+++ /dev/null
-#!/usr/bin/env python
-"""
-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:
-
- * Flowcell ID
- * run dates
- * start/stop cycle numbers
- * Firecrest, bustard, gerald version numbers
- * Eland analysis types, and everything in the eland configuration file.
- * cluster numbers and other values from the Summary.htm
- LaneSpecificParameters table.
- * How many reads mapped to a genome from an eland file
-
-The ELAND "mapped reads" counter will also check for eland squashed file
-that were symlinked from another directory. This is so I can track how
-many reads landed on the genome of interest and on the spike ins.
-
-Basically my subdirectories something like:
-
-genomes/hg18
-genomes/hg18/chr*.2bpb <- files for hg18 genome
-genomes/hg18/chr*.vld
-genomes/hg18/VATG.fa.2bp <- symlink to genomes/spikeins
-genomes/spikein
-
-runfolder.py can also spit out a simple summary report (-s option)
-that contains the per lane post filter cluster numbers and the mapped
-read counts. (The report isn't currently very pretty)
-"""
-from glob import glob
-import logging
-import optparse
-import os
-import sys
-
-from htsworkflow.pipelines import runfolder
-from htsworkflow.pipelines.runfolder import ElementTree
-
-def make_parser():
- usage = 'usage: %prog [options] runfolder_root_dir'
- parser = optparse.OptionParser(usage)
-
- parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
- default=False,
- help='turn on verbose mode')
- parser.add_option('--dry-run', action='store_true', default=False,
- help="Don't delete anything (in clean mode)")
-
- commands = optparse.OptionGroup(parser, 'Commands')
-
- commands.add_option('-s', '--summary', dest='summary', action='store_true',
- default=False,
- help='produce summary report')
- commands.add_option('-a', '--archive', dest='archive', action='store_true',
- default=False,
- help='generate run configuration archive')
- commands.add_option('--extract-results', action='store_true',
- default=False,
- help='create run-xml summary, compress the eland result files, build srf files and '
- 'copy all that and the Summary.htm file into an archival directory.')
- commands.add_option('-c', '--clean', action='store_true', default=False,
- help='Clean runfolder, preparing it for long-term storage')
- parser.add_option_group(commands)
-
- parser.add_option('-j', '--max-jobs', default=1,
- help='sepcify the maximum number of processes to run '
- '(used in extract-results)')
- parser.add_option('-o', '--output-dir', default=None,
- help="specify the default output directory for extract results")
- parser.add_option('--run-xml', dest='run_xml',
- default=None,
- help='specify a run_<FlowCell>.xml file for summary reports')
- parser.add_option('--site', default=None,
- help='create srf files tagged with the provided site name')
- parser.add_option('-u', '--use-run', dest='use_run', default=None,
- help='Specify which run to use instead of autoscanning '
- 'the runfolder. You do this by providing the final '
- ' GERALD directory, and it assumes the parent '
- 'directories are the bustard and image processing '
- 'directories.')
-
- return parser
-
-def main(cmdlist=None):
- parser = make_parser()
- opt, args = parser.parse_args(cmdlist)
-
- logging.basicConfig()
- if opt.verbose:
- root_log = logging.getLogger()
- root_log.setLevel(logging.INFO)
-
- logging.info('Starting htsworkflow illumina runfolder processing tool.')
- runs = []
- if opt.run_xml:
- # handle ~ shortcut
- opt.run_xml = os.path.expanduser(opt.run_xml)
- tree = ElementTree.parse(opt.run_xml).getroot()
- runs.append(runfolder.PipelineRun(xml=tree))
-
- # look for manually specified run
- if opt.use_run is not None:
- specific_run = runfolder.get_specific_run(opt.use_run)
- if specific_run is not None:
- runs.append(specific_run)
- else:
- logging.warn("Couldn't find a run in %s" % (opt.use_run,))
-
- # scan runfolders for runs
- for run_pattern in args:
- # expand args on our own if needed
- for run_dir in glob(run_pattern):
- runs.extend(runfolder.get_runs(run_dir))
-
- if len(runs) > 0:
- command_run = False
- if opt.summary:
- print runfolder.summary_report(runs)
- command_run = True
- if opt.archive:
- runfolder.extract_run_parameters(runs)
- command_run = True
- if opt.extract_results:
- if opt.dry_run:
- parser.error("Dry-run is not supported for extract-results")
- runfolder.extract_results(runs,
- opt.output_dir,
- opt.site,
- opt.max_jobs)
- command_run = True
- if opt.clean:
- runfolder.clean_runs(runs, opt.dry_run)
- command_run = True
-
- if command_run == False:
- print "You need to specify a command."+os.linesep
- parser.print_help()
- else:
- print "You need to specify some run folders to process..."+os.linesep
- parser.print_help()
-
- return 0
-
-if __name__ == "__main__":
- sys.exit(main(sys.argv[1:]))
projects / htsworkflow.git / blobdiff