sys.exit(1) # Set up and run pipeline pipeline = Pipeline.PipelineRunner(runner,max_concurrent_jobs=options.max_concurrent_jobs, jobCompletionHandler=JobCleanup, groupCompletionHandler=lambda group,jobs, email=options.email_addr: SendReport(email,group,jobs)) for data_dir in data_dirs: # Get for this directory print "Collecting data from %s" % data_dir if options.input_type == "solid": run_data = Pipeline.GetSolidDataFiles(data_dir,pattern=options.pattern) elif options.input_type == "solid_paired_end": run_data = Pipeline.GetSolidPairedEndFiles(data_dir,pattern=options.pattern) elif options.input_type == "fastq": run_data = Pipeline.GetFastqFiles(data_dir,pattern=options.pattern) elif options.input_type == "fastqgz": run_data = Pipeline.GetFastqGzFiles(data_dir,pattern=options.pattern) else: logging.error("Unknown input type: '%s'" % options.input_type) sys.exit(1) # Add jobs to pipeline runner (up to limit of max_total_jobs) for data in run_data: if options.max_total_jobs > 0 and pipeline.nWaiting() == options.max_total_jobs: print "Maximum number of jobs queued (%d)" % options.max_total_jobs break label = os.path.splitext(os.path.basename(data[0]))[0] group = os.path.basename(data_dir) # Set up argument list for script args = [] if script_args:
# Set up and run pipeline pipeline = Pipeline.PipelineRunner( runner, max_concurrent_jobs=options.max_concurrent_jobs, jobCompletionHandler=JobCleanup, groupCompletionHandler=lambda group, jobs, email=options.email_addr: SendReport(email, group, jobs)) for data_dir in data_dirs: # Get for this directory print "Collecting data from %s" % data_dir if options.input_type == "solid": run_data = Pipeline.GetSolidDataFiles(data_dir) elif options.input_type == "solid_paired_end": run_data = Pipeline.GetSolidPairedEndFiles(data_dir) elif options.input_type == "fastq": run_data = Pipeline.GetFastqFiles(data_dir) else: logging.error("Unknown input type: '%s'" % options.input_type) sys.exit(1) # Add jobs to pipeline runner (up to limit of max_total_jobs) for data in run_data: if options.max_total_jobs > 0 and pipeline.nWaiting( ) == options.max_total_jobs: print "Maximum number of jobs queued (%d)" % options.max_total_jobs break label = os.path.splitext(os.path.basename(data[0]))[0] group = os.path.basename(data_dir) # Set up argument list for script args = [] if script_args: for arg in script_args: