumps(config, indent=4)
+    out_file = os.path.join(options.dir_output, 'config.json')
     with open("info.json", "w") as outfile:
         outfile.write(json_config)
-    os.system("mv info.json src/workflow/workflows/")
 
     os.chdir('src/workflow/workflows/w_sMRI')
-    if int(options.dry_run) == 1:
-        os.system("snakemake -np")
-    else:
-        os.system(f"snakemake --cores {options.cores}")
+        os.system(f"snakemake --cores 1")