Fixes for Aviti demux emails

VERSIONLOG.md

@@ -1,5 +1,9 @@
 # TACA Version Log
 
+##20260127.1
+
+Email when MismatchThreshold is set to 0 for AVITI runs
+
 ##20251127.1
 
 Enable archiving of Aviti Teton runs to PDC

taca/__init__.py

@@ -1,3 +1,3 @@
 """Main TACA module"""
 
-__version__ = "1.6.14"
+__version__ = "1.6.15"

taca/analysis/analysis_element.py

@@ -153,7 +153,7 @@ def _process(run_to_process):
             email_subject = f"{run} has been transferred to the analysis cluster"
             email_message = (
                 f"Rsync of data for run {run} to the analysis cluster has finished!\n"
-                f"The run is available at https://genomics-status.scilifelab.se/flowcells_element/{run}"
+                f"The run is available at https://genomics-status.scilifelab.se/flowcells_element/{run.NGI_run_id}"
             )
             send_mail(email_subject, email_message, CONFIG["mail"]["recipients"])
 

taca/element/Element_Runs.py

@@ -13,7 +13,9 @@
 import pandas as pd
 from Levenshtein import distance
 
+from taca.utils.config import CONFIG
 from taca.utils.filesystem import chdir
+from taca.utils.misc import send_mail
 from taca.utils.statusdb import ElementRunsConnection
 
 logger = logging.getLogger(__name__)
@@ -724,7 +726,22 @@ def make_demux_manifests(
                 )
                 settings_kvs["I1MismatchThreshold"] = str(i1_mm_threshold)
                 settings_kvs["I2MismatchThreshold"] = str(i2_mm_threshold)
-
+                if i1_mm_threshold == 0 or i2_mm_threshold == 0:
+                    email_subject = (
+                        f"MismatchThreshold(s) set to 0 for {self.NGI_run_id}"
+                    )
+                    email_message = (
+                        f"During demultiplexing manifest generation for run {self.NGI_run_id}, "
+                        "the minimum distance between some index sequences was at or below 2. "
+                        "As a result, the I1MismatchThreshold and/or I2MismatchThreshold was set to 0.\n\n"
+                        f"Lanes: {', '.join(map(str, group['Lane'].unique()))}\n"
+                        f"I1MismatchThreshold: {i1_mm_threshold}\n"
+                        f"I2MismatchThreshold: {i2_mm_threshold}\n\n"
+                        "Please check that this is acceptable and inform the user."
+                    )
+                    send_mail(
+                        email_subject, email_message, CONFIG["mail"]["recipients"]
+                    )
                 # Add PhiX to group
                 group = pd.concat([group, group_controls], axis=0, ignore_index=True)
 

tests/analysis/test_analysis_element.py

@@ -154,6 +154,14 @@ def test_process_on_finished_run(aviti_fixture):
     # Sub-mock configuration
     mocks["mock_db"].return_value.check_db_run_status.return_value = "ongoing"
     mocks["mock_db"].return_value.upload_to_statusdb.return_value = None
+    # set mocks["mock_mail"] to mock taca.element.Element_Runs.send_mail instead
+    # of taca.analysis.analysis_element.send_mail
+    mocks["mock_mail"].stop()
+    mocks["mock_mail"] = patch("taca.element.Element_Runs.send_mail").start()
+    patch(
+        "taca.element.Element_Runs.CONFIG",
+        new={**get_config(tmp), "mail": {"recipients": ["<EMAIL>"]}},
+    ).start()
 
     # Add metadata files
     run_dir = create_element_run_dir(