diff --git a/workflow/main.nf b/workflow/main.nf
index 2d89d8179bec42d15d2d0fc7905e4613ce798dc7..a8c50272131ced87f134cf63241032ceddda2f98 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -395,7 +395,7 @@ process consensusPeaks {
 // Annotate Peaks
 process peakAnnotation {
 
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -416,7 +416,7 @@ process peakAnnotation {
 // Motif Search  Peaks
 process motifSearch {
 
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -441,7 +441,7 @@ uniqueExperimentsList = uniqueExperiments
 // Calculate Differential Binding Activity
 process diffPeaks {
 
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input: