diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
index 87a372846d6536699ef7c3a420561376139c2a23..ece556aaa238f17cb3db8a42f52791ad0638951c 100644
--- a/src/nf_modules/UrQt/urqt.nf
+++ b/src/nf_modules/UrQt/urqt.nf
@@ -21,6 +21,7 @@ Channel
 process trimming {
   tag "$pair_id"
   cpus 4
+  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
@@ -53,6 +54,7 @@ Channel
 process trimming {
   tag "$reads.baseName"
   cpus 4
+  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   file reads from fastq_files
diff --git a/src/nf_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
index bebdf41ad8c2c8fe5c9e8fd9b418ae34582e1e97..094f30b9483c241b308bc245c5e51d3bbf896a1a 100644
--- a/src/nf_modules/cutadapt/cutadapt.nf
+++ b/src/nf_modules/cutadapt/cutadapt.nf
@@ -21,6 +21,7 @@ Channel
 
 process adaptor_removal {
   tag "$pair_id"
+  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
@@ -51,6 +52,7 @@ Channel
 
 process adaptor_removal {
   tag "$reads.baseName"
+  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   file reads from fastq_files
@@ -83,6 +85,7 @@ Channel
 
 process trimming {
   tag "$pair_id"
+  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
@@ -113,6 +116,7 @@ Channel
 
 process trimming {
   tag "$reads.baseName"
+  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   file reads from fastq_files