Allow 0 mismatch for all indexes that are shorter than 8nt

taca/illumina/NovaSeqXPlus_Runs.py

@@ -83,6 +83,12 @@ def _generate_samplesheet_subset(
                                     or "BarcodeMismatchesIndex" not in k
                                 ):
                                     output += f"{k},{v}{os.linesep}"
+                    # Allow 0 mismatch for all indexes that are shorter than 8nt
+                    else:
+                        if index1_size != 0 and index1_size < 8:
+                            output += f"BarcodeMismatchesIndex1,0{os.linesep}"
+                        if index2_size != 0 and index2_size < 8:
+                            output += f"BarcodeMismatchesIndex2,0{os.linesep}"
         # Data
         output += f"[Data]{os.linesep}"
         datafields = []
@@ -107,11 +113,15 @@ def _generate_samplesheet_subset(
                         if field == "index2" and noindex_flag:
                             if software == "bclconvert":
                                 line[field] = (
-                                    "T" * index_cycles[1] if index_cycles[1] != 0 else ""
+                                    "T" * index_cycles[1]
+                                    if index_cycles[1] != 0
+                                    else ""
                                 )
                             else:
                                 line[field] = (
-                                    "A" * index_cycles[1] if index_cycles[1] != 0 else ""
+                                    "A" * index_cycles[1]
+                                    if index_cycles[1] != 0
+                                    else ""
                                 )
                             noindex_flag = False
                         # Case of IDT UMI