From 783bcdac7504df66476f4e7f06b4479af41360c1 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Wed, 2 Aug 2023 17:18:49 +0200
Subject: [PATCH 1/2] update config

---
 conf/modules/qc_bam.config | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config
index 080f988f..f0296709 100644
--- a/conf/modules/qc_bam.config
+++ b/conf/modules/qc_bam.config
@@ -52,22 +52,22 @@ process {
     }
 
     withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS' {
-        ext.when = params.aligner.equals("bwamem2")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("bwamem2") }
         ext.prefix = { "${meta.id}_wgsmetrics" }
     }
 
     withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_Y' {
-        ext.when = params.aligner.equals("bwamem2")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("bwamem2") }
         ext.prefix = { "${meta.id}_wgsmetrics_y" }
     }
 
     withName: '.*QC_BAM:SENTIEON_WGSMETRICS' {
-        ext.when = params.aligner.equals("sentieon")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("sentieon") }
         ext.prefix = { "${meta.id}_wgsmetrics" }
     }
 
     withName: '.*QC_BAM:SENTIEON_WGSMETRICS_Y' {
-        ext.when = params.aligner.equals("sentieon")
+        ext.when = { params.analysis_type.equals("wgs") && params.aligner.equals("sentieon") }
         ext.prefix = { "${meta.id}_wgsmetrics_y" }
     }
 }

From cb2dfafffc6adcbee260fa5e0d3020c633aef193 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Wed, 2 Aug 2023 17:20:20 +0200
Subject: [PATCH 2/2] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ab9e831b..bb9bc7bf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Invalid GATK4 container which caused incorrect singularity downloads with nf-core download [nf-core/modules #3668](https://github.com/nf-core/modules/issues/3668)
 - Make the default cram prefix same as markduplicates prefix [#392](https://github.com/nf-core/raredisease/pull/392)
+- Added constraints to block the pipeline from running CollectWgsMetrics on WES samples [#396](https://github.com/nf-core/raredisease/pull/396)
 
 ## v1.1.1 - Abu (Patch) [2023-07-26]