From d124d8ba737b4c377fb10ea5e3084d5ac3bad56e Mon Sep 17 00:00:00 2001
From: Kiah McIntosh <kiah.mcintosh@nanoporetech.com>
Date: Wed, 20 May 2026 16:31:24 +0000
Subject: [PATCH] Sort joint bambu inputs to fix caching [CW-7264]

---
 subworkflows/transcriptome.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/transcriptome.nf b/subworkflows/transcriptome.nf
index 6e99251..221b2fd 100644
--- a/subworkflows/transcriptome.nf
+++ b/subworkflows/transcriptome.nf
@@ -221,7 +221,7 @@ workflow transcriptome_analysis {
 
         joint_discover = runJointBambuDiscover(
             alignments
-                .collect(flat: false)
+                .toSortedList { a, b -> a[0].alias <=> b[0].alias }
                 .map { rows ->
                     // transform [meta, bam, bai] rows to 
                     // [meta, [alias1...aliasN], [bam1...bamN], [bai1...baiN], sample_sheet]