also add -Y for umi mapping

FriederikeHanssen · FriederikeHanssen · commit f5f49eaef307 · 2022-07-17T12:34:55.000+02:00
diff --git a/conf/modules.config b/conf/modules.config
@@ -234,7 +234,7 @@ process {
 
     if (params.umi_read_structure) {
         withName: "NFCORE_SAREK:SAREK:CREATE_UMI_CONSENSUS:MAPPING_UMI:BWAMEM.*_MEM" {
-            ext.args         = { "-p -C -M -R ${meta.read_group}" }
+            ext.args         = { "-K 100000000 -p -C -Y -R ${meta.read_group}" }
             ext.args2        = '-bS'
             ext.prefix       = {"${meta.id}.umi_unsorted"}
         }

Original file line number	Diff line number	Diff line change
`@@ -234,7 +234,7 @@ process {`
`234`	`234`
`235`	`235`	`if (params.umi_read_structure) {`
`236`	`236`	`withName: "NFCORE_SAREK:SAREK:CREATE_UMI_CONSENSUS:MAPPING_UMI:BWAMEM.*_MEM" {`
`237`		`- ext.args = { "-p -C -M -R ${meta.read_group}" }`
	`237`	`+ ext.args = { "-K 100000000 -p -C -Y -R ${meta.read_group}" }`
`238`	`238`	`ext.args2 = '-bS'`
`239`	`239`	`ext.prefix = {"${meta.id}.umi_unsorted"}`
`240`	`240`	`}`