Pass map.single_read to feature counts

Author: JoseEspinosa

subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf

@@ -90,8 +90,8 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
         }
         .join(ch_bams)
         .map {
-            antibody, meta, saf, bams ->
-                [ meta, bams.flatten().sort(), saf ]
+            antibody, meta, saf, bams, meta_single_end ->
+                [ meta + meta_single_end, bams.flatten().sort(), saf ]
         }
         .set { ch_bam_saf }
 

workflows/chipseq.nf

@@ -130,7 +130,6 @@ workflow CHIPSEQ {
     )
     ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.versions)
 
-
     //
     // SUBWORKFLOW: Alignment with BWA & BAM QC
     //
@@ -474,9 +473,14 @@ workflow CHIPSEQ {
         ch_ip_control_bam
             .map {
                 meta, ip_bam, control_bam ->
-                    [ meta.antibody, ip_bam ]
+                    [ meta.antibody, meta.single_end, ip_bam ]
             }
             .groupTuple()
+            .map {
+                antibody, single_end, ip_bams ->
+                    def single_end_map = single_end.unique().size() == 1 ? [single_end: single_end[0]] : false
+                    [ antibody, ip_bams, single_end_map ]
+            }
             .set { ch_antibody_bams }
 
         BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 (