diff --git a/pipeline.nf b/pipeline.nf
index f91617f..1f2f379 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -192,8 +192,8 @@ process footprint_extraction {
 	conda "${path_env}"
 
 	tag{name}
-	publishDir "${params.out}/footprint_extraction/", mode: 'copy', pattern: '*.bed'
-	publishDir "${params.out}/footprint_extraction/log", mode: 'copy', pattern: '*.log'
+	publishDir "${params.out}/1.1_footprint_extraction/", mode: 'copy', pattern: '*.bed'
+	publishDir "${params.out}/1.1_footprint_extraction/log", mode: 'copy', pattern: '*.log'
 
 	input:
 	set name, file (bigWig), file (bed) from footprint_in
@@ -216,7 +216,7 @@ process extract_known_TFBS {
 
 	conda "${path_env}"
 
-	publishDir "${params.out}/known_TFBS/", mode: 'copy', pattern: '*.bed'
+	publishDir "${params.out}/1.2_filter_motifs/TFBSscan/", mode: 'copy', pattern: '*.bed'
 
 	input:
 	set file (fasta), file (db), file (bed) from for_tfbs
@@ -252,7 +252,7 @@ if(params.tfbs_path == "") {
 process overlap_with_known_TFBS {
 	conda "${path_env}"
 
-	publishDir "${params.out}/unknown_overlap/", mode :'copy'
+	publishDir "${params.out}/1.2_filter_motifs/compareBed/", mode :'copy'
 
 	input:
 	set name, file (bed_footprints), val (bed_motifs), file (fasta) from for_overlap
@@ -274,7 +274,7 @@ Reduce each sequence to its most conserved region.
 process reduce_sequence {
 	conda "${path_env}"
 	echo true
-	publishDir "${params.out}/cluster/reduced_bed/", mode: 'copy'
+	publishDir "${params.out}/2.1_clustering/reduced_bed/", mode: 'copy'
 
 	input:
 	set name, file (bed) from bed_for_reducing
@@ -296,7 +296,7 @@ process clustering {
 	conda "${path_env}"
 	echo true
 
-	publishDir "${params.out}/cluster/", mode: 'copy', pattern: '*.bed'
+	publishDir "${params.out}/2.1_clustering/", mode: 'copy', pattern: '*.bed'
 
 	input:
 	set name, file (bed) from bed_for_clustering
@@ -316,7 +316,7 @@ Converting BED-File to one FASTA-File per cluster
 */
 process bed_to_clustered_fasta {
 	conda "${path_env}"
-	publishDir "${params.out}/esimated_motifs/clustered_motifs/clustered_fasta/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/fasta/", mode: 'copy'
     tag{name}
 
     input:
@@ -345,7 +345,7 @@ Generating Motifs through alignment and scoring best local matches.
 process glam2 {
 
     tag{name}
-	publishDir "${params.out}/esimated_motifs/clustered_motifs/${name}/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/glam2/${name}/", mode: 'copy'
 
     input:
     set name, file (fasta) from fasta_for_glam2
@@ -368,7 +368,7 @@ The paths are sorted numerically depending on the cluster number.
 */
 process merge_meme {
 
-	publishDir "${params.out}/esimated_motifs/merged_meme/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/cluster_motifs/merged_meme/", mode: 'copy'
 
 	input:
 	val (memelist) from meme_to_merge.toList()
@@ -395,7 +395,7 @@ Output table has the information which clusters are similar to each other.
 */
 process find_similar_motifs {
 
-	publishDir "${params.out}/esimated_motifs/cluster_similarity/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/cluster_motifs/cluster_similarity/", mode: 'copy'
 	input:
 	file (merged_meme) from merged_meme
 
@@ -420,7 +420,7 @@ Merging FASTA-files of similar clusters
 */
 process merge_fasta {
 	conda "${path_env}"
-	publishDir "${params.out}/esimated_motifs/merged_fasta/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/cluster_motifs/merged_fasta/", mode: 'copy'
 	echo true
 	input:
 	set file (motiv_sim), val (fasta_list) from files_for_merge_fasta
@@ -446,7 +446,7 @@ motif_clustered_fasta_flat = motif_clustered_fasta_list.flatten()
 
 process clustered_glam2 {
 
-	publishDir "${params.out}/final_esimated_motifs/${name}/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/cluster_motifs/glam2/${name}/", mode: 'copy'
 
 	input:
 	file (fasta) from motif_clustered_fasta_flat
@@ -482,7 +482,7 @@ Tomtom searches motifs in databases.
 process tomtom {
 
     tag{name}
-	publishDir "${params.out}/esimated_motifs/tomtom/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/tomtom/", mode: 'copy'
 
     input:
     set name, file (meme) from for_tomtom
@@ -529,7 +529,7 @@ process check_for_unknown_motifs {
 process get_best_motif {
 	conda "${path_env}"
 
-	publishDir "${params.out}/esimated_motifs/unknown_motifs/", mode: 'copy'
+	publishDir "${params.out}/2.2_motif_estimation/best_unknown_motifs/", mode: 'copy'
 
 	input:
 	set name, file(meme), file(tsv) from meme_for_scan
@@ -579,7 +579,7 @@ process cluster_quality {
 process create_GTF {
 	conda "${path_env}"
 
-	publishDir "${params.out}/gtf/", mode: 'copy'
+	publishDir "${params.out}/3.1_create_gtf/", mode: 'copy'
 
 	output:
 	file ('*.gtf') into gtf