code: def _run_workflow(items, paired, workflow_file, work_dir):
      
      utils.remove_safe(os.path.join(work_dir, "workspace"))
      data = paired.tumor_data if paired else items[0]
      cmd = [utils.get_program_python("configManta.py"), workflow_file, "-m", "local", "-j", dd.get_num_cores(data)]
      do.run(cmd, "Run manta SV analysis")
      utils.remove_safe(os.path.join(work_dir, "workspace"))
docs: Run manta analysis inside prepared workflow directory.