From 18366c9ef255b27da4e47866622dd745521de31d Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Wed, 24 Jan 2024 17:57:37 +0000
Subject: [PATCH 1/2] Swap NGSCheckMate bed file for GATK.GRCh37

---
 conf/igenomes.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/igenomes.config b/conf/igenomes.config
index 1ae02673d7..9157284fc0 100644
--- a/conf/igenomes.config
+++ b/conf/igenomes.config
@@ -35,7 +35,7 @@ params {
             known_indels_tbi      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.gz.tbi"
             known_indels_vqsr     = '--resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_phase1.indels.b37.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
             mappability           = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/Control-FREEC/out100m2_hg19.gem"
-            ngscheckmate_bed      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_wChr.bed"
+            ngscheckmate_bed      = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/NGSCheckMate/SNP_GRCh37_hg19_woChr.bed"
             snpeff_db             = 87
             snpeff_genome         = 'GRCh37'
             vep_cache_version     = 110

From 42d3fd02233acc4dfe72dbe566f428343b3fa36c Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Wed, 24 Jan 2024 17:59:20 +0000
Subject: [PATCH 2/2] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 824f616280..766c417dc8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1351](https://github.com/nf-core/sarek/pull/1351) - Fix params name for test profiles (`bcftools_annotations`)
 - [#1357](https://github.com/nf-core/sarek/pull/1364) - Fixed bug where samples were dropped while reconstituting BAM files
 - [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming
+- [#1373](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix
 
 ### Removed