code: def _bowtie2_args_from_config(config, curcl):
      
      qual_format = config["algorithm"].get("quality_format", "")
      if qual_format.lower() == "illumina":
          qual_flags = ["--phred64-quals"]
      else:
          qual_flags = []
      num_cores = config["algorithm"].get("num_cores", 1)
      core_flags = ["-p", str(num_cores)] if num_cores > 1 else []
      user_opts = config_utils.get_resources("bowtie2", config).get("options", [])
      for flag_opt in (o for o in user_opts if str(o).startswith("-")):
          if flag_opt in curcl:
              raise ValueError("Duplicate option %s in resources and bcbio commandline: %s %s" %
                               flag_opt, user_opts, curcl)
      return core_flags + qual_flags + user_opts
docs: Configurable high level options for bowtie2.