diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_nov.py b/deep_sequencing_unit/source/Jython/createSampleSheet_nov.py index 6e76f4ec9ebda292e52b3f227ecc38a7ce112644..a6da0077a0ab9d39b3c075d9fab26ea1da410162 100644 --- a/deep_sequencing_unit/source/Jython/createSampleSheet_nov.py +++ b/deep_sequencing_unit/source/Jython/createSampleSheet_nov.py @@ -114,6 +114,11 @@ def parseOptions(logger): default=False, action='store_true', help='Verbose debug logging. Default: False') + parser.add_option('-v', '--verbose', + dest='verbose', + default=False, + action='store_true', + help='Write Sample Sheet to stout. Default: False') (options, args) = parser.parse_args() @@ -143,7 +148,6 @@ def readConfig(logger): configMap = {} - logger.info('Reading config file') configParameters = parseConfigurationFile(logger) configMap['facilityName'] = configParameters.get(GENERAL, 'facilityName') @@ -366,10 +370,12 @@ def writeSampleSheet(flowCellName, sampleSheetDict, sortedSampleSheetList, myopt try: with open(myFile, 'w') as sampleSheetFile: for listElement in sortedSampleSheetList: + if myoptions.verbose: + print sampleSheetDict[listElement][0] sampleSheetFile.write(sampleSheetDict[listElement][0] + newline) logger.info('Writing file ' + myFile) - print ('Written ' + myFile) + except IOError: logger.error('File error: ' + str(err)) print ('File error: ' + str(err)) @@ -398,7 +404,6 @@ def main(): createHiseqSampleSheet(laneParentDict, flowCellDict, configMap, service, logger, myoptions) logout(service, logger) - print('DONE') if __name__ == "__main__": main()