This is the final module in the pipeline.  It will call the rank boosting R
    script.

    This module corresponds to node 21 in the tree

def boost_ranks(job, isoform_expression, merged_mhc_calls, transgene_out, univ_options,
                rank_boost_options):
    """
    This is the final module in the pipeline.  It will call the rank boosting R
    script.

    This module corresponds to node 21 in the tree
    """
    job.fileStore.logToMaster('Running boost_ranks on %s' % univ_options['patient'])
    work_dir = os.path.join(job.fileStore.getLocalTempDir(), univ_options['patient'])
    os.mkdir(work_dir)
    input_files = {
        'rsem_quant.tsv': isoform_expression,
        'mhci_merged_files.tsv': merged_mhc_calls['mhci_merged_files.list'],
        'mhcii_merged_files.tsv': merged_mhc_calls['mhcii_merged_files.list'],
        'mhci_peptides.faa': transgene_out['transgened_tumor_10_mer_snpeffed.faa'],
        'mhcii_peptides.faa': transgene_out['transgened_tumor_15_mer_snpeffed.faa']}
    input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
    output_files = {}
    for mhc in ('mhci', 'mhcii'):
        parameters = [mhc,
                      input_files[''.join([mhc, '_merged_files.tsv'])],
                      input_files['rsem_quant.tsv'],
                      input_files[''.join([mhc, '_peptides.faa'])],
                      rank_boost_options[''.join([mhc, '_combo'])]
                      ]
        docker_call(tool='rankboost', tool_parameters=parameters, work_dir=work_dir,
                    dockerhub=univ_options['dockerhub'])
        output_files[mhc] = {
            ''.join([mhc, '_concise_results.tsv']):
                job.fileStore.writeGlobalFile(''.join([work_dir, '/', mhc,
                                                       '_merged_files_concise_results.tsv'])),
            ''.join([mhc, '_detailed_results.tsv']):
                job.fileStore.writeGlobalFile(''.join([work_dir, '/', mhc,
                                                       '_merged_files_detailed_results.tsv']))}
    export_results(work_dir, univ_options)
    return output_files