diff --git a/conf/modules.config b/conf/modules.config
index f79a251..d0dca0d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -192,7 +192,7 @@ if (!params.skip_qc){
             ]
         }
     }
-
+    
     process {
         withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${meta.id}.dedup.sorted" }
@@ -229,6 +229,22 @@ if (!params.skip_qc) {
 
 }
 
+// READ COUNTS
+if (!params.skip_qc) {
+
+    process {
+        withName:'.*:READ_COUNTS' {
+            publishDir = [
+                path: { "${params.outdir}/batch_qcs/read_counts" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
+    }
+
+}
+
 /////////////////////
 // REFERENCE FILES //
 /////////////////////
@@ -306,7 +322,7 @@ process {
 
 // GUNZIP
 process {
-    withName: '.*:GUNZIP' {
+    withName: '.*:GUNZIP.*' {
         publishDir = [
             enabled: false
         ]
@@ -506,6 +522,15 @@ process {
     }
 }
 
+process {
+    withName:'.*:BAM_SORT_STATS_SAMTOOLS_TAGGED:.*' {
+        ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            enabled: false
+        ]
+    }
+}
+
 process {
     withName:'.*:BAM_SORT_STATS_SAMTOOLS_DEDUP:SAMTOOLS_SORT' {
         ext.prefix = { "${meta.id}.dedup.sorted" }