From e1bd22155bc98b244d6c071260b91fa418ac042c Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 11 Dec 2023 11:47:48 +0100
Subject: [PATCH] Fix end run detection

---
 .../aozan3/dataprovider/IlluminaRawRunDataProvider.java   | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/main/java/fr/ens/biologie/genomique/aozan/aozan3/dataprovider/IlluminaRawRunDataProvider.java b/src/main/java/fr/ens/biologie/genomique/aozan/aozan3/dataprovider/IlluminaRawRunDataProvider.java
index 25c7ac69..901aa7a8 100644
--- a/src/main/java/fr/ens/biologie/genomique/aozan/aozan3/dataprovider/IlluminaRawRunDataProvider.java
+++ b/src/main/java/fr/ens/biologie/genomique/aozan/aozan3/dataprovider/IlluminaRawRunDataProvider.java
@@ -201,12 +201,14 @@ public static boolean runCompleted(Path runDirectory) {
     // RTA 2
     if (new File(dir, "RunParameters.xml").exists()) {
 
-      return fileExists(dir, "RTAComplete.txt", "RunCompletionStatus.xml")
-          && completeFileExists(dir, "RTARead", "Complete.txt");
+      if (fileExists(dir, "RTAComplete.txt", "RunCompletionStatus.xml")
+          && completeFileExists(dir, "RTARead", "Complete.txt")) {
+            return true
+          }
     }
 
     // RTA 1
-    if (new File(dir, "runParameters.xml").exists()) {
+    if (new File(dir, "runParameters.xml").exists() || new File(dir, "RunParameters.xml").exists()) {
 
       return fileExists(dir, "RTAComplete.txt",
           "ImageAnalysis_Netcopy_complete.txt")