code: def _prep_inputs(align_bams, ref_file, items):
      
      broad_runner = broad.runner_from_path("picard", items[0]["config"])
      broad_runner.run_fn("picard_index_ref", ref_file)
      for x in align_bams:
          bam.index(x, items[0]["config"])
docs: Ensure inputs to calling are indexed as expected.