[MODIF] deal with technical replicates

subworkflows/local/hicpro.nf

@@ -70,16 +70,16 @@ workflow HICPRO {
   //**************************************
   // MERGE AND REMOVE DUPLICATES
   
-  if (params.split_fastq){
-    ch_valid_pairs = ch_valid_pairs.map{ it -> removeChunks(it)}.groupTuple()
-    ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.map{it->removeChunks(it)}.groupTuple()
-                        .concat(HICPRO_MAPPING.out.pairstats.map{it->removeChunks(it)}.groupTuple(),
-			        ch_valid_stats.map{it->removeChunks(it)}.groupTuple())
-  }else{
-    ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.groupTuple()
-                        .concat(HICPRO_MAPPING.out.pairstats.groupTuple(),
-                                ch_valid_stats.groupTuple())
-  }
+  //if (params.split_fastq){
+  ch_valid_pairs = ch_valid_pairs.map{ it -> removeChunks(it)}.groupTuple()
+  ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.map{it->removeChunks(it)}.groupTuple()
+                      .concat(HICPRO_MAPPING.out.pairstats.map{it->removeChunks(it)}.groupTuple(),
+		        ch_valid_stats.map{it->removeChunks(it)}.groupTuple())
+  //}else{
+  //  ch_hicpro_stats = HICPRO_MAPPING.out.mapstats.groupTuple()
+  //                      .concat(HICPRO_MAPPING.out.pairstats.groupTuple(),
+  //                              ch_valid_stats.groupTuple())
+  //}
 
   MERGE_VALID_INTERACTION (
     ch_valid_pairs

subworkflows/local/input_check.nf

@@ -30,6 +30,9 @@ workflow INPUT_CHECK {
         .splitCsv ( header:true, sep:',' )
         .map { create_fastq_channels(it) }
 	.map { it -> [it[0], [it[1], it[2]]]}
+	.groupTuple(by: [0])
+        .flatMap { it -> setMetaChunk(it) }
+        .collate(2)
         .set { reads }
    }
 
@@ -53,3 +56,15 @@ def create_fastq_channels(LinkedHashMap row) {
   array = [ meta, file(row.fastq_1), file(row.fastq_2) ]
   return array
 }
+
+// Set the meta.chunk value in case of technical replicates
+def setMetaChunk(row){
+  def map = []
+  row[1].eachWithIndex() { file,i ->
+    meta = row[0].clone()
+    meta.chunks = i
+    map += [meta, file]
+  }
+  return map
+}                                                                                                                                                                                                            
+                                                                                                                                                                                                             

workflows/hic.nf

@@ -143,16 +143,6 @@ Channel.fromPath( params.fasta )
 // Info required for completion email and summary
 def multiqc_report = []
 
-def setMetaChunk(row){
-  def map = []
-  row[1].eachWithIndex() { file,i ->
-    meta = row[0].clone()
-    meta.chunks = i
-    map += [meta, file]
-  }
-  return map
-}
-
 workflow HIC {
 
   ch_versions = Channel.empty()
@@ -163,19 +153,8 @@ workflow HIC {
   INPUT_CHECK (
     ch_input
   )
-  .reads
-  //.map {
-  //    meta, fastq ->
-  //        meta.id = meta.id.split('_')[0..-2].join('_')
-  //        [ meta, fastq ] }
-  .groupTuple(by: [0])
-  .flatMap { it -> setMetaChunk(it) }
-  .collate(2)
-  .set { ch_fastq }
-
-  ch_fastq.view()
 
-  //INPUT_CHECK.out.reads.view()
+  INPUT_CHECK.out.reads.view()
 
   //
   // SUBWORKFLOW: Prepare genome annotation
@@ -190,7 +169,7 @@ workflow HIC {
   // MODULE: Run FastQC
   //
   FASTQC (
-    ch_fastq
+    INPUT_CHECK.out.reads
   )
   ch_versions = ch_versions.mix(FASTQC.out.versions)
 
@@ -198,7 +177,7 @@ workflow HIC {
   // SUB-WORFLOW: HiC-Pro
   //
   HICPRO (
-    ch_fastq,
+    INPUT_CHECK.out.reads,
     PREPARE_GENOME.out.index,
     PREPARE_GENOME.out.res_frag,
     PREPARE_GENOME.out.chromosome_size,