diff --git a/graphstorm-processing/graphstorm_processing/config/data_config_base.py b/graphstorm-processing/graphstorm_processing/config/data_config_base.py
index 0014348b6a..f737adaded 100644
--- a/graphstorm-processing/graphstorm_processing/config/data_config_base.py
+++ b/graphstorm-processing/graphstorm_processing/config/data_config_base.py
@@ -15,7 +15,7 @@
 """
 
 from dataclasses import dataclass
-from typing import Sequence, Optional
+from typing import Optional
 
 from graphstorm_processing.constants import SUPPORTED_FILE_TYPES
 
@@ -27,7 +27,7 @@ class DataStorageConfig:
     """
 
     format: str
-    files: Sequence[str]
+    files: list[str]
     separator: Optional[str] = None
 
     def __post_init__(self):
@@ -39,3 +39,7 @@ def __post_init__(self):
                     raise ValueError(
                         f"File paths need to be relative (not starting with '/'), got : {file}"
                     )
+
+        for idx, file in enumerate(self.files):
+            if file.startswith("./"):
+                self.files[idx] = file[2:]
diff --git a/graphstorm-processing/graphstorm_processing/graph_loaders/dist_heterogeneous_loader.py b/graphstorm-processing/graphstorm_processing/graph_loaders/dist_heterogeneous_loader.py
index db56720840..af76ab40e8 100644
--- a/graphstorm-processing/graphstorm_processing/graph_loaders/dist_heterogeneous_loader.py
+++ b/graphstorm-processing/graphstorm_processing/graph_loaders/dist_heterogeneous_loader.py
@@ -939,7 +939,7 @@ def process_node_data(self, node_configs: Sequence[NodeConfig]) -> Dict:
         self.graph_info["ntype_to_label_masks"] = defaultdict(list)
         for node_config in node_configs:
             files = node_config.files
-            file_paths = [f"{self.input_prefix}/{f}" for f in files]
+            file_paths = [os.path.join(self.input_prefix, f) for f in files]
 
             node_type = node_config.ntype
             node_col = node_config.node_col
diff --git a/graphstorm-processing/tests/resources/small_heterogeneous_graph/gsprocessing-config.json b/graphstorm-processing/tests/resources/small_heterogeneous_graph/gsprocessing-config.json
index d06cfd283e..675109bb53 100644
--- a/graphstorm-processing/tests/resources/small_heterogeneous_graph/gsprocessing-config.json
+++ b/graphstorm-processing/tests/resources/small_heterogeneous_graph/gsprocessing-config.json
@@ -17,7 +17,7 @@
                 "data": {
                     "format": "csv",
                     "files": [
-                        "nodes/movie.csv"
+                        "./nodes/movie.csv"
                     ],
                     "separator": ","
                 },
@@ -104,7 +104,7 @@
                 "data": {
                     "format": "csv",
                     "files": [
-                        "edges/movie-included_in-genre.csv"
+                        "./edges/movie-included_in-genre.csv"
                     ],
                     "separator": ","
                 },