From 19f75ddd4b4a3d8ae67c640528a02b9ab36b9f0a Mon Sep 17 00:00:00 2001
From: Lorenzo Gaifas <brisvag@gmail.com>
Date: Thu, 31 Aug 2023 13:53:10 +0200
Subject: [PATCH] default to denoising and using patch 4

---
 src/waretomo/main.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/waretomo/main.py b/src/waretomo/main.py
index 32504a0..cee19b2 100644
--- a/src/waretomo/main.py
+++ b/src/waretomo/main.py
@@ -89,6 +89,7 @@ def __str__(self):
     "-p",
     "--patches",
     type=int,
+    default=4,
     help="number of patches for local alignment in aretomo (NxN), if any",
 )
 @click.option(
@@ -135,7 +136,7 @@ def __str__(self):
 @click.option(
     "--stop-at",
     type=click.Choice(ProcessingStep.__members__),
-    default="reconstruct",
+    default="denoise",
     help="terminate processing after this step",
 )
 @click.option("--ccderaser", type=str, default="ccderaser", help="ccderaser executable")