diff --git a/workflow/main.nf b/workflow/main.nf
index 4fa5d9f62bc75b3c283f39a07e1f8e849a294bef..4b1fa5bdbe6ef4c48f92a2f4d121d9a238be45f8 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -13,6 +13,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
 params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
 params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
 params.cutoffRatio = 1.2
+params.outDir= "$outDir"
 
 // Check inputs
 if( params.bwaIndex ){
@@ -36,10 +37,11 @@ designFile = params.designFile
 genomeSize = params.genomeSize
 chromSizes = params.chromSizes
 cutoffRatio = params.cutoffRatio
+outDir = params.outDir
 
 process checkDesignFile {
 
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "$outDir/design", mode: 'copy'
 
   input:
 
@@ -80,7 +82,7 @@ rawReads = designFilePaths
 process trimReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -110,7 +112,7 @@ process trimReads {
 process alignReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -141,7 +143,7 @@ process alignReads {
 process filterReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -174,13 +176,13 @@ process filterReads {
 dedupReads
 .map{ sampleId, bam, bai, experimentId, biosample, factor, treatment, replicate, controlId ->
 "$sampleId\t$bam\t$bai\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
-.collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+.collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
 .into { dedupDesign; preDiffDesign }
 
 // Quality Metrics using deeptools
 process experimentQC {
 
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -202,7 +204,7 @@ process experimentQC {
 process convertReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -231,7 +233,7 @@ process convertReads {
 process crossReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -261,12 +263,12 @@ process crossReads {
 xcorDesign = xcorReads
               .map{ sampleId, seTagAlign, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId ->
               "$sampleId\t$seTagAlign\t$tagAlign\t$xcor\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
-              .collectFile(name:'design_xcor.tsv', seed:"sample_id\tse_tag_align\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+              .collectFile(name:'design_xcor.tsv', seed:"sample_id\tse_tag_align\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
 
 // Make Experiment design files to be read in for downstream analysis
 process defineExpDesignFiles {
 
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "$outDir/design", mode: 'copy'
 
   input:
 
@@ -290,7 +292,7 @@ process poolAndPsuedoReads {
 
 
   tag "${experimentObjs.baseName}"
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "$outDir/design", mode: 'copy'
 
   input:
 
@@ -324,7 +326,7 @@ experimentRows = experimentPoolObjs
 process callPeaksMACS {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
   set sampleId, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId, controlTagAlign from experimentRows
@@ -352,12 +354,12 @@ process callPeaksMACS {
 peaksDesign = experimentPeaks
               .map{ sampleId, peak, fcSignal, pvalueSignal, experimentId, biosample, factor, treatment, replicate, controlId ->
               "$sampleId\t$peak\t$fcSignal\t$pvalueSignal\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
-              .collectFile(name:'design_peak.tsv', seed:"sample_id\tpeaks\tfc_signal\tpvalue_signal\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+              .collectFile(name:'design_peak.tsv', seed:"sample_id\tpeaks\tfc_signal\tpvalue_signal\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
 
 // Calculate Consensus Peaks
 process consensusPeaks {
 
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input: