diff --git a/conf/modules.config b/conf/modules.config
index 7c1ceba..e367a67 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -268,7 +268,7 @@ process {
         // one run with multiple samples, so fix ID to just db name to ensure clean log name
         ext.prefix = { "${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/malt/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{rma6,log,sam}'
         ]
@@ -278,7 +278,7 @@ process {
         ext.args = "-c2c Taxonomy"
         ext.prefix = { "${meta.id}" }
         publishDir = [
-            path: { "${params.outdir}/malt/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/malt/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{txt.gz,megan}'
         ]
@@ -288,7 +288,7 @@ process {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/kraken2/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/kraken2/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{txt,report,fastq.gz}'
         ]
@@ -297,7 +297,7 @@ process {
     withName: KRONA_CLEANUP {
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/krona/${ext.prefix}" },
+            path: { "${params.outdir}/krona/" },
             mode: params.publish_dir_mode,
             pattern: '*.{html}'
         ]
@@ -306,7 +306,7 @@ process {
     withName: KRONA_KTIMPORTTEXT {
         ext.prefix = { "${meta.tool}-${meta.id}" }
         publishDir = [
-            path: { "${params.outdir}/krona/${ext.prefix}" },
+            path: { "${params.outdir}/krona/" },
             mode: params.publish_dir_mode,
             pattern: '*.{html}'
         ]
@@ -321,7 +321,7 @@ process {
         ext.args = "-i"
         ext.prefix = { "${meta.tool}-${meta.id}" }
         publishDir = [
-            path: { "${params.outdir}/krona/${ext.prefix}" },
+            path: { "${params.outdir}/krona/" },
             mode: params.publish_dir_mode,
             pattern: '*.{html}'
         ]
@@ -331,7 +331,7 @@ process {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/metaphlan3/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{biom,txt}'
         ]
@@ -339,7 +339,7 @@ process {
 
     withName: CENTRIFUGE_CENTRIFUGE {
         publishDir = [
-            path: { "${params.outdir}/centrifuge/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{txt,sam,gz}'
         ]
@@ -352,7 +352,7 @@ process {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" }
         publishDir = [
-            path: { "${params.outdir}/centrifuge/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{txt}'
         ]
@@ -361,7 +361,7 @@ process {
     withName: KAIJU_KAIJU {
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/kaiju/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/kaiju/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.tsv'
         ]
@@ -385,7 +385,7 @@ process {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/diamond/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/diamond/${meta.db_name}/" },
             mode: params.publish_dir_mode,
             pattern: '*.{blast,xml,txt,daa,sam,tsv,paf,log}'
         ]
@@ -394,7 +394,7 @@ process {
     withName: MOTUS_PROFILE {
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
-            path: { "${params.outdir}/motus/${meta.db_name}/${ext.prefix}" },
+            path: { "${params.outdir}/motus/${meta.db_name}/" },
             mode: params.publish_dir_mode
         ]
     }