From 010c5cdc9213ecd840d86d6929441ce30b39222a Mon Sep 17 00:00:00 2001
From: Stephen Watts <hello@stephen.ac>
Date: Fri, 3 May 2024 15:13:59 +1000
Subject: [PATCH] Set bwa-mem2 batch size for reproducibility

Parameter value set to match Sarek default configuration.
---
 modules/local/bwa-mem2/mem/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/local/bwa-mem2/mem/main.nf b/modules/local/bwa-mem2/mem/main.nf
index 9c44d086..4d894eb9 100644
--- a/modules/local/bwa-mem2/mem/main.nf
+++ b/modules/local/bwa-mem2/mem/main.nf
@@ -28,6 +28,7 @@ process BWAMEM2_ALIGN {
 
     bwa-mem2 mem \\
         -Y \\
+        -K 100000000 \\
         -R '${read_group_tag}' \\
         -t ${task.cpus} \\
         ${genome_fasta} \\