These results exist for 'DEFAULT_SAMPLE_NAME': Read_type
Traceback (most recent call last):
File "/home/drc/pepatac_tutorial//tools/pepatac/pipelines/pepatac.py", line 2779, in <module>
sys.exit(main())
File "/home/drc/pepatac_tutorial//tools/pepatac/pipelines/pepatac.py", line 731, in main
pm.report_result("Read_type", args.single_or_paired)
File "/home/drc/anaconda3/envs/pepatac38/lib/python3.8/site-packages/pypiper/manager.py", line 1615, in report_result
for r in reported_result:
TypeError: 'bool' object is not iterable
pipestat.report returns False if it cannot report the result which then causes an issue in line 1691.
Solution:
-create a new parameter in pypiper that allows the user to toggle force_overwrite and default it to False.
-implement handling a False value instead of crashing pypiper.
I noticed that, when managing pipelines via pypiper, if the results already exist, the pipeline will fail. This is because pypiper uses pipestat to report and does not use
pipestat.report
'sforce_overwrite
parameter: https://github.com/databio/pypiper/blob/8aaede5d75f374fd475573dfd875e3d742c581ea/pypiper/manager.py#L1686-L1692Example of error (while using PEPATAC):
pipestat.report
returnsFalse
if it cannot report the result which then causes an issue in line 1691.Solution: -create a new parameter in pypiper that allows the user to toggle
force_overwrite
and default it to False. -implement handling aFalse
value instead of crashing pypiper.