fix(_run): terminate loop on config parse errors (#14)

README.rst

@@ -262,6 +262,14 @@ during their execution too. These can be obtained as follows:
 Changelog
 ---------
 
+Release 0.13.1
+~~~~~~~~~~~~~~
+
+`26th May, 2026`
+
+* Fix run loop hanging when Nextflow exits with a config parse error (#14).
+
+
 Release 0.13.0
 ~~~~~~~~~~~~~~
 

nextflow/command.py

@@ -94,17 +94,19 @@ def _run(
         params=params
     )
 
-    execution, log_start = None, 0
+    execution, log_start, rc_seen = None, 0, False
     while True:
         time.sleep(sleep)
         execution, diff = get_execution(
             submission.output_path, submission.log_path, submission.nextflow_command, execution, log_start, timezone, io
         )
         log_start += diff
         if execution and poll: yield execution
-        if execution and execution.return_code and execution.finished:
+        if execution and execution.return_code and (execution.finished or rc_seen):
             if not poll: yield execution
             break
+        if execution and execution.return_code:
+            rc_seen = True
 
 
 def submit_execution(
@@ -207,9 +209,10 @@ def make_nextflow_command(run_path, output_path, log_path, pipeline_path, resume
     profiles = make_nextflow_command_profiles_string(profiles)
     reports = make_reports_string(output_path, report, timeline, dag, trace)
     command = f"{env}{nf} {log}{configs}run {pipeline_path} {resume}{params} {profiles} {reports}"
+    prefix = (str(output_path) + os.path.sep) if output_path != run_path else ""
+    command = f":>{prefix}rc.txt; {command}"
     abspath = io.abspath if io else os.path.abspath
     if run_path != abspath("."): command = f"cd {run_path}; {command}"
-    prefix = (str(output_path) + os.path.sep) if output_path != run_path else ""
     command = command.rstrip() + f" >{prefix}"
     command += f"stdout.txt 2>{prefix}"
     command += f"stderr.txt; echo $? >{prefix}rc.txt"

setup.py

@@ -5,13 +5,13 @@
 
 setup(
     name="nextflowpy",
-    version="0.13.0",
+    version="0.13.1",
     description="A Python wrapper around Nextflow.",
     long_description=long_description,
     long_description_content_type="text/x-rst",
     url="https://github.com/goodwright/nextflow.py",
-    author="Sam Ireland",
-    author_email="sam@goodwright.com",
+    author="Goodwright Ltd",
+    author_email="engineering@flow.bio",
     license="GPLv3+",
     classifiers=[
         "Development Status :: 4 - Beta",

tests/unit/test_command.py

@@ -43,13 +43,26 @@ def test_can_run_with_custom_values(self, mock_ex, mock_sleep, mock_submit):
         self.assertEqual(executions, [mock_executions[1]])
 
 
+    @patch("nextflow.command.submit_execution")
+    @patch("time.sleep")
+    @patch("nextflow.command.get_execution")
+    def test_loop_terminates_when_return_code_set_but_finished_never_arrives(self, mock_ex, mock_sleep, mock_submit):
+        submission = Mock()
+        mock_submit.return_value = submission
+        execution = Mock(return_code="1", finished=None)
+        mock_ex.side_effect = [(execution, 100), (execution, 0)]
+        executions = list(_run("main.nf"))
+        self.assertEqual(executions, [execution])
+        self.assertEqual(mock_ex.call_count, 2)
+
+
     @patch("nextflow.command.submit_execution")
     @patch("time.sleep")
     @patch("nextflow.command.get_execution")
     def test_can_run_and_poll(self, mock_ex, mock_sleep, mock_submit):
         submission = Mock()
         mock_submit.return_value = submission
