code: def run_star(job, fastqs, univ_options, star_options):
      assert star_options['type'] in ('star', 'starlong')
      job.fileStore.logToMaster('Running STAR on %s' %univ_options['patient'])
      work_dir = job.fileStore.getLocalTempDir()
      input_files = {
          'rna_cutadapt_1.fastq': fastqs['rna_cutadapt_1.fastq'],
          'rna_cutadapt_2.fastq': fastqs['rna_cutadapt_2.fastq'],
          'star_index.tar.gz': star_options['index_tar']}
      input_files = get_files_from_filestore(job, input_files, work_dir,
                                             docker=True)
      parameters = ['--runThreadN', str(star_options['n']),
                    '--genomeDir', input_files['star_index'],
                    '--outFileNamePrefix', 'rna',
                    '--readFilesIn',
                    input_files['rna_cutadapt_1.fastq'],
                    input_files['rna_cutadapt_2.fastq'],
                    '--outSAMattributes', 'NH', 'HI', 'AS', 'NM', 'MD',
                    '--outSAMtype', 'BAM', 'SortedByCoordinate',
                    '--quantMode', 'TranscriptomeSAM',
                    '--outSAMunmapped', 'Within']
      if star_options['type'] == 'star':
          docker_call(tool='star', tool_parameters=parameters, work_dir=work_dir,
                      dockerhub=univ_options['dockerhub'])
      else:
          docker_call(tool='starlong', tool_parameters=parameters, work_dir=work_dir,
                      dockerhub=univ_options['dockerhub'])
      output_files = defaultdict()
      for bam_file in ['rnaAligned.toTranscriptome.out.bam',
                       'rnaAligned.sortedByCoord.out.bam']:
          output_files[bam_file] = job.fileStore.writeGlobalFile('/'.join([
              work_dir, bam_file]))
      job.fileStore.deleteGlobalFile(fastqs['rna_cutadapt_1.fastq'])
      job.fileStore.deleteGlobalFile(fastqs['rna_cutadapt_2.fastq'])
      index_star = job.wrapJobFn(index_bamfile,
                                 output_files['rnaAligned.sortedByCoord.out.bam'],
                                 'rna', univ_options, disk='120G')
      job.addChild(index_star)
      output_files['rnaAligned.sortedByCoord.out.bam'] = index_star.rv()
      return output_files