From 84902d23522749600177f7faa52c6a976a7e5f34 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Tue, 24 Jun 2025 11:50:38 +0100
Subject: [PATCH] Support CSI files too

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

diff --git a/subworkflows/local/convert_stats.nf b/subworkflows/local/convert_stats.nf
index 76e3f6d1..c24110d6 100644
--- a/subworkflows/local/convert_stats.nf
+++ b/subworkflows/local/convert_stats.nf
@@ -81,7 +81,7 @@ workflow CONVERT_STATS {
 
         // Set the BAM and BAI channels for emission
         ch_bam = SAMTOOLS_REINDEX.out.bam
-        ch_bai = SAMTOOLS_REINDEX.out.bai
+        ch_bai = SAMTOOLS_REINDEX.out.bai.mix(SAMTOOLS_REINDEX.out.csi)
 
         // If using BAM for stats, use the reindexed BAM
         if ( !("cram" in outfmt_options) ) {