3 Runfolder.py can generate a xml file capturing all the 'interesting' parameters from a finished pipeline run. (using the -a option). The information currently being captured includes:
7 * start/stop cycle numbers
8 * Firecrest, bustard, gerald version numbers
9 * Eland analysis types, and everything in the eland configuration file.
10 * cluster numbers and other values from the Summary.htm
11 LaneSpecificParameters table.
12 * How many reads mapped to a genome from an eland file
14 The ELAND "mapped reads" counter will also check for eland squashed file
15 that were symlinked from another directory. This is so I can track how
16 many reads landed on the genome of interest and on the spike ins.
18 Basically my subdirectories something like:
21 genomes/hg18/chr*.2bpb <- files for hg18 genome
23 genomes/hg18/VATG.fa.2bp <- symlink to genomes/spikeins
26 runfolder.py can also spit out a simple summary report (-s option)
27 that contains the per lane post filter cluster numbers and the mapped
28 read counts. (The report isn't currently very pretty)
34 from gaworkflow.pipeline import runfolder
35 from gaworkflow.pipeline.runfolder import ElementTree
38 usage = 'usage: %prog [options] runfolder_root_dir'
39 parser = optparse.OptionParser(usage)
40 parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
42 help='turn on verbose mode')
43 parser.add_option('-s', '--summary', dest='summary', action='store_true',
45 help='produce summary report')
46 parser.add_option('-a', '--archive', dest='archive', action='store_true',
48 help='generate run configuration archive')
49 parser.add_option('--run-xml', dest='run_xml',
51 help='specify a run_<FlowCell>.xml file for summary reports')
55 def main(cmdlist=None):
56 parser = make_parser()
57 opt, args = parser.parse_args(cmdlist)
61 root_log = logging.getLogger()
62 root_log.setLevel(logging.INFO)
66 tree = ElementTree.parse(opt.run_xml).getroot()
67 runs.append(runfolder.PipelineRun(xml=tree))
69 runs.extend(runfolder.get_runs(run_dir))
73 print runfolder.summary_report(runs)
75 runfolder.extract_run_parameters(runs)
79 if __name__ == "__main__":
80 sys.exit(main(sys.argv[1:]))