diff --git a/phys2denoise/cli/run.py b/phys2denoise/cli/run.py
index ccaf7ab..71d34b4 100644
--- a/phys2denoise/cli/run.py
+++ b/phys2denoise/cli/run.py
@@ -69,7 +69,8 @@ def _get_parser():
         dest="mode",
         type=str,
         help="Format of the input physiological data. Options are: "
-        "physio or bids. Default is physio.",
+        "auto, physio or bids. Default is auto, which determines the input file mode automatically.",
+        default="auto",
     )
 
     # Important optional arguments
diff --git a/phys2denoise/workflow.py b/phys2denoise/workflow.py
index 0db25c7..2f3459c 100644
--- a/phys2denoise/workflow.py
+++ b/phys2denoise/workflow.py
@@ -77,7 +77,7 @@ def build(
     metrics,
     metric_args,
     metrics_to_export,
-    mode="physio",
+    mode="auto",
     fs=None,
     bids_parameters=dict(),
     bids_channel=None,