Added RG tag info to BWA mem command

nf-core · Feb 7, 2024 · b6cf17e · b6cf17e
1 parent 63bf3e7
commit b6cf17e
Showing 1 changed file with 5 additions and 1 deletion.
diff --git 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