diff --git a/CHANGELOG.md b/CHANGELOG.md
index ded8856651..5422ec5614 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -63,6 +63,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#454](https://github.com/nf-core/sarek/pull/454) - Input is optional (can actually be found automatically by `Sarek` if previously run)
 - [#463](https://github.com/nf-core/sarek/pull/463), [#468](https://github.com/nf-core/sarek/pull/468) - Fix `nf-core lint`
 - [#513](https://github.com/nf-core/sarek/pull/513), [#527](https://github.com/nf-core/sarek/pull/527) - CNV is back
+- [#529](https://github.com/nf-core/sarek/pull/529) - Do not save `versions.yml` files
 
 ### Deprecated
 
diff --git a/conf/modules.config b/conf/modules.config
index 37a66ee735..e622d76c50 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -199,17 +199,17 @@ process {
             [
                 path: { "${params.outdir}/reports/trimgalore/${meta.id}/fastqc" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{html,zip}"
+                pattern: "*{html,zip}"
             ],
             [
                 path: { "${params.outdir}/trimgalore/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.fq.gz"
+                pattern: "*fq.gz"
             ],
             [
                 path: { "${params.outdir}/reports/trimgalore/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.txt"
+                pattern: "*txt"
             ]
         ]
     }
@@ -244,8 +244,9 @@ process {
         ext.when         = { params.split_fastq > 1 }
         publishDir       = [
             enabled: params.save_split_fastqs,
+            mode: params.publish_dir_mode,
             path: { "${params.outdir}/preprocessing/${meta.sample}/seqkit" },
-            mode: params.publish_dir_mode
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -273,7 +274,7 @@ process {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/preprocessing/${meta.id}/mapped" },
-            pattern: "*.bam",
+            pattern: "*bam",
             saveAs: { (params.save_bam_mapped || (params.skip_tools && params.skip_tools.contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? it : null }
         ]
     }
@@ -293,24 +294,21 @@ process {
 
 // MARKDUPLICATES
 
-    withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
+    withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY|GATK4_MARKDUPLICATES' {
         ext.prefix       = { "${meta.id}.md" }
-        ext.when         = { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" },
-            pattern: "*metrics"
+            path: { "${params.outdir}/reports/${meta.id}/markduplicates" },
+            pattern: "metrics"
         ]
     }
 
+    withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
+        ext.when         = { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) }
+    }
+
     withName: 'GATK4_MARKDUPLICATES' {
         ext.args         = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
-        ext.prefix       = { "${meta.id}.md" }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/${meta.id}/markduplicates" },
-            pattern: "*metrics"
-        ]
     }
 
     withName: 'GATK4_MARKDUPLICATES_SPARK' {
@@ -351,7 +349,7 @@ process {
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/preprocessing/${meta.id}/recal_table" },
-            pattern: "*.table"
+            pattern: "*table"
         ]
     }
 
@@ -398,7 +396,7 @@ process {
             [
                 path: { "${params.outdir}/reports/fastqc/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{html,zip}"
+                pattern: "*{html,zip}"
             ]
         ]
     }
@@ -409,7 +407,8 @@ process {
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('bamqc')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/qualimap/${meta.id}" }
+            path: { "${params.outdir}/reports/qualimap/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -417,7 +416,8 @@ process {
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/samtools_stats/${meta.id}" }
+            path: { "${params.outdir}/reports/samtools_stats/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -425,7 +425,8 @@ process {
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('deeptools')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/deeptools/${meta.id}" }
+            path: { "${params.outdir}/reports/deeptools/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -435,7 +436,8 @@ process {
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('bamqc')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/qualimap/${meta.id}" }
+            path: { "${params.outdir}/reports/qualimap/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -443,7 +445,8 @@ process {
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/samtools_stats/${meta.id}" }
+            path: { "${params.outdir}/reports/samtools_stats/${meta.id}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 }
@@ -502,7 +505,8 @@ process{
         publishDir       = [
             enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: 'FREEBAYES' {
@@ -511,13 +515,15 @@ process{
         publishDir       = [
             enabled: params.no_intervals,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName : 'TABIX_VC_FREEBAYES' {
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -527,7 +533,8 @@ process{
         publishDir       = [
             enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: 'HAPLOTYPECALLER' {
@@ -630,7 +637,7 @@ process{
             enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
-            pattern: "*{mpileup}"
+            pattern: "*mpileup"
         ]
     }
 
@@ -680,7 +687,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
-            pattern: "*{.bed}"
+            pattern: "*bed"
         ]
     }
 
@@ -689,7 +696,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
-            pattern: "*{.circos.txt}"
+            pattern: "*circos.txt"
         ]
     }
 
@@ -698,7 +705,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
-            pattern: "*{png}"
+            pattern: "*png"
         ]
     }
 
@@ -708,7 +715,7 @@ process{
             enabled: params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/controlfreec" },
-            pattern: "*{mpileup}"
+            pattern: "*mpileup"
         ]
     }
 
@@ -721,7 +728,8 @@ process{
     withName: 'GATK4_CALCULATECONTAMINATION' {
         publishDir        = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -738,7 +746,8 @@ process{
         ext.prefix       = {"${meta.id}.filtered"}
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -748,7 +757,8 @@ process{
         publishDir       = [
             enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -756,7 +766,8 @@ process{
         publishDir        = [
             enabled: params.no_intervals,
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -764,7 +775,8 @@ process{
         ext.prefix       = { "${meta.id}.vcf.gz" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" }
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -865,6 +877,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -874,8 +887,9 @@ process{
             enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             //use ${meta.tumor_id}_vs_${meta_normal_id} to publish in the same directory as the remainders of the
-            //somatic output whilst keeping the filename prefix identifieable for status type
-            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" }
+            //somatic output whilst keeping the filename prefix identifiable for status type
+            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -884,6 +898,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -892,6 +907,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/msisensorpro" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -910,6 +926,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/bcftools" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -919,6 +936,7 @@ process{
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/vcftools" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }