diff --git a/src/workflow/CommandExecutor.py b/src/workflow/CommandExecutor.py
index 6cc49301..74ffff49 100644
--- a/src/workflow/CommandExecutor.py
+++ b/src/workflow/CommandExecutor.py
@@ -166,9 +166,15 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> N
             # Add non-default TOPP tool parameters
             if tool in params.keys():
                 for k, v in params[tool].items():
-                    command += [f"-{k}"]
+                    # Handle the case where f is a flag and v is false by just skipping
+                    if v != False:
+                      command += [f"-{k}"]
+                    # add the value if we aren't a flag
                     if isinstance(v, str) and "\n" in v:
                         command += v.split("\n")
+                    # If we are a flag don't append the value
+                    elif isinstance(v, bool):
+                        continue
                     else:
                         command += [str(v)]
             # Add custom parameters
@@ -265,4 +271,4 @@ def run_python(self, script_file: str, input_output: dict = {}) -> None:
             # run command
             self.run_command(["python", str(path), str(tmp_params_file)])
             # remove tmp params file
-            tmp_params_file.unlink()
\ No newline at end of file
+            tmp_params_file.unlink()