code: def sort_bamfile(job, bamfile, sample_type, univ_options, samtools_options):
      work_dir = os.getcwd()
      in_bamfile = ''.join([sample_type, '.bam'])
      out_bamfile = '_'.join([sample_type, 'sorted.bam'])
      input_files = {
          in_bamfile: bamfile}
      input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
      parameters = ['sort',
                    '-o', docker_path(out_bamfile),
                    '-O', 'bam',
                    '-T', 'temp_sorted',
                    '-@', str(samtools_options['n']),
                    input_files[in_bamfile]]
      docker_call(tool='samtools', tool_parameters=parameters, work_dir=work_dir,
                  dockerhub=univ_options['dockerhub'], tool_version=samtools_options['version'])
      job.fileStore.deleteGlobalFile(bamfile)
      job.fileStore.logToMaster('Ran samtools-sort on %s:%s successfully'
                                % (univ_options['patient'], sample_type))
      return job.fileStore.writeGlobalFile(out_bamfile)