adding merging of input control BAM files

dunnart/Snakefile

@@ -198,16 +198,20 @@ rule indexBam:
 rule mergeBAMreplicates:
     input:
         H3K4me3 = ["results/bowtie2/A-2_H3K4me3_PPq30.sorted.dedup.bam",  "results/bowtie2/B-2_H3K4me3_PPq30.sorted.dedup.bam"],
-        H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam", "results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"]
+        H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam", "results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"],
+        control = ["results/bowtie2/A-1_input_PPq30.sorted.dedup.bam", "results/bowtie2/B-1_input_PPq30.sorted.dedup.bam"]
     output:
         H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
-        H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam"
+        H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+        control = "results/bowtie2/input_pooled_PPq30.sorted.dedup.bam"
     log:
         H3K4me3 = "logs/H3K4me3.mergeBAM",
-        H3K27ac = "logs/H3K27ac.mergeBAM"
+        H3K27ac = "logs/H3K27ac.mergeBAM",
+        control = "logs/input.mergeBAM"
     run:
         shell("samtools merge {output.H3K4me3} {input.H3K4me3} 2> {log.H3K4me3}")
-        shell("samtools merge {output.H3K27ac} {input.H3K427ac} 2> {log.H3K27ac}")
+        shell("samtools merge {output.H3K27ac} {input.H3K27ac} 2> {log.H3K27ac}")
+        shell("samtools merge {output.control} {input.control} 2> {log.control}")
 
 # ===============================================================================================
 #  4. GENERAL ALIGNMENT QC