code: def _run_germline(align_bams, items, ref_file, target, out_file):
      
      align_bams = " ".join(align_bams)
      cores = dd.get_num_cores(items[0])
      cmd = ("octopus --threads {cores} --reference {ref_file} --reads {align_bams} "
             "--regions-file {target} "
             "--working-directory {tmp_dir} "
             "-o {tx_out_file} --legacy")
      with file_transaction(items[0], out_file) as tx_out_file:
          tmp_dir = os.path.dirname(tx_out_file)
          do.run(cmd.format(**locals()), "Octopus germline calling")
          _produce_compatible_vcf(tx_out_file, items[0])
      return out_file
docs: Run germline calling, handling populations.
  
      TODO:
        - We could better handle trio calling with ped inputs as octopus
          has special support.