Issue
Error while trying to validate empty CNV files:
[I 220517 15:24:52] ... checking genomebuild consistency ...
Traceback (most recent call last):
File "MINICONDA/bin/cubi-tk", line 33, in <module>
sys.exit(load_entry_point('cubi-tk', 'console_scripts', 'cubi-tk')())
File "PATH/cubi-tk/cubi_tk/__main__.py", line 123, in main
res = cmds[args.cmd](args, parser, subparsers.choices[args.cmd] if args.cmd else None)
File "PATH/cubi-tk/cubi_tk/snappy/__init__.py", line 97, in run
return args.snappy_cmd(args, parser, subparser)
File "PATH/cubi-tk/cubi_tk/snappy/varfish_upload.py", line 263, in run
return SnappyVarFishUploadCommand(args).execute()
File "PATH/cubi-tk/cubi_tk/snappy/varfish_upload.py", line 180, in execute
self._process_dataset(dataset)
File "PATH/cubi-tk/cubi_tk/snappy/varfish_upload.py", line 254, in _process_dataset
varfish_cli_main(args[1:])
File "MINICONDA/lib/python3.8/site-packages/varfish_cli/__main__.py", line 109, in main
res = cmds[args.cmd](
File "MINICONDA/lib/python3.8/site-packages/varfish_cli/case/__init__.py", line 31, in run
return args.case_cmd(config, toml_config, args, parser, subparser)
File "MINICONDA/lib/python3.8/site-packages/varfish_cli/case/create_case_import.py", line 861, in run
return CaseImporter(config).run()
File "MINICONDA/lib/python3.8/site-packages/varfish_cli/case/create_case_import.py", line 281, in run
self._check_genomebuild_consistency()
File "MINICONDA/lib/python3.8/site-packages/varfish_cli/case/create_case_import.py", line 433, in _check_genomebuild_consistency
line = inputf.readline().splitlines(keepends=False)[0].split("\t")
To Reproduce
Steps to reproduce the behavior:
Go to 'NAMSE' directory
Run cubi-tk snappy varfish-upload --min-batch 210 --yes <UUID>
Batch contains empty file for XHMM:
.gts.tsv.gz
Issue Error while trying to validate empty CNV files:
To Reproduce Steps to reproduce the behavior:
cubi-tk snappy varfish-upload --min-batch 210 --yes <UUID>
Batch contains empty file for XHMM:.gts.tsv.gz
.feature-effects.tsv.gz
Expected behavior Expected to validate header as to check the pipeline ran correctly. Ignore line if file is contains no entries.