From c758568d016fe420f71babcb3421bb0e507e96f3 Mon Sep 17 00:00:00 2001 From: adRn-s Date: Thu, 19 Sep 2024 13:19:57 +0200 Subject: [PATCH] tidy-up --- BRB/run.py | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/BRB/run.py b/BRB/run.py index b72bd73..1b6c272 100755 --- a/BRB/run.py +++ b/BRB/run.py @@ -63,7 +63,7 @@ def validate_fcid_with_stats(ctx, param, value): "--stats", required=False, is_flag=True, - help='Standalone run, will not run any pipelines. Requires --fcid to indicate target.' + help='Standalone run, use only on finished flowcells. Requires --fcid to indicate target.' ) @click.option('--fcid', callback=validate_fcid_with_stats, help='Flowcell ID to push stats.') def run_brb(configfile, stats, fcid): @@ -89,14 +89,13 @@ def run_brb(configfile, stats, fcid): else: # Push stats on-demand - log.info(f"Pushing stats for flowcell: {fcid}") d = [d for d in glob.glob("{}/*/fastq.made".format(config.get('Paths', 'baseData'))) if fcid in d] dual_lane = len(d) == 2 if len(d) == 0: - log.error(f"No fastq.made files found for {fcid}") + print(f"ERROR: No fastq.made files found for {fcid}") return # Exit BRB if no files found. elif len(d) > 2: - log.error(f"How many lanes does {fcid} have?!") + print(f"ERROR: How many lanes does {fcid} have?!") return # Exit BRB this error shouldn't happen at all. config.set('Options','runID',d[0].split("/")[-2]) @@ -111,14 +110,11 @@ def run_brb(configfile, stats, fcid): if not dual_lane: logFile = Path(config['Paths']['logPath'], config.get('Options','runID') + '.log') else: - logFile = Path(config['Paths']['logPath'], config.get('Options','runID')[:-1] + '_both' + '.log') + logFile = Path(config['Paths']['logPath'], config.get('Options','runID')[:-1] + 'both' + '.log') print(f"Logging into: {logFile}") setLog(logFile) - - if dual_lane: - log.info("Same log-file is being used for both lanes. Hopefully this is not too confusing :$") - - + log.info(f"Pushing stats for flowcell: {fcid}") + # Process each group's data, ignore cases where the project isn't in the lanes being processed process_data(config, ParkourDict)