code: def get_patient_vcf(job, patient_dict):
      
      temp = job.fileStore.readGlobalFile(patient_dict['mutation_vcf'],
                                          os.path.join(os.getcwd(), 'temp.gz'))
      if is_gzipfile(temp):
          outfile = job.fileStore.writeGlobalFile(gunzip(temp))
          job.fileStore.deleteGlobalFile(patient_dict['mutation_vcf'])
      else:
          outfile = patient_dict['mutation_vcf']
      return outfile
docs: Convenience function to get the vcf from the patient dict
  
      :param dict patient_dict: dict of patient info
      :return: The vcf
      :rtype: toil.fileStore.FileID