code: def run(items):
      
      paired = vcfutils.get_paired(items)
      data = paired.tumor_data if paired else items[0]
      work_dir = _sv_workdir(data)
      variant_file = _get_out_file(work_dir, paired)
      if not utils.file_exists(variant_file):
          with file_transaction(data, work_dir) as tx_work_dir:
              utils.safe_makedir(tx_work_dir)
              tx_workflow_file = _prep_config(items, paired, tx_work_dir)
              _run_workflow(items, paired, tx_workflow_file, tx_work_dir)
      assert utils.file_exists(variant_file), "Manta finished without output file %s" % variant_file
      variant_file = shared.annotate_with_depth(variant_file, items)
      out = []
      upload_counts = collections.defaultdict(int)
      for data in items:
          if "break-point-inspector" in dd.get_tools_on(data):
              if paired and paired.normal_bam and paired.tumor_name == dd.get_sample_name(data):
                  variant_file = _run_break_point_inspector(data, variant_file, paired, work_dir)
          if "sv" not in data:
              data["sv"] = []
          final_vcf = shared.finalize_sv(variant_file, data, items)
          vc = {"variantcaller": "manta",
                "do_upload": upload_counts[final_vcf] == 0,  # only upload a single file per batch
                "vrn_file": final_vcf}
          evidence_bam = _get_evidence_bam(work_dir, data)
          if evidence_bam:
              vc["read_evidence"] = evidence_bam
          data["sv"].append(vc)
          upload_counts[final_vcf] += 1
          out.append(data)
      return out
docs: Perform detection of structural variations with Manta.