call peaks rule for pooled replicates

mouse/Snakefile

@@ -457,6 +457,67 @@ rule call_peaks_macs2:
         -n {params.name} \
         -g mm 2> {log} "
 
+rule call_peaks_macs2_pooled_replicates:
+    input:
+        E10 = "results/bwa/E10.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+        E11 = "results/bwa/E11.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+        E12 = "results/bwa/E12.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+        E13 = "results/bwa/E13.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+        E14 = "results/bwa/E14.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+        E15 = "results/bwa/E15.5_H3K27ac_q30.sorted.pooled.dedup.bam",
+        E10C = "results/bwa/input_E10.5_H3K27ac_q30.sorted.dedup.bam",
+        E11C = "results/bwa/input_E11.5_H3K27ac_q30.sorted.dedup.bam",
+        E12C = "results/bwa/input_E12.5_H3K27ac_q30.sorted.dedup.bam",
+        E13C = "results/bwa/input_E13.5_H3K27ac_q30.sorted.dedup.bam",
+        E14C = "results/bwa/input_E14.5_H3K27ac_q30.sorted.dedup.bam",
+        E15C = "results/bwa/input_E15.5_H3K27ac_q30.sorted.dedup.bam",
+    output:
+        directory("results/macs2/pooled")
+    log:
+        E10 = "results/qc/E10.5_H3K27ac.pooled.macs2",
+        E11 = "results/qc/E11.5_H3K27ac.pooled.macs2",
+        E12 = "results/qc/E12.5_H3K27ac.pooled.macs2",
+        E13 = "results/qc/E13.5_H3K27ac.pooled.macs2",
+        E14 = "results/qc/E14.5_H3K27ac.pooled.macs2",
+        E15 = "results/qc/E15.5_H3K27ac.pooled.macs2",
+    params:
+        E10 = "E10.5_H3K27ac.pooled.macs2",
+        E11 = "E11.5_H3K27ac.pooled.macs2",
+        E12 = "E12.5_H3K27ac.pooled.macs2",
+        E13 = "E13.5_H3K27ac.pooled.macs2",
+        E14 = "E14.5_H3K27ac.pooled.macs2",
+        E15 = "E15.5_H3K27ac.pooled.macs2",
+    run:
+        shell("macs2 callpeak -f BAM -t {input.E10} \
+        -c {input.E10C} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.E10} \
+        -g mm 2> {log.E10}" )
+        shell("macs2 callpeak -f BAM -t {input.E11} \
+        -c {input.E11C} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.E11} \
+        -g mm 2> {log.E11}" )
+        shell("macs2 callpeak -f BAM -t {input.E12} \
+        -c {input.E12C} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.E12} \
+        -g mm 2> {log.E12}" )
+        shell("macs2 callpeak -f BAM -t {input.E13} \
+        -c {input.E13C} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.E13} \
+        -g mm 2> {log.E13}" )
+        shell("macs2 callpeak -f BAM -t {input.E14} \
+        -c {input.E14C} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.E14} \
+        -g mm 2> {log.E14}" )
+        shell("macs2 callpeak -f BAM -t {input.E15} \
+        -c {input.E15C} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.E15} \
+        -g mm 2> {log.E15}" )
 
 # ===============================================================================================
 #  8. Peak QC