From 10f6e3a1db21988ee48a404454ffda66a2bcbd87 Mon Sep 17 00:00:00 2001 From: Mark Kennedy Date: Wed, 18 Feb 2026 01:32:46 +0000 Subject: [PATCH] feat: add support for ignore_unspecified_barcodes in start_protocol helper --- python/minknow_api/examples/start_protocol.py | 6 ++++++ python/minknow_api/tools/protocols.py | 7 +++++++ 2 files changed, 13 insertions(+) diff --git a/python/minknow_api/examples/start_protocol.py b/python/minknow_api/examples/start_protocol.py index 79baa2d..3a249e3 100644 --- a/python/minknow_api/examples/start_protocol.py +++ b/python/minknow_api/examples/start_protocol.py @@ -191,6 +191,11 @@ def parse_args(): action="store_true", help="bar-code filtering (both ends of a strand must have a matching barcode)", ) + parser.add_argument( + "--ignore-unspecified-barcodes", + action="store_true", + help="ignore unspecified barcodes", + ) # ALIGNMENT ARGUMENTS parser.add_argument( @@ -904,6 +909,7 @@ def _make_request(request_body): args.barcode_kits, args.trim_barcodes, args.barcodes_both_ends, + args.ignore_unspecified_barcodes, ) if args.alignment_reference: diff --git a/python/minknow_api/tools/protocols.py b/python/minknow_api/tools/protocols.py index 9d327a9..ab2f51f 100644 --- a/python/minknow_api/tools/protocols.py +++ b/python/minknow_api/tools/protocols.py @@ -192,6 +192,7 @@ def find_protocol( "kits", "trim_barcodes", "barcodes_both_ends", + "ignore_unspecified_barcodes", ], ) AlignmentArgs = collections.namedtuple("AlignmentArgs", ["reference_files", "bed_file"]) @@ -341,6 +342,12 @@ def on_off(value: bool): "require_barcodes_both_ends=" + on_off(basecalling.barcoding.barcodes_both_ends) ) + if basecalling.barcoding.ignore_unspecified_barcodes: + # ignore_unspecified_barcodes=on/off + barcoding_args.append( + "ignore_unspecified_barcodes=" + + on_off(basecalling.barcoding.ignore_unspecified_barcodes) + ) protocol_args.extend(["--barcoding"] + barcoding_args)