code: def organize_noalign(data):
      
      data = utils.to_single_data(data[0])
      work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data)))
      work_bam = os.path.join(work_dir, "%s-input.bam" % dd.get_sample_name(data))
      if data.get("files"):
          if data["files"][0].endswith(".cram"):
              work_bam = cram.to_bam(data["files"][0], work_bam, data)
          else:
              assert data["files"][0].endswith(".bam"), data["files"][0]
              utils.copy_plus(data["files"][0], work_bam)
          bam.index(work_bam, data["config"])
      else:
          work_bam = None
      data["align_bam"] = work_bam
      return data
docs: CWL target to skip alignment and organize input data.