Update _BaseWorker to avoid creating a new Pipeline in the main t…

…hread

src/pyhmmer/hmmer/_base.py

@@ -255,7 +255,9 @@ def __init__(
         super().__init__()
         self.options = options
         self.targets: _T = targets
-        self.pipeline = pipeline_class(**options)
+        # self.pipeline = pipeline_class(**options)
+        self.pipeline_options = options
+        self.pipeline_class = pipeline_class
         self.query_queue: "queue.Queue[typing.Optional[_BaseChore[_Q, _R]]]" = query_queue
         self.query_count = query_count
         self.callback: typing.Optional[typing.Callable[[_Q, int], None]] = (
@@ -265,6 +267,7 @@ def __init__(
         self.builder = builder
 
     def run(self) -> None:
+        self.pipeline = self.pipeline_class(**self.pipeline_options)
         while not self.is_killed():
             # attempt to get the next argument, with a timeout
             # so that the thread can periodically check if it has