Merge pull request NationalGenomicsInfrastructure#455 from kedhammar/…

…free-prom-col3

Free column 3 of PromethION

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # TACA Version Log
 
+## 20241211.1
+
+No longer reserve PromethION column 3 for Clinical Genomics.
+
 ## 20241210.4
 
 Change server_status nas to update statusdb by default

taca/nanopore/instrument_transfer.py

@@ -12,10 +12,9 @@
 from glob import glob
 
 RUN_PATTERN = re.compile(
-    # Run folder name expected as yyyymmdd_HHMM_1A-3H/MN19414_flowCellId_randomHash
+    # Run folder name expected as yyyymmdd_HHMM_positionOrInstrument_flowCellId_randomHash
     # Flow cell names starting with "CTC" are configuration test cells and should not be included
-    # As of december 2023, the third column (3A-3H) is excluded, because it will be used by Clinical Genomics
-    r"^\d{8}_\d{4}_(([1-2][A-H])|(MN19414))_(?!CTC)[A-Za-z0-9]+_[A-Za-z0-9]+$"
+    r"^\d{8}_\d{4}_(([1-3][A-H])|(MN19414))_(?!CTC)[A-Za-z0-9]+_[A-Za-z0-9]+$"
 )
 
 

tests/nanopore/test_instrument_transfer.py

@@ -135,28 +135,6 @@ def test_main_ignore_CTC(setup_test_fixture):
         mock_dump_path.assert_not_called()
 
 
-def test_main_ignore_col3(setup_test_fixture):
-    """Check so that runs on column 3 (set aside for Clinical Genomics as of december 2023)
-    are not picked up.
-    """
-
-    # Run fixture
-    args, tmp, file_paths = setup_test_fixture
-
-    # Setup run
-    run_path = (
-        f"{args.source_dir}/experiment/sample/{DUMMY_RUN_NAME.replace('MN19414', '3A')}"
-    )
-    os.makedirs(run_path)
-
-    with patch("taca.nanopore.instrument_transfer.dump_path") as mock_dump_path:
-        # Start testing
-        instrument_transfer.main(args)
-
-        # Check dump_path was not called
-        mock_dump_path.assert_not_called()
-
-
 @pytest.mark.parametrize(
     "finished, qc", [(True, True), (True, False), (False, True), (False, False)]
 )