From b6cf17ee055bb0aa9adc366eda7569511000f516 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Wed, 7 Feb 2024 16:45:13 +0100
Subject: [PATCH] Added RG tag info to BWA mem command

---
 conf/modules.config | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index ea1d8d927..98e8e9238 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -431,7 +431,11 @@ process {
 
     withName: BWA_MEM {
         tag = { "${meta.reference}|${meta.sample_id}_${meta.library_id}_L${meta.lane}" }
-        ext.args = { "-k ${params.mapping_bwamem_k} -r ${params.mapping_bwamem_r}" }
+        ext.args = {[
+            "-k ${params.mapping_bwamem_k}",
+            "-r ${params.mapping_bwamem_r}",
+            "-R '@RG\\tID:ILLUMINA-${meta.library_id}\\tSM:${meta.sample_id}\\tPL:illumina\\tPU:ILLUMINA-${meta.library_id}-${meta.strandedness}'"
+            ].join(' ').trim() }
         ext.prefix = { "${meta.sample_id}_${meta.library_id}_L${meta.lane}_${meta.reference}" }
         publishDir = [
             enabled: false