diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml
index ebc68faf..89499d1a 100644
--- a/.github/workflows/build-windows-executable-app.yaml
+++ b/.github/workflows/build-windows-executable-app.yaml
@@ -14,7 +14,7 @@ env:
   OPENMS_VERSION: 3.2.0 
   PYTHON_VERSION: 3.11.0
   # Name of the installer
-  APP_NAME: FLASHApp-0.9.4
+  APP_NAME: FLASHApp-0.9.5
   APP_UpgradeCode: "69ae44ad-d554-4e3c-8715-7c4daf60f8bb"
 
 jobs:
diff --git a/settings.json b/settings.json
index b1da5790..edf13059 100644
--- a/settings.json
+++ b/settings.json
@@ -1,7 +1,7 @@
 {
     "app-name": "FLASHApp",
     "github-user": "OpenMS",
-    "version": "0.9.4",
+    "version": "0.9.5",
     "repository-name": "FLASHApp",
     "analytics": {
         "google-analytics": {
diff --git a/src/workflow/CommandExecutor.py b/src/workflow/CommandExecutor.py
index 383dadc5..297adf8f 100644
--- a/src/workflow/CommandExecutor.py
+++ b/src/workflow/CommandExecutor.py
@@ -173,6 +173,8 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> N
                             command += [f"-{k}"]
                         elif v == 'false':
                             pass
+                        else:
+                            command += [f"-{k}", v]
                     else:
                         command += [f"-{k}", str(v)]
             # Add custom parameters