old_contents: """Next gen sequence alignments with Bowtie (http://bowtie-bio.sourceforge.net).
  """
  import os
  
  from bcbio.pipeline import config_utils
  from bcbio.utils import file_exists
  from bcbio.distributed.transaction import file_transaction
  from bcbio.provenance import do
  
  galaxy_location_file = "bowtie_indices.loc"
  
  def _bowtie_args_from_config(config):
      """Configurable high level options for bowtie.
      """
      qual_format = config["algorithm"].get("quality_format", None)
      if qual_format is None or qual_format.lower() == "illumina":
          qual_flags = ["--phred64-quals"]
      else:
          qual_flags = []
      multi_mappers = config["algorithm"].get("multiple_mappers", True)
      multi_flags = ["-M", 1] if multi_mappers else ["-m", 1]
      cores = config.get("resources", {}).get("bowtie", {}).get("cores", None)
      num_cores = config["algorithm"].get("num_cores", 1)
      core_flags = ["-p", str(num_cores)] if num_cores > 1 else []
      return core_flags + qual_flags + multi_flags
  
  def align(fastq_file, pair_file, ref_file, out_base, align_dir, data,
            extra_args=None, names=None):
      """Do standard or paired end alignment with bowtie.
      """
      config = data['config']
      out_file = os.path.join(align_dir, "%s.sam" % out_base)
      if not file_exists(out_file):
          with file_transaction(out_file) as tx_out_file:
              cl = [config_utils.get_program("bowtie", config)]
              cl += _bowtie_args_from_config(config)
              cl += extra_args if extra_args is not None else []
              cl += ["-q",
                     "-v", config["algorithm"]["max_errors"],
                     "-k", 1,
                     "-X", 2000, # default is too selective for most data
                     "--best",
                     "--strata",
                     "--sam",
                     ref_file]
              if pair_file:
                  cl += ["-1", fastq_file, "-2", pair_file]
              else:
                  cl += [fastq_file]
              cl += [tx_out_file]
              cl = [str(i) for i in cl]
              do.run(cl)
      return out_file
  
new_contents: """Next gen sequence alignments with Bowtie (http://bowtie-bio.sourceforge.net).
  """
  import os
  
  from bcbio.pipeline import config_utils
  from bcbio.utils import file_exists
  from bcbio.distributed.transaction import file_transaction
  from bcbio.provenance import do
  
  galaxy_location_file = "bowtie_indices.loc"
  
  def _bowtie_args_from_config(config):
      """Configurable high level options for bowtie.
      """
      qual_format = config["algorithm"].get("quality_format", None)
      if qual_format is None or qual_format.lower() == "illumina":
          qual_flags = ["--phred64-quals"]
      else:
          qual_flags = []
      multi_mappers = config["algorithm"].get("multiple_mappers", True)
      multi_flags = ["-M", 1] if multi_mappers else ["-m", 1]
      cores = config.get("resources", {}).get("bowtie", {}).get("cores", None)
      num_cores = config["algorithm"].get("num_cores", 1)
      core_flags = ["-p", str(num_cores)] if num_cores > 1 else []
      return core_flags + qual_flags + multi_flags
  
  def align(fastq_file, pair_file, ref_file, out_base, align_dir, data,
            extra_args=None, names=None):
      """Do standard or paired end alignment with bowtie.
      """
      config = data['config']
      out_file = os.path.join(align_dir, "%s.sam" % out_base)
      if not file_exists(out_file):
          with file_transaction(out_file) as tx_out_file:
              cl = [config_utils.get_program("bowtie", config)]
              cl += _bowtie_args_from_config(config)
              cl += extra_args if extra_args is not None else []
              cl += ["-q",
                     "-v", config["algorithm"]["max_errors"],
                     "-k", 1,
                     "-X", 2000, # default is too selective for most data
                     "--best",
                     "--strata",
                     "--sam",
                     ref_file]
              if pair_file:
                  cl += ["-1", fastq_file, "-2", pair_file]
              else:
                  cl += [fastq_file]
              cl += [tx_out_file]
              cl = [str(i) for i in cl]
              do.run(cl, "Running Bowtie on %s and %s." % (fastq_file, pair_file), None)
      return out_file
  
subject: Use do.run properly.