code: def run_coral(clus_obj, out_dir, args):
      
      if not args.bed:
          raise ValueError("This module needs the bed file output from cluster subcmd.")
      workdir = op.abspath(op.join(args.out, 'coral'))
      safe_dirs(workdir)
      bam_in = op.abspath(args.bam)
      bed_in = op.abspath(args.bed)
      reference = op.abspath(args.ref)
      with chdir(workdir):
          bam_clean = coral.prepare_bam(bam_in, bed_in)
          out_dir = op.join(workdir, "regions")
          safe_dirs(out_dir)
          prefix = "seqcluster"
          loci_file = coral.detect_regions(bam_clean, bed_in, out_dir, prefix)
          coral.create_features(bam_clean, loci_file, reference, out_dir)
docs: Run some CoRaL modules to predict small RNA function