def run_phlat(job, fastqs, sample_type, univ_options, phlat_options):
    """
    This module will run PHLAT on SAMPLE_TYPE fastqs.

    ARGUMENTS -- <ST> depicts the sample type. Substitute with 'tumor_dna',
                 'normal_dna', or 'tumor_rna'
    1. fastqs: Dict of list of input WGS/WXS fastqs
         fastqs
              +- '<ST>': [<JSid for 1.fastq> , <JSid for 2.fastq>]
    2. sample_type: string of 'tumor' or 'normal'
    3. univ_options: Dict of universal arguments used by almost all tools
         univ_options
                +- 'dockerhub': <dockerhub to use>
    4. phlat_options: Dict of parameters specific to phlat
         phlat_options
              |- 'index_tar': <JSid for the PHLAT index tarball>
              +- 'n': <number of threads to allocate>

    RETURN VALUES
    1. output_file: <JSid for the allele predictions for ST>

    This module corresponds to nodes 5, 6 and 7 on the tree
    """
    job.fileStore.logToMaster('Running phlat on %s:%s' % (univ_options['patient'], sample_type))
    work_dir = job.fileStore.getLocalTempDir()
    fq_extn = '.gz' if fastqs['gzipped'] else ''
    input_files = {
        'input_1.fastq' + fq_extn: fastqs[sample_type][0],
        'input_2.fastq' + fq_extn: fastqs[sample_type][1],
        'phlat_index.tar.gz': phlat_options['index_tar']}
    input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
    parameters = ['-1', input_files['input_1.fastq'],
                  '-2', input_files['input_2.fastq'],
                  '-index', input_files['phlat_index'],
                  '-b2url', '/usr/local/bin/bowtie2',
                  '-tag', sample_type,
                  '-e', '/home/phlat-1.0',  # Phlat directory home
                  '-o', '/data',  # Output directory
                  '-p', str(phlat_options['n'])]  # Number of threads
    docker_call(tool='phlat', tool_parameters=parameters, work_dir=work_dir,
                dockerhub=univ_options['dockerhub'])
    output_file = job.fileStore.writeGlobalFile(''.join([work_dir, '/', sample_type, '_HLA.sum']))
    return output_file
This module will run PHLAT on SAMPLE_TYPE fastqs.

    ARGUMENTS -- <ST> depicts the sample type. Substitute with 'tumor_dna',
                 'normal_dna', or 'tumor_rna'
    1. fastqs: Dict of list of input WGS/WXS fastqs
         fastqs
              +- '<ST>': [<JSid for 1.fastq> , <JSid for 2.fastq>]
    2. sample_type: string of 'tumor' or 'normal'
    3. univ_options: Dict of universal arguments used by almost all tools
         univ_options
                +- 'dockerhub': <dockerhub to use>
    4. phlat_options: Dict of parameters specific to phlat
         phlat_options
              |- 'index_tar': <JSid for the PHLAT index tarball>
              +- 'n': <number of threads to allocate>

    RETURN VALUES
    1. output_file: <JSid for the allele predictions for ST>

    This module corresponds to nodes 5, 6 and 7 on the tree