varfish-upload: allow empty SV files

[eudesbarbosa]

Issue
XHMM might return an empty VCF for a CNV analysis if it considers that sample is an outlier. This should not stop VarFish upload.
Call:

$ cubi-tk snappy varfish-upload --min-batch 201 <UUID> --yes
[I 220311 09:11:27] Starting cubi-tk varfish-upload
[I 220311 09:11:27]   args: Namespace(answer_yes=True, base_path=PosixPath('/data/gpfs-1/work/projects/medgen_namse/2019-07-03_NAMSE_Translate/GRCh37'), cmd='snappy', config=None, min_batch=201, project=['<UUID>'], samples='', snappy_cmd=<function run at 0x149010a35d30>, sodar_api_token=None, sodar_server_url=None, steps=('ngs_mapping', 'targeted_seq_cnv_export', 'variant_export', 'wgs_cnv_export', 'wgs_sv_export'), varfish_api_token=None, varfish_config=None, varfish_server_url=None, verbose=False)
[I 220311 09:11:27] Loading data sets from /data/.../GRCh37/.snappy_pipeline/config.yaml
[I 220311 09:11:27] Loaded 4 data sets, 2 with SODAR UUID
[I 220311 09:11:27] Processing Dataset <UUID>
[I 220311 09:11:27]   loading from /data/...namse
                ...
[I 220311 09:11:28] ... checking genomebuild consistency ...
Traceback (most recent call last):
  File "/PATH/work/miniconda3.barbosae_c/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 119, 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 89, 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 "/PATH/work/miniconda3.barbosae_c/lib/python3.8/site-packages/varfish_cli/__main__.py", line 109, in main
    res = cmds[args.cmd](
  File "/PATH/work/miniconda3.barbosae_c/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 "/PATH/work/miniconda3.barbosae_c/lib/python3.8/site-packages/varfish_cli/case/create_case_import.py", line 861, in run
    return CaseImporter(config).run()
  File "/PATH/work/miniconda3.barbosae_c/lib/python3.8/site-packages/varfish_cli/case/create_case_import.py", line 281, in run
    self._check_genomebuild_consistency()
  File "/PATH/work/miniconda3.barbosae_c/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")
IndexError: list index out of range

Expected behavior
Either the code will gracefully stop and ask user if it is acceptable to have an empty file; or just throw a warning if flag --allow-empty-sv-files is enabled.

Additional context
Relevant code: https://github.com/bihealth/varfish-cli/blob/e0627cf42ff1774f533ca0cb932b0c18c61960df/varfish_cli/case/create_case_import.py#L433