diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index bd4a1890040e57fb996c3c6ffbd45f7a3f9d5d70..f0bef1310ad3bdaaf8d5f4575b355471cae51240 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -5,7 +5,6 @@ process fasta_from_bed {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "${bed.baseName}"
-  publishDir "results/fasta/", mode: 'copy'
 
   input:
   path fasta
@@ -25,7 +24,6 @@ process bam_to_fastq_singleend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "${bam_id}"
-  publishDir "results/mapping/fastq/", mode: 'copy'
 
   input:
   tuple val(bam_id), path(bam)
@@ -44,7 +42,6 @@ process bam_to_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "${bam_id}"
-  publishDir "results/mapping/fastq/", mode: 'copy'
 
   input:
   tuple val(bam_id), path(bam)
diff --git a/src/nf_modules/bowtie/main.nf b/src/nf_modules/bowtie/main.nf
index d507b6b4950ed12733e0b4b61a8d6ba7aee0a086..c95c47f087dac91274a4c255d3ea1e535d2ffe63 100644
--- a/src/nf_modules/bowtie/main.nf
+++ b/src/nf_modules/bowtie/main.nf
@@ -5,7 +5,6 @@ process index_fasta {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
 
   input:
     path fasta
@@ -31,7 +30,6 @@ process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$pair_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index
@@ -69,7 +67,6 @@ process mapping_fastq_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index
diff --git a/src/nf_modules/bowtie2/main.nf b/src/nf_modules/bowtie2/main.nf
index 22465baef0cf8fa73cccff0a431afc93f1956c79..c852c31df95fe86d2dbb644056a0152bca0fd391 100644
--- a/src/nf_modules/bowtie2/main.nf
+++ b/src/nf_modules/bowtie2/main.nf
@@ -5,7 +5,6 @@ process index_fasta {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
 
   input:
     path fasta
@@ -32,7 +31,6 @@ process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$pair_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index
@@ -71,7 +69,6 @@ process mapping_fastq_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/mapping/bams/", mode: 'copy'
 
   input:
   path index
diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf
index 0859ea9232e284713adaf19a69f8b96f4b7e760e..020101fe0d7ac3557a748f7d0225ce3bda9844d9 100644
--- a/src/nf_modules/cutadapt/main.nf
+++ b/src/nf_modules/cutadapt/main.nf
@@ -10,7 +10,6 @@ process adaptor_removal_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
@@ -31,7 +30,6 @@ process adaptor_removal_singleend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/fastq/adaptor_removal/", mode: 'copy'
 
   input:
   tuple val(file_id), path(reads)
@@ -52,7 +50,6 @@ process trimming_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index 3d0127967d6dfdb17f31f79602eb2133a09e3fd9..4a60dabe98c4544f531c52ecc3bf349d20392394 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -23,7 +23,6 @@ process bam_to_bigwig {
   label "big_mem_multi_cpus"
   tag "$file_id"
 
-  publishDir "results/mapping/bigwig/", mode: 'copy'
 
   input:
     tuple val(file_id), path(bam), path(idx)
@@ -42,7 +41,6 @@ process compute_matrix {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "${bed_file_id}"
-  publishDir "results/metagene/region_matrix/", mode: 'copy'
 
   input:
     tuple val(file_id), path(bw)
@@ -66,7 +64,6 @@ process plot_profile {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/metagene/region_matrix/", mode: 'copy'
 
   input:
     tuple val(file_id), path(matrix)
diff --git a/src/nf_modules/fastqc/main.nf b/src/nf_modules/fastqc/main.nf
index 4a2095014a6af3e8330e8fc13e71c4c191fd4708..599101f6c76a2dc9a3b518dbbd485450fb186963 100644
--- a/src/nf_modules/fastqc/main.nf
+++ b/src/nf_modules/fastqc/main.nf
@@ -5,7 +5,6 @@ process fastqc_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$pair_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
@@ -24,7 +23,6 @@ process fastqc_fastq_singleend {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/fastq/fastqc/", mode: 'copy'
 
   input:
   tuple val(file_id), path(reads)
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 0517a1b54f2106c1ce64bfcb805b368d0424db67..bb80e4b361d08b3a34598ee1857268005545a030 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -5,7 +5,6 @@ process index_fasta {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$fasta.baseName"
-  publishDir "results/mapping/index/", mode: 'copy'
 
   input:
     path fasta
@@ -26,7 +25,6 @@ process mapping_fastq_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$pair_id"
-  publishDir "results/mapping/counts/", mode: 'copy'
 
   input:
   path index
@@ -50,7 +48,6 @@ process mapping_fastq_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/mapping/counts/", mode: 'copy'
 
   input:
   path index
diff --git a/src/nf_modules/macs2/main.nf b/src/nf_modules/macs2/main.nf
index e30e0ee241640abc357d716ec5288ba0eba1a934..139a8db66029324a2340be8ac9bb7b485e3c0baa 100644
--- a/src/nf_modules/macs2/main.nf
+++ b/src/nf_modules/macs2/main.nf
@@ -5,7 +5,6 @@ process peak_calling {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "${file_id}"
-  publishDir "results/peak_calling/${file_id}", mode: 'copy'
 
   input:
     tuple val(file_id), path(bam_ip), path(bam_control)
diff --git a/src/nf_modules/multiqc/main.nf b/src/nf_modules/multiqc/main.nf
index 1a3efda7065f61abf709171533c9406c0d500890..3b360f35cf129d2e43e27a88f673387cbaf367dc 100644
--- a/src/nf_modules/multiqc/main.nf
+++ b/src/nf_modules/multiqc/main.nf
@@ -5,7 +5,6 @@ process multiqc {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$report[0].baseName"
-  publishDir "results/QC/multiqc/", mode: 'copy'
 
   input:
     path report
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index 0faec2e001ce79e92c6377abfc07e2a7b6138b22..a7326f3dacc341bc1dfe7ffb2cb81cea380791d0 100644
--- a/src/nf_modules/picard/main.nf
+++ b/src/nf_modules/picard/main.nf
@@ -5,7 +5,6 @@ process mark_duplicate {
   container = "${container_url}"
   label "big_mem_mono_cpus"
   tag "$file_id"
-  publishDir "results/mapping/ddup/", mode: 'copy'
 
   input:
     tuple val(file_id), path(bam)
diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf
index 48a1a3ecb75a17ecab60dc0735df715afbf5ec9e..6744856a0fe455a52a2df221fdf6baf4311be651 100644
--- a/src/nf_modules/urqt/main.nf
+++ b/src/nf_modules/urqt/main.nf
@@ -7,7 +7,6 @@ process trimming_pairedend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "${reads}"
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   tuple val(pair_id), path(reads)
@@ -29,7 +28,6 @@ process trimming_singleend {
   container = "${container_url}"
   label "big_mem_multi_cpus"
   tag "$file_id"
-  publishDir "results/fastq/trimming/", mode: 'copy'
 
   input:
   tuple val(file_id), path(reads)