remove counting number of peaks

mouse/Snakefile

@@ -391,41 +391,27 @@ rule call_peaks_macs2:
 #   > fraction of reads in peaks (convert BAM to bed first then do intersect with peaks)
 # ===============================================================================================
 
-#peak counts in a format that multiqc can handle
-# rule get_narrow_peak_counts_for_multiqc:
-#     input:
-#         peaks = "results/macs2/{case}_vs_{control}_{stage}_{mark}_macs2_peaks.narrowPeak"
-#     output:
-#         "results/macs2/{case}-vs-{control}_{stage}_{mark}-narrowpeak-count_mqc.json"
-#     params:
-#         peakType = "narrowPeak"
-#     shell:
-#         "python2.7 scripts/count_peaks.py \
-#         --peak_type {params.peakType} \
-#         --peaks {input.peaks} --sample_name {wildcards.case} > {output}"
-#
+## Convert BAM to tagAlign file for calculating FRiP QC metric (Fraction of reads in peaks)
+rule bamToBed:
+    input:
+        "results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bam"
+    output:
+        "results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bed"
+    log:
+        "logs/{case}_{stage}_{mark}.bamToBed"
+    shell:
+        "samtools sort -n {input} | bedtools bamtobed -i - > {output}"
 
-# ## Convert BAM to tagAlign file for calculating FRiP QC metric (Fraction of reads in peaks)
-# rule bamToBed:
-#     input:
-#         "results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bam"
-#     output:
-#         "results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bed"
-#     log:
-#         "logs/{case}_{stage}_{mark}.bamToBed"
-#     shell:
-#         "samtools sort -n {input} | bedtools bamtobed -i - > {output}"
-#
-# #
-# # ## Fraction of reads in peaks
-# rule frip:
-#     input:
-#         bed = "results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bed",
-#         peak = "results/macs2/{case}_vs_{control}_{stage}_{mark}_macs2_peaks.narrowPeak"
-#     output:
-#         "results/frip/{case}_vs_{control}_{stage}_{mark}.frip.txt"
-#     shell:
-#         "python2.7 scripts/encode_frip.py {input.bed} {input.peak} > {output}"
+
+# ## Fraction of reads in peaks
+rule frip:
+    input:
+        bed = "results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bed",
+        peak = "results/macs2/{case}_vs_{control}_{stage}_{mark}_macs2_peaks.narrowPeak"
+    output:
+        "results/frip/{case}_vs_{control}_{stage}_{mark}.frip.txt"
+    shell:
+        "python2.7 scripts/encode_frip.py {input.bed} {input.peak} > {output}"
 
 
 # ===============================================================================================