cleanup

                }

                .filter { !it.isEmpty() }

                .set { ch_bedgraph_combined }

            ch_bedgraph_combined | view

            /*

             * CHANNEL: Recombines and maps igg control replicates to the target replicate

             */

            // ch_bedgraph_split.target

            //     .combine(ch_bedgraph_split.control)

            //     .filter { row -> row[0].replicate == row[2].replicate }

            //     .map { row -> [ row[0], row[1], row[3] ] }

            //     .set { ch_bedgraph_combined }

            //EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false,

            // bt2_total_reads_target:9616, bt2_align1_target:315, bt2_align_gt1_target:449, bt2_non_aligned_target:8852, bt2_total_aligned_target:764,

            // bt2_total_reads_spikein:9616, bt2_align1_spikein:1, bt2_align_gt1_spikein:0, bt2_non_aligned_spikein:9615, bt2_total_aligned_spikein:1,

        /*

        * MODULE: DESeq2 QC Analysis

        */

        if (false){

        DESEQ2_DIFF (

            ch_groups_no_igg,

            ch_seacr_bed.collect{it[1]},

            ch_samtools_bam.collect{it[1]}

        )

        ch_software_versions = ch_software_versions.mix(DESEQ2_DIFF.out.version.ifEmpty(null))

        }

        /*

        * MODULE: Compute DeepTools matrix used in heatmap plotting for Genes