-        mock_executions = [Mock(finished=False), Mock(finished=True)]
+        mock_executions = [Mock(return_code=""), Mock(return_code="0")]
         mock_ex.side_effect = [[None, 20], [mock_executions[0], 40], [mock_executions[1], 20]]
         executions = list(_run("main.nf", poll=True, output_path="/out"))
         mock_sleep.assert_called_with(1)
@@ -181,7 +194,7 @@ def test_can_get_full_nextflow_command(self, mock_report, mock_prof, mock_params
         mock_params.assert_called_with({"param": "2"})
         mock_prof.assert_called_with(["docker"])
         mock_report.assert_called_with("/out", "report.html", "time.html", "dag.html", "trace.html")
-        self.assertEqual(command, "cd /exdir; A=B C=D nextflow -Duser.country=US -log '.nextflow.log' -c conf1 -c conf2 run main.nf -resume X --p1=10 --p2=20 -profile docker,test --dag.html >/out/stdout.txt 2>/out/stderr.txt; echo $? >/out/rc.txt")
+        self.assertEqual(command, "cd /exdir; :>/out/rc.txt; A=B C=D nextflow -Duser.country=US -log '.nextflow.log' -c conf1 -c conf2 run main.nf -resume X --p1=10 --p2=20 -profile docker,test --dag.html >/out/stdout.txt 2>/out/stderr.txt; echo $? >/out/rc.txt")
 
 
     @patch("nextflow.command.make_nextflow_command_env_string")
@@ -208,7 +221,7 @@ def test_can_get_minimal_nextflow_command(self, mock_abspath, mock_report, mock_
         mock_params.assert_called_with({"param": "2"})
         mock_prof.assert_called_with(["docker"])
         mock_report.assert_called_with("/exdir", None, None, None, None)
-        self.assertEqual(command, "nextflow -Duser.country=US run main.nf >stdout.txt 2>stderr.txt; echo $? >rc.txt")
+        self.assertEqual(command, ":>rc.txt; nextflow -Duser.country=US run main.nf >stdout.txt 2>stderr.txt; echo $? >rc.txt")
 
 
     @patch("nextflow.command.make_nextflow_command_env_string")
@@ -235,7 +248,29 @@ def test_can_use_custom_io(self, mock_report, mock_prof, mock_params, mock_resum
         mock_params.assert_called_with({"param": "2"})
         mock_prof.assert_called_with(["docker"])
         mock_report.assert_called_with("/exdir", None, None, None, None)
-        self.assertEqual(command, "nextflow -Duser.country=US run main.nf >stdout.txt 2>stderr.txt; echo $? >rc.txt")
+        self.assertEqual(command, ":>rc.txt; nextflow -Duser.country=US run main.nf >stdout.txt 2>stderr.txt; echo $? >rc.txt")
+
+
+    @patch("nextflow.command.make_nextflow_command_env_string")
+    @patch("nextflow.command.make_nextflow_command_log_string")
+    @patch("nextflow.command.make_nextflow_command_config_string")
+    @patch("nextflow.command.make_nextflow_command_resume_string")
+    @patch("nextflow.command.make_nextflow_command_params_string")
+    @patch("nextflow.command.make_nextflow_command_profiles_string")
+    @patch("nextflow.command.make_reports_string")
+    def test_command_truncates_stale_rc_before_running(self, mock_report, mock_prof, mock_params, mock_resume, mock_conf, mock_log, mock_env):
+        mock_env.return_value = ""
+        mock_log.return_value = ""
+        mock_conf.return_value = ""
+        mock_resume.return_value = ""
+        mock_params.return_value = ""
+        mock_prof.return_value = ""
+        mock_report.return_value = ""
+        io = Mock()
+        io.abspath.return_value = "/exdir"
+        command = make_nextflow_command("/exdir", "/out", "/log", "main.nf", False, None, None, None, None, None, None, None, None, None, None, io)
+        self.assertIn(":>/out/rc.txt;", command)
+        self.assertLess(command.index(":>/out/rc.txt;"), command.index("nextflow"))