try picard hicpro + delete temp bam sorted files

conf/modules.config

@@ -424,9 +424,5 @@ process {
         ext.args = { [
             "-n"
         ].join('').trim() }
-        publishDir = [
-            path: { "${params.outdir}/picard/bam" },
-            mode: 'copy'
-        ]
     }
 }

nextflow.config

@@ -10,7 +10,7 @@
 params {
 
     // Choice of the workflow ('hicpro' or 'hicstuff')
-    workflow = 'hicstuff'
+    workflow = 'hicpro'
 
     // Input options
     input = null

subworkflows/local/filter_pcr_dup.nf

@@ -32,6 +32,7 @@ workflow FILTER_PCR_DUP {
     )
     SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
 
+    if (params.workflow == "hicstuff"){
         FILTER_PAIR(
         ch_bam.combine(ch_bam)
         .map {
@@ -39,6 +40,11 @@ workflow FILTER_PCR_DUP {
                 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

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

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 (