Add flag parameter support for TOPP tools

.github/workflows/ci.yml

@@ -1,6 +1,6 @@
 name: continuous-integration
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   test:

src/workflow/CommandExecutor.py

@@ -268,6 +268,15 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}, tool
 
         # Load merged parameters (_defaults + user overrides) for this tool instance
         merged_params = self.parameter_manager.get_merged_params(params_key)
+
+        # Load flag parameter names: params.json takes priority (survives session restart),
+        # session_state is the live fallback during the current session.
+        flag_map = self.parameter_manager.get_parameters_from_json().get("_flag_params", {})
+        flag_list = flag_map.get(params_key)
+        if flag_list is None:
+            flag_list = st.session_state.get("_topp_flag_params", {}).get(params_key, [])
+        flag_params: set = set(flag_list)
+
         # Construct commands for each process
         for i in range(n_processes):
             command = [tool]
@@ -288,25 +297,42 @@ def run_topp(self, tool: str, input_output: dict, custom_params: dict = {}, tool
                     command += [value[i]]
             # Add merged TOPP tool parameters (_defaults + user overrides)
             for k, v in merged_params.items():
-                command += [f"-{k}"]
-                # 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")
+                if k in flag_params:
+                    # CLI flag: include "-k" only when truthy, omit when false
+                    if isinstance(v, str):
+                        is_enabled = v.lower() == "true"
                     else:
-                        command += [str(v)]
+                        is_enabled = bool(v)
+                    if is_enabled:
+                        command += [f"-{k}"]
+                    continue
+                # Regular parameter: skip empty/None/empty-list, append value otherwise
+                if v == "" or v is None or (isinstance(v, list) and not v):
+                    continue
+                command += [f"-{k}"]
+                if isinstance(v, str) and "\n" in v:
+                    command += v.split("\n")
+                elif isinstance(v, list):
+                    command += [str(x) for x in v]
+                else:
+                    command += [str(v)]
             # Add custom parameters
             for k, v in custom_params.items():
-                command += [f"-{k}"]
-
-                # 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]
+                if k in flag_params:
+                    if isinstance(v, str):
+                        is_enabled = v.lower() == "true"
                     else:
-                        command += [str(v)]
+                        is_enabled = bool(v)
+                    if is_enabled:
+                        command += [f"-{k}"]
+                    continue
+                if v == "" or v is None or (isinstance(v, list) and not v):
+                    continue
+                command += [f"-{k}"]
+                if isinstance(v, list):
+                    command += [str(x) for x in v]
+                else:
+                    command += [str(v)]
             # Add threads parameter for TOPP tools
             command += ["-threads", str(threads_per_command)]
             commands.append(command)

src/workflow/StreamlitUI.py

@@ -826,6 +826,7 @@ def input_TOPP(
         num_cols: int = 4,
         exclude_parameters: List[str] = [],
         include_parameters: List[str] = [],
+        flag_parameters: List[str] = [],
         display_tool_name: bool = True,
         display_subsections: bool = True,
         display_subsection_tabs: bool = False,
@@ -862,6 +863,18 @@ def input_TOPP(
             st.session_state["_topp_tool_instance_map"] = {}
         st.session_state["_topp_tool_instance_map"][tool_instance_name] = topp_tool_name
 
+        # Persist flag_parameters to session_state and params.json so run_topp
+        # can skip appending a value for these boolean CLI flags.
+        if "_topp_flag_params" not in st.session_state:
+            st.session_state["_topp_flag_params"] = {}
+        st.session_state["_topp_flag_params"][tool_instance_name] = list(flag_parameters)
+        _fp = self.parameter_manager.get_parameters_from_json()
+        if "_flag_params" not in _fp:
+            _fp["_flag_params"] = {}
+        _fp["_flag_params"][tool_instance_name] = list(flag_parameters)
+        with open(self.parameter_manager.params_file, "w", encoding="utf-8") as _f:
+            json.dump(_fp, _f, indent=4)
+
         if not display_subsections:
             display_subsection_tabs = False
         if display_subsection_tabs:

tests/test_queue_manager_cancel.py

@@ -153,9 +153,7 @@ def test_stopped_status_is_mapped_in_get_job_info(monkeypatch):
 
     info = qm.get_job_info("stopped-job")
     assert info is not None
-    assert info.status == __import__(
-        "src.workflow.QueueManager", fromlist=["JobStatus"]
-    ).JobStatus.CANCELED, (
+    assert info.status.name == "CANCELED", (
         "RQ 'stopped' status should be reported as CANCELED to the UI; "
         "otherwise stopped jobs appear stuck in 'queued'."
     )