From 764cd85cb41444c196bcf01c8a58d74631a476a1 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Fri, 21 Oct 2011 11:37:02 -0700 Subject: [PATCH] Yes generate regular gerald config file. --- htsworkflow/pipelines/retrieve_config.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py index 2292cb9..48b581e 100644 --- a/htsworkflow/pipelines/retrieve_config.py +++ b/htsworkflow/pipelines/retrieve_config.py @@ -320,15 +320,15 @@ def saveConfigFile(options): genome_map = constructMapperDict(available_genomes) logging.debug('available genomes: %s' % ( unicode( genome_map.keys() ),)) - #config = format_gerald_config(options, flowcell_info, genome_map) - # - #if options.output_filepath is not None: - # outstream = open(options.output_filepath, 'w') - # logging.info('Writing config file to %s' % (options.output_filepath,)) - #else: - # outstream = sys.stdout - # - #outstream.write(config) + config = format_gerald_config(options, flowcell_info, genome_map) + + if options.output_filepath is not None: + outstream = open(options.output_filepath, 'w') + logging.info('Writing config file to %s' % (options.output_filepath,)) + else: + outstream = sys.stdout + + outstream.write(config) if options.sample_sheet is None: pass -- 2.30.2