if you only specify output_dir in the looper config, you get this error:
Traceback (most recent call last):
File "/home/nsheff/.local/bin/looper", line 8, in <module>
sys.exit(main())
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/looper.py", line 1200, in main
CheckerOld(prj)(flags=args.flags)
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/looper.py", line 201, in __call__
files_by_flag = fetch_flag_files(prj=self.prj, flags=flags)
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/utils.py", line 65, in fetch_flag_files
folder = sample_folder(prj, s)
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/utils.py", line 133, in sample_folder
return os.path.join(prj.results_folder, sample[prj.sample_table_index])
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/project.py", line 65, in __getattr__
return getattr(self.prj, item)
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/project.py", line 214, in results_folder
return self._out_subdir_path(RESULTS_SUBDIR_KEY, default="results_pipeline")
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/project.py", line 235, in _out_subdir_path
parent = getattr(self, OUTDIR_KEY)
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/project.py", line 174, in output_dir
return self._extra_cli_or_cfg(OUTDIR_KEY, strict=True)
File "/home/nsheff/.local/lib/python3.8/site-packages/looper/project.py", line 201, in _extra_cli_or_cfg
raise MisconfigurationException(
looper.exceptions.MisconfigurationException: 'output_dir' is missing. Provide it in the 'looper' section of the project configuration file
if you only specify
output_dir
in the looper config, you get this error: