subworkflows/local/hicstuff_sub.nf: update

subworkflows/local/hicstuff_sub.nf

@@ -9,8 +9,10 @@ include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event'
 include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law'
 include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
 include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/custom/gatk4/markduplicates/main'
-include { SAMTOOLS_SORT } from '../../modules/nf-core/custom/samtools/sort/main'
+include { SAMTOOLS_SORT as  SAMTOOLS_SORT1} from '../../modules/nf-core/custom/samtools/sort/main'
+include { SAMTOOLS_SORT as  SAMTOOLS_SORT2} from '../../modules/nf-core/custom/samtools/sort/main'
 include { SAMTOOLS_SORT_N } from '../../modules/nf-core/custom/samtools_n/sort/main'
+include { FILTER_PAIR } from '../../modules/nf-core/custom/filterbam/main'
 include { SAMTOOLS_INDEX } from '../../modules/nf-core/custom/samtools/index/main'
 include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/custom/picard/markduplicates/main'
 
@@ -65,27 +67,13 @@ workflow HICSTUFF_SUB {
         error "Error: filter_pcr and filter_pcr_picard can't both be true at the same time! Set one of them false in the config file"
     }
     else if (params.filter_pcr_picard){
-        SAMTOOLS_SORT(
+        SAMTOOLS_SORT1(
             BOWTIE2_ALIGNMENT.out.bam
         )
 
-/*         GATK4_MARKDUPLICATES(
-            SAMTOOLS_SORT.out.bam,
-            fasta.map{ it[1] }.collect(),
-            index.map{ it[1] }.collect()
-        )
-
-        SAMTOOLS_SORT_N(
-            GATK4_MARKDUPLICATES.out.bam
-        )
-
-        SAMTOOLS_INDEX(
-            SAMTOOLS_SORT_N.out.bam
-        )
- */
 
         PICARD_MARKDUPLICATES(
-            SAMTOOLS_SORT.out.bam,
+            SAMTOOLS_SORT1.out.bam,
             fasta.collect(),
             index.collect()
         )
@@ -94,24 +82,35 @@ workflow HICSTUFF_SUB {
             PICARD_MARKDUPLICATES.out.bam
         )
 
-        SAMTOOLS_INDEX(
-            SAMTOOLS_SORT_N.out.bam
-        )
-
         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
+        })
+
+        FILTER_PAIR.out.bam.set{ new_ch_bam }
+
     }
     else {
 
-        BOWTIE2_ALIGNMENT.out.bam.set{ ch_bam }
+        // BOWTIE2_ALIGNMENT.out.bam.set{ ch_bam }
+        SAMTOOLS_SORT_N(BOWTIE2_ALIGNMENT.out.bam)
+        SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
 
-    }
-    BAM2PAIRS(
         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
-        },
+        }.set{ new_ch_bam }
+
+    }
+    new_ch_bam.view()
+
+    BAM2PAIRS(
+        new_ch_bam,
         FRAGMENT_ENZYME.out.info_contigs.collect(),
         digestion,
         fasta.collect()