diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index ee2f344..2b395ef 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -26,3 +26,7 @@ jobs:
       - name: Run NSIQCppStyle RULES tests
         timeout-minutes: 5
         run: PYTHONPATH=./:./rules python -m unittest discover -s rules -p "*.py"
+
+      - name: Run NSIQCppStyle App tests
+        timeout-minutes: 5
+        run: python nsiqcppstyle_exe.py -f nsiqunittest/rules/comment_and_empty_lines.txt --ci nsiqunittest/src/simple_main.cpp
diff --git a/nsiqcppstyle_exe.py b/nsiqcppstyle_exe.py
index 102b2a0..0741889 100755
--- a/nsiqcppstyle_exe.py
+++ b/nsiqcppstyle_exe.py
@@ -374,7 +374,7 @@ def _ProcessFilterLine(self, filter, raw_line):
 
         if line.startswith("#") or len(line) == 0:
             # Comment or empty line, just return
-            return None
+            return filter
         if line.startswith("*"):
             if len(line[1:].strip()) != 0:
                 filterName = line[1:].strip()
@@ -567,6 +567,9 @@ def AddVarMap(self, keyValuePairString, where):
 
 
 def GetCliKeyValueMap(kvList):
+    if kvList == None:
+        return {}
+
     varMap = {}
     for kv in kvList:
         kvPair = kv.split(":", 1)
@@ -575,6 +578,7 @@ def GetCliKeyValueMap(kvList):
                 f"Error!: No key found in {kv}. Please use KEY:VALUE style to provide key and value",
             )
         varMap[kvPair[0]] = kvPair[1]
+
     return varMap
 
 
diff --git a/nsiqcppstyle_util.py b/nsiqcppstyle_util.py
index 2a584b3..9553b28 100644
--- a/nsiqcppstyle_util.py
+++ b/nsiqcppstyle_util.py
@@ -66,6 +66,10 @@ def CmpObjects(a, b):
 
 def RemoveOuterQuotes(raw_string):
     final_string = raw_string.strip()
-    if final_string[0] == final_string[-1] and final_string[0] in [SINGLE_QUOTE, DOUBLE_QUOTE]:
+    if (
+        len(final_string) >= 2
+        and final_string[0] == final_string[-1]
+        and final_string[0] in [SINGLE_QUOTE, DOUBLE_QUOTE]
+    ):
         final_string = final_string[1:-1].strip()
     return final_string
diff --git a/nsiqunittest/rules/comment_and_empty_lines.txt b/nsiqunittest/rules/comment_and_empty_lines.txt
new file mode 100644
index 0000000..d8930b8
--- /dev/null
+++ b/nsiqunittest/rules/comment_and_empty_lines.txt
@@ -0,0 +1,11 @@
+# This filefilter is here to ensure that the app:
+#   - handles comments properly
+#   - handles empty lines correctly
+
+~ RULE_3_1_A_do_not_start_filename_with_underbar
+~ RULE_3_3_A_start_function_name_with_lowercase_unix
+~ RULE_3_3_B_start_private_function_name_with_underbar
+~ RULE_4_5_B_use_braces_even_for_one_statement
+~ RULE_7_2_B_do_not_use_goto_statement
+~ RULE_9_1_A_do_not_use_hardcorded_include_path
+~ RULE_9_2_D_use_reentrant_function
diff --git a/nsiqunittest/src/simple_main.cpp b/nsiqunittest/src/simple_main.cpp
new file mode 100644
index 0000000..c9b4d4d
--- /dev/null
+++ b/nsiqunittest/src/simple_main.cpp
@@ -0,0 +1,4 @@
+int main(int argc, char* argv[])
+{
+    return 1;
+}