From 3dd1e0355a5c58e4e2cd98a91114dbf742f67d39 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 2a8ac501..d12f7356 100644
--- a/modules/local/bwa-mem2/mem/main.nf
+++ b/modules/local/bwa-mem2/mem/main.nf
@@ -33,6 +33,7 @@ process BWAMEM2_ALIGN {
     bwa-mem2 mem \\
         ${args} \\
         -Y \\
+        -K 100000000 \\
         -R '${read_group_tag}' \\
         -t ${task.cpus} \\
         ${genome_fasta} \\