def run_strelka_full(job, tumor_bam, normal_bam, univ_options, strelka_options):
    """
    Run strelka on the DNA bams.

    :param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
    :param dict normal_bam: Dict of bam and bai for normal DNA-Seq
    :param dict univ_options: Dict of universal options used by almost all tools
    :param dict strelka_options: Options specific to strelka
    :return: Dict of fsIDs snv and indel prediction files
             output_dict:
                 |-'snvs': fsID
                 +-'indels': fsID
    :rtype: dict
    """
    work_dir = os.getcwd()
    input_files = {
        'tumor.bam': tumor_bam['tumor_dna_fix_pg_sorted.bam'],
        'tumor.bam.bai': tumor_bam['tumor_dna_fix_pg_sorted.bam.bai'],
        'normal.bam': normal_bam['normal_dna_fix_pg_sorted.bam'],
        'normal.bam.bai': normal_bam['normal_dna_fix_pg_sorted.bam.bai'],
        'genome.fa.tar.gz': strelka_options['genome_fasta'],
        'genome.fa.fai.tar.gz': strelka_options['genome_fai'],
        'config.ini.tar.gz': strelka_options['config_file']
    }
    input_files = get_files_from_filestore(job, input_files, work_dir, docker=False)

    for key in ('genome.fa', 'genome.fa.fai', 'config.ini'):
        input_files[key] = untargz(input_files[key + '.tar.gz'], work_dir)
    input_files = {key: docker_path(path) for key, path in input_files.items()}

    parameters = [input_files['config.ini'],
                  input_files['tumor.bam'],
                  input_files['normal.bam'],
                  input_files['genome.fa'],
                  str(job.cores)
                  ]
    docker_call(tool='strelka', tool_parameters=parameters, work_dir=work_dir,
                dockerhub=univ_options['dockerhub'], tool_version=strelka_options['version'])
    output_dict = {}
    for mutation_type in ['snvs', 'indels']:
        output_dict[mutation_type] = job.fileStore.writeGlobalFile(os.path.join(
            work_dir, 'strelka_out', 'results', 'passed.somatic.' + mutation_type + '.vcf'))
    job.fileStore.logToMaster('Ran strelka on %s successfully' % univ_options['patient'])
    return output_dict
def run_strelka_full ( job , tumor_bam , normal_bam , univ_options , strelka_options ) : work_dir = os . getcwd ( ) input_files = { 'tumor.bam' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam' ] , 'tumor.bam.bai' : tumor_bam [ 'tumor_dna_fix_pg_sorted.bam.bai' ] , 'normal.bam' : normal_bam [ 'normal_dna_fix_pg_sorted.bam' ] , 'normal.bam.bai' : normal_bam [ 'normal_dna_fix_pg_sorted.bam.bai' ] , 'genome.fa.tar.gz' : strelka_options [ 'genome_fasta' ] , 'genome.fa.fai.tar.gz' : strelka_options [ 'genome_fai' ] , 'config.ini.tar.gz' : strelka_options [ 'config_file' ] } input_files = get_files_from_filestore ( job , input_files , work_dir , docker = False ) for key in ( 'genome.fa' , 'genome.fa.fai' , 'config.ini' ) : input_files [ key ] = untargz ( input_files [ key + '.tar.gz' ] , work_dir ) input_files = { key : docker_path ( path ) for key , path in input_files . items ( ) } parameters = [ input_files [ 'config.ini' ] , input_files [ 'tumor.bam' ] , input_files [ 'normal.bam' ] , input_files [ 'genome.fa' ] , str ( job . cores ) ] docker_call ( tool = 'strelka' , tool_parameters = parameters , work_dir = work_dir , dockerhub = univ_options [ 'dockerhub' ] , tool_version = strelka_options [ 'version' ] ) output_dict = { } for mutation_type in [ 'snvs' , 'indels' ] : output_dict [ mutation_type ] = job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'strelka_out' , 'results' , 'passed.somatic.' + mutation_type + '.vcf' ) ) job . fileStore . logToMaster ( 'Ran strelka on %s successfully' % univ_options [ 'patient' ] ) return output_dict
Run strelka on the DNA bams.

    :param dict tumor_bam: Dict of bam and bai for tumor DNA-Seq
    :param dict normal_bam: Dict of bam and bai for normal DNA-Seq
    :param dict univ_options: Dict of universal options used by almost all tools
    :param dict strelka_options: Options specific to strelka
    :return: Dict of fsIDs snv and indel prediction files
             output_dict:
                 |-'snvs': fsID
                 +-'indels': fsID
    :rtype: dict