Fix TOPP parameter handling for zero values

Changed truthiness check `if v:` to explicit `if v != "" and v is not None:`
to properly handle numeric zero values (0, 0.0) which are valid parameters.

Previously, setting fragment_bin_offset=0 would skip the value entirely,
causing malformed command lines where the next flag was interpreted as
the previous parameter's value.

Author: t0mdavid-m

src/workflow/CommandExecutor.py

@@ -236,15 +236,19 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}) -> b
             if tool in params.keys():
                 for k, v in params[tool].items():
                     command += [f"-{k}"]
-                    if v:  # Skip empty values (pass flag with no value)
+                    # Skip only empty strings (pass flag with no value)
+                    # Note: 0 and 0.0 are valid values, so use explicit check
+                    if v != "" and v is not None:
                         if isinstance(v, str) and "\n" in v:
                             command += v.split("\n")
                         else:
                             command += [str(v)]
             # Add custom parameters
             for k, v in custom_params.items():
                 command += [f"-{k}"]
-                if v:
+                # Skip only empty strings (pass flag with no value)
+                # Note: 0 and 0.0 are valid values, so use explicit check
+                if v != "" and v is not None:
                     if isinstance(v, list):
                         command += [str(x) for x in v]
                     else: