code: def run(bam_file, sample, out_dir):
      
      out = {}
      # if "rchipqc" in dd.get_tools_on(sample):
      #    out = chipqc(bam_file, sample, out_dir)
  
      peaks = sample.get("peaks_files", {}).get("main")
      if peaks:
          out.update(_reads_in_peaks(bam_file, peaks, sample))
      return out
docs: Standard QC metrics for chipseq