celloracle ns fixed:2

src/methods/multi_omics/celloracle/script.py

@@ -2,6 +2,7 @@
 import anndata as ad
 import sys
 import os
+import argparse
 
 ## VIASH START
 par = {
@@ -13,12 +14,32 @@
   "prediction": "output/celloracle_test.h5ad",
 }
 ## VIASH END
-par['links'] = f"{par['temp_dir']}/links.celloracle.links" 
 
+parser = argparse.ArgumentParser(description="Process multiomics RNA data.")
+parser.add_argument('--multiomics_rna', type=str, help='Path to the multiomics RNA file')
+parser.add_argument('--multiomics_atac', type=str, help='Path to the multiomics atac file')
+parser.add_argument('--prediction', type=str, help='Path to the prediction file')
+parser.add_argument('--resources_dir', type=str, help='Path to the prediction file')
+parser.add_argument('--tf_all', type=str, help='Path to the tf_all')
+parser.add_argument('--num_workers', type=str, help='Number of cores')
+args = parser.parse_args()
 
-meta = {
-  "resources_dir":'src/methods/multi_omics/celloracle'
-}
+if args.multiomics_rna:
+    par['multiomics_rna'] = args.multiomics_rna
+if args.multiomics_atac:
+    par['multiomics_atac'] = args.multiomics_atac
+if args.prediction:
+    par['prediction'] = args.prediction
+if args.tf_all:
+    par['tf_all'] = args.tf_all
+if args.num_workers:
+    par['num_workers'] = args.num_workers
+
+if args.resources_dir:
+    meta['resources_dir'] = args.resources_dir   
+
+
+par['links'] = f"{par['temp_dir']}/links.celloracle.links" 
 
 
 import argparse