diff --git a/conf/modules.config b/conf/modules.config
index 01715bf1c7d45610e10a6436c9eded6b97330f3a..0b13690a235b85a2732700b2317f59c3af13f440 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -424,9 +424,5 @@ process {
         ext.args = { [
             "-n"
         ].join('').trim() }
-        publishDir = [
-            path: { "${params.outdir}/picard/bam" },
-            mode: 'copy'
-        ]
     }
 }
diff --git a/nextflow.config b/nextflow.config
index f4f369bc08250880367476c6f09e4f6354a4f45d..6582b79628b595766fff6ace5a7048d75341bd2f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,7 +10,7 @@
 params {
 
     // Choice of the workflow ('hicpro' or 'hicstuff')
-    workflow = 'hicstuff'
+    workflow = 'hicpro'
 
     // Input options
     input = null
diff --git a/subworkflows/local/filter_pcr_dup.nf b/subworkflows/local/filter_pcr_dup.nf
index 3530d6fdbae5cd69fe8b1a23d4433bf076abe379..344c1c9c8f30f6da04591a395c94a4c01f43fae8 100644
--- a/subworkflows/local/filter_pcr_dup.nf
+++ b/subworkflows/local/filter_pcr_dup.nf
@@ -32,13 +32,19 @@ workflow FILTER_PCR_DUP {
     )
     SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
 
-    FILTER_PAIR(
-    ch_bam.combine(ch_bam)
-    .map {
-        meta1, bam1, meta2, bam2 ->
-            meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1,  bam1,  meta2, bam2 ] : null
+    if (params.workflow == "hicstuff"){
+        FILTER_PAIR(
+        ch_bam.combine(ch_bam)
+        .map {
+            meta1, bam1, meta2, bam2 ->
+                meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1,  bam1,  meta2, bam2 ] : null
     })
     FILTER_PAIR.out.bam.set{ new_ch_bam }
+    }
+    else{
+        ch_bam.set{ new_ch_bam }
+    }
+
 
     emit:
     bam = new_ch_bam
diff --git a/subworkflows/local/hicpro.nf b/subworkflows/local/hicpro.nf
index 17543d05c060c2924d2b65d20fad3e3b1f7f5568..6d2e07d7055e6fc6a105a4334a30791fcb5533ab 100644
--- a/subworkflows/local/hicpro.nf
+++ b/subworkflows/local/hicpro.nf
@@ -12,6 +12,7 @@ include { MERGE_STATS } from '../../modules/local/hicpro/merge_stats'
 include { HICPRO2PAIRS } from '../../modules/local/hicpro/hicpro2pairs'
 include { BUILD_CONTACT_MAPS } from '../../modules/local/hicpro/build_contact_maps'
 include { ICE_NORMALIZATION } from '../../modules/local/hicpro/run_ice'
+include { FILTER_PCR_DUP } from './filter_pcr_dup'
 
 // Remove meta.chunks
 def removeChunks(row){
@@ -44,7 +45,22 @@ workflow HICPRO {
     ch_versions = ch_versions.mix(HICPRO_MAPPING.out.versions)
 
     HICPRO_MAPPING.out.bam.set{ ch_bam }
-    ch_bam.view()
+
+    //***************************************
+    // FILTER PCR DUPLICATES
+
+    if (params.filter_pcr_picard && !params.keep_dups){
+        error "Error: cannot filter PCR duplicates with both methods! If filter_pcr_picard is true, keep_dups should be true too"
+    }
+    else if (params.filter_pcr_picard){
+        FILTER_PCR_DUP(
+            HICPRO_MAPPING.out.bam,
+            fasta,
+            index
+        )
+        FILTER_PCR_DUP.out.bam
+            .set {ch_bam}
+    }
 
     //***************************************
     // DIGESTION PROTOCOLS
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index 3e36cf0eb20e4879907ffccc586f4569b0679c99..61a95a85ace406b808bcc3c157504e026d96d92e 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -9,7 +9,6 @@ include { BOWTIE2_ALIGN as BOWTIE2_ALIGN_TRIMMED } from '../../modules/nf-core/b
 include { MERGE_BOWTIE2 } from '../../modules/local/hicpro/bowtie2_merge'
 include { COMBINE_MATES} from '../../modules/local/hicpro/combine_mates'
 include { MAPPING_STATS_DNASE } from '../../modules/local/hicpro/dnase_mapping_stats'
-include { FILTER_PCR_DUP } from './filter_pcr_dup'
 
 // Paired-end to Single-end
 def pairToSingle(row, mates) {
@@ -31,12 +30,12 @@ def singleToPair(row){
   return [ meta, row[1] ]
 }
 
-def singleToPairPCR(row){
+/* def singleToPairPCR(row){
     def meta = row[0].clone()
     meta.remove('mates')
     meta.single_end = false
     return [ meta, [row[1], row[3]] ]
-}
+} */
 
 
 workflow HICPRO_MAPPING {
@@ -111,28 +110,7 @@ workflow HICPRO_MAPPING {
       .set {ch_bams}
   }
 
-  //***************************************
-    // FILTER PCR DUPLICATES
-
-    if (params.filter_pcr_picard && !params.keep_dups){
-        error "Error: cannot filter PCR duplicates with both methods! If filter_pcr_picard is true, keep_dups should be true too"
-    }
-    else if (params.filter_pcr_picard){
-        if (!params.dnase){
-            MERGE_BOWTIE2.out.bam.set{ch_2filter}
-        }
-        else{
-            BOWTIE2_ALIGN.out.bamx.set{ch_2filter}
-        }
-        FILTER_PCR_DUP(
-            ch_2filter,
-            fasta,
-            index
-        )
-        FILTER_PCR_DUP.out.bam
-            .map { singleToPairPCR(it) }
-            .set {ch_bams}
-    }
+
 
 
   COMBINE_MATES (