From cafa635cdf2e185e475b5d9740aa99014420728a Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Wed, 27 Aug 2025 14:34:50 +0200
Subject: [PATCH] adding output path

---
 python/minknow_api/examples/start_protocol.py |  7 ++++++
 python/minknow_api/tools/protocols.py         | 25 ++++++++++++++-----
 2 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/python/minknow_api/examples/start_protocol.py b/python/minknow_api/examples/start_protocol.py
index 6d88d68..a4dd418 100644
--- a/python/minknow_api/examples/start_protocol.py
+++ b/python/minknow_api/examples/start_protocol.py
@@ -273,6 +273,12 @@ def parse_args():
         help="Duration (in seconds) of a single bam file batch; if set to 0, time-based batching is disabled",
     )
 
+    parser.add_argument(
+        "--output-path",
+        type=str,
+        help="Path to output data to.",
+    )
+
     # Read until
     parser.add_argument(
         "--read-until-reference",
@@ -1034,6 +1040,7 @@ def build_output_arguments(args, name):
             mux_scan_period=args.mux_scan_period,
             stop_criteria=stop_criteria,
             simulation_path=args.simulation,
+            output_path=args.output_path,
             args=args.extra_args,  # Any extra args passed.
         )
 
diff --git a/python/minknow_api/tools/protocols.py b/python/minknow_api/tools/protocols.py
index 6a18234..06c524e 100644
--- a/python/minknow_api/tools/protocols.py
+++ b/python/minknow_api/tools/protocols.py
@@ -2,19 +2,20 @@
 
 import collections
 import dataclasses
-from pathlib import Path
 import logging
-from typing import Optional, List, Sequence, Tuple
+from pathlib import Path
+from typing import List, Optional, Sequence, Tuple
 
 import grpc
 
-from .. import Connection
-from minknow_api import protocol_pb2, run_until_pb2, acquisition_pb2
+from minknow_api import acquisition_pb2, protocol_pb2, run_until_pb2
+from minknow_api.analysis_workflows_pb2 import AnalysisWorkflowRequest
 from minknow_api.manager_pb2 import FindBasecallConfigurationsResponse
 from minknow_api.protocol_pb2 import BarcodeUserData
-from minknow_api.analysis_workflows_pb2 import AnalysisWorkflowRequest
 from minknow_api.tools.any_helpers import make_float_any, make_uint64_any
 
+from .. import Connection
+
 LOGGER = logging.getLogger(__name__)
 
 
@@ -57,7 +58,6 @@ def find_simplex_model(
     ],
     simplex_model_name: str,
 ) -> Tuple[FindBasecallConfigurationsResponse.SimplexModel]:
-
     searched_configs = set()
     for config in available_basecall_configs:
         for simplex in config.simplex_models:
@@ -269,6 +269,7 @@ def make_protocol_arguments(
     disable_active_channel_selection: bool = False,
     mux_scan_period: float = 1.5,
     simulation_path: Optional[Path] = None,
+    output_path: Optional[Path] = None,
     args: Optional[List[str]] = None,
     is_flongle: bool = False,
 ) -> List[str]:
@@ -286,6 +287,7 @@ def make_protocol_arguments(
         disable_active_channel_selection(bool): Disable active channel selection
         mux_scan_period(float):                 Period of time between mux scans in hours.
         simulation_path(:obj:`Path`):           An optional fast5 bulk path to use for simulated playback.
+        output_path(:obj:`Path`):                An optional output path.
         args(:obj:`list`):                      Extra arguments to pass to protocol.
         is_flongle(bool):                       Specify if the flow cell to be sequenced on is a flongle.
 
@@ -441,6 +443,11 @@ def on_off(value: bool):
             )
         protocol_args.extend(["--simulation", str(simulation_path)])
 
+    if output_path:
+        if not output_path.exists():
+            raise Exception(f"Non-existent path '{output_path}' passed for output.")
+        protocol_args.extend(["--output_path", str(output_path)])
+
     if args:
         protocol_args.extend(args)
 
@@ -500,6 +507,7 @@ def start_protocol(
     stop_criteria: Optional[CriteriaValues] = None,
     experiment_duration: Optional[float] = None,
     analysis_workflow_request: Optional[AnalysisWorkflowRequest] = None,
+    output_path: Optional[Path] = None,
     *args,
     **kwargs,
 ) -> str:
@@ -552,6 +560,11 @@ def start_protocol(
     if analysis_workflow_request is not None:
         additional_params["analysis_workflow_request"] = analysis_workflow_request
 
+    if output_path:
+        additional_params["offload_location_info"] = protocol_pb2.OffloadLocationInfo(
+            offload_location_path=output_path
+        )
+
     result = device_connection.protocol.start_protocol(
         identifier=identifier,
         args=protocol_arguments,