Help manual is missing options

[danidey]

Describe the bug When trying to import GRCh38 data, the following error occurs: [E 230329 14:36:33 create_case_import:312] Inconsistent genome build from file: GRCh38 and from args: GRCh37

Using varfish-cli --help only lists the following options:

positional arguments:
  {case,varannos}
    case                Work with cases.
    varannos            Work with varannos module.

optional arguments:
  -h, --help            show this help message and exit
  --verbose             Increase verbosity.
  --version             show program's version number and exit

Basic Configuration:
  --no-verify-ssl       Disable HTTPS SSL verification
  --config CONFIG       Path to configuration file.
  --varfish-server-url VARFISH_SERVER_URL
                        VarFish server URL key to use, defaults to env VARFISH_SERVER_URL.
  --varfish-api-token VARFISH_API_TOKEN
                        VarFish API token to use, defaults to env VARFISH_API_TOKEN.

The option --genomebuild can be found in the source code, but it is not listed when using the help function. Especially when more users are switching to hg38, this option is going to be needed.

To Reproduce Steps to reproduce the behavior:

1. Use GRCh38 when annotating vcf files
2. Try to load into varfish using varfish-cli

Expected behavior Amend help function to show all available arguments.

[holtgrewe]

The upcoming version will be be better in terms of self-documentation:

varfish-cli importer caseimportinfo-create --help

 Usage: varfish-cli importer caseimportinfo-create [OPTIONS] PROJECT_UUID                                                            
                                                   [PATHS]...                                                                        

╭─ Arguments ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ *    project_uuid      UUID        UUID of project to list cases for [default: None] [required]                                   │
│      paths             [PATHS]...  Path(s) to files to use for the import. