diff --git a/conf/modules.config b/conf/modules.config
index 67e030eef..fcb14b4f1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -47,7 +47,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/fastqc_raw/" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -58,7 +58,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/fastqc_processed/" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -78,7 +78,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/falco_raw/" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -89,7 +89,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/falco_processed/" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -709,7 +709,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapstats/preseq" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -728,7 +728,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapstats/preseq" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -749,7 +749,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapstats/bedtools" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -760,7 +760,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapstats/bedtools" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -1076,7 +1076,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapstats/qualimap/${meta.reference}/" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -1094,7 +1094,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/damage_estimation/damageprofiler/" },
             mode: params.publish_dir_mode,
-            pattern: '*[!versions.yml]'
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }