nodes: 0, module; 1, function_definition; 2, function_name:main; 3, parameters; 4, block; 5, expression_statement; 6, comment:# Define Parser object and add to toil; 7, expression_statement; 8, expression_statement; 9, expression_statement; 10, comment:# Store inputs from argparse; 11, expression_statement; 12, comment:# Launch jobs; 13, expression_statement; 14, comment:"""
      This is a Toil pipeline for the UNC best practice RNA-Seq analysis.
      RNA-seq fastqs are combined, aligned, sorted, filtered, and quantified.
  
      Please read the README.md located in the same directory.
      """; 15, assignment; 16, call; 17, assignment; 18, assignment; 19, call; 20, identifier:parser; 21, call; 22, attribute; 23, argument_list; 24, identifier:args; 25, call; 26, identifier:inputs; 27, dictionary; 28, attribute; 29, argument_list; 30, identifier:build_parser; 31, argument_list; 32, attribute; 33, identifier:addToilOptions; 34, identifier:parser; 35, attribute; 36, argument_list; 37, pair; 38, pair; 39, pair; 40, pair; 41, pair; 42, pair; 43, pair; 44, pair; 45, pair; 46, pair; 47, pair; 48, pair; 49, pair; 50, pair; 51, pair; 52, pair; 53, pair; 54, pair; 55, pair; 56, attribute; 57, identifier:startToil; 58, call; 59, identifier:args; 60, identifier:Job; 61, identifier:Runner; 62, identifier:parser; 63, identifier:parse_args; 64, string; 65, attribute; 66, string; 67, attribute; 68, string; 69, attribute; 70, string; 71, attribute; 72, string; 73, attribute; 74, string; 75, attribute; 76, string; 77, attribute; 78, string; 79, attribute; 80, string; 81, attribute; 82, string; 83, attribute; 84, string; 85, attribute; 86, string; 87, attribute; 88, string; 89, attribute; 90, string; 91, attribute; 92, string; 93, attribute; 94, string; 95, attribute; 96, string; 97, None; 98, string; 99, None; 100, string; 101, None; 102, identifier:Job; 103, identifier:Runner; 104, attribute; 105, argument_list; 106, string_content:config; 107, identifier:args; 108, identifier:config; 109, string_content:config_fastq; 110, identifier:args; 111, identifier:config_fastq; 112, string_content:input; 113, identifier:args; 114, identifier:input; 115, string_content:unc.bed; 116, identifier:args; 117, identifier:unc; 118, string_content:hg19.transcripts.fa; 119, identifier:args; 120, identifier:fasta; 121, string_content:composite_exons.bed; 122, identifier:args; 123, identifier:composite_exons; 124, string_content:normalize.pl; 125, identifier:args; 126, identifier:normalize; 127, string_content:output_dir; 128, identifier:args; 129, identifier:output_dir; 130, string_content:rsem_ref.zip; 131, identifier:args; 132, identifier:rsem_ref; 133, string_content:chromosomes.zip; 134, identifier:args; 135, identifier:chromosomes; 136, string_content:ebwt.zip; 137, identifier:args; 138, identifier:ebwt; 139, string_content:ssec; 140, identifier:args; 141, identifier:ssec; 142, string_content:s3_dir; 143, identifier:args; 144, identifier:s3_dir; 145, string_content:sudo; 146, identifier:args; 147, identifier:sudo; 148, string_content:single_end_reads; 149, identifier:args; 150, identifier:single_end_reads; 151, string_content:upload_bam_to_s3; 152, identifier:args; 153, identifier:upload_bam_to_s3; 154, string_content:uuid; 155, string_content:sample.tar; 156, string_content:cpu_count; 157, identifier:Job; 158, identifier:wrapJobFn; 159, identifier:download_shared_files; 160, identifier:inputs
code: def main():
      """
      This is a Toil pipeline for the UNC best practice RNA-Seq analysis.
      RNA-seq fastqs are combined, aligned, sorted, filtered, and quantified.
  
      Please read the README.md located in the same directory.
      """
      # Define Parser object and add to toil
      parser = build_parser()
      Job.Runner.addToilOptions(parser)
      args = parser.parse_args()
      # Store inputs from argparse
      inputs = {'config': args.config,
                'config_fastq': args.config_fastq,
                'input': args.input,
                'unc.bed': args.unc,
                'hg19.transcripts.fa': args.fasta,
                'composite_exons.bed': args.composite_exons,
                'normalize.pl': args.normalize,
                'output_dir': args.output_dir,
                'rsem_ref.zip': args.rsem_ref,
                'chromosomes.zip': args.chromosomes,
                'ebwt.zip': args.ebwt,
                'ssec': args.ssec,
                's3_dir': args.s3_dir,
                'sudo': args.sudo,
                'single_end_reads': args.single_end_reads,
                'upload_bam_to_s3': args.upload_bam_to_s3,
                'uuid': None,
                'sample.tar': None,
                'cpu_count': None}
  
      # Launch jobs
      Job.Runner.startToil(Job.wrapJobFn(download_shared_files, inputs), args)