Merge branch 'master' into aviti_bioinfo_tab

VERSIONLOG.md

@@ -4,6 +4,10 @@
 
 Add element instruments to bioinfo_tab
 
+## 20241031.1
+
+Fix extra postfix in sample names for BCL Convert
+
 ## 20241029.3
 
 Fix missing settings for BCL Convert

taca/illumina/Runs.py

@@ -703,6 +703,22 @@ def _process_simple_lane_with_single_demux(
                 os.unlink(dest)
         os.symlink(source, dest)
 
+        # Replace the file laneBarcode.html
+        html_report_laneBarcode = os.path.join(
+            source, "html", self.flowcell_id, "all", "all", "all", "laneBarcode.html"
+        )
+        if os.path.exists(html_report_laneBarcode):
+            html_report_laneBarcode_parser = LaneBarcodeParser(html_report_laneBarcode)
+            # Remove the trailing "_SX" postfix from samples names for BCL Convert when it handles SmartSeq3 libraries
+            for entry in html_report_laneBarcode_parser.sample_data:
+                if "_S" in entry["Sample"]:
+                    entry["Sample"] = "_".join(entry["Sample"].split("_")[:-1])
+            html_report_laneBarcode_parser.sample_data = sorted(
+                html_report_laneBarcode_parser.sample_data,
+                key=lambda k: (k["Lane"].lower(), k["Sample"]),
+            )
+            _generate_lane_html(html_report_laneBarcode, html_report_laneBarcode_parser)
+
     def _fix_html_reports_for_complex_lanes(
         self,
         demux_folder,