From 8ccbb5c0d4d841688936b795460115fee6a64c2b Mon Sep 17 00:00:00 2001
From: chuan-wang <chuan.wang@scilifelab.se>
Date: Fri, 25 Oct 2024 13:39:16 +0200
Subject: [PATCH] Support MiSeq V2 Micro

---
 VERSIONLOG.md                            | 4 ++++
 scripts/illumina_run_parameter_parser.py | 5 +++++
 scripts/manage_demux_stats_thresholds.py | 3 +++
 3 files changed, 12 insertions(+)

diff --git a/VERSIONLOG.md b/VERSIONLOG.md
index 88f37f98..9c47143a 100644
--- a/VERSIONLOG.md
+++ b/VERSIONLOG.md
@@ -1,5 +1,9 @@
 # Scilifelab_epps Version Log
 
+## 20241025.1
+
+Support MiSeq V2 Micro
+
 ## 20241016.1
 
 Remove index orientation checker
diff --git a/scripts/illumina_run_parameter_parser.py b/scripts/illumina_run_parameter_parser.py
index c2558636..65edc0f9 100644
--- a/scripts/illumina_run_parameter_parser.py
+++ b/scripts/illumina_run_parameter_parser.py
@@ -337,6 +337,11 @@ def lims_for_miseq(process, run_dir):
         and runParameters["Setup"]["NumTilesPerSwath"] == "2"
     ):
         process.udf["Run Type"] = "Version2Nano"
+    elif (
+        runParameters["Setup"]["SupportMultipleSurfacesInUI"] == "true"
+        and runParameters["Setup"]["NumTilesPerSwath"] == "4"
+    ):
+        process.udf["Run Type"] = "Version2Micro"
     else:
         process.udf["Run Type"] = "null"
     # Runs with single read return a dict object
diff --git a/scripts/manage_demux_stats_thresholds.py b/scripts/manage_demux_stats_thresholds.py
index 0567832a..28cc25a0 100644
--- a/scripts/manage_demux_stats_thresholds.py
+++ b/scripts/manage_demux_stats_thresholds.py
@@ -25,6 +25,7 @@ def __init__(self, instrument, chemistry, paired, read_length):
             "Version3",
             "Version2",
             "Version2Nano",
+            "Version2Micro",
             "SP",
             "S1",
             "S2",
@@ -131,6 +132,8 @@ def set_exp_lane_clust(self):
                 self.exp_lane_clust = 10e6
             elif self.chemistry == "Version2Nano":
                 self.exp_lane_clust = 750000
+            elif self.chemistry == "Version2Micro":
+                self.exp_lane_clust = 3000000
             else:
                 if self.read_length >= 76 and self.read_length <= 301:
                     self.exp_lane_clust = 18e6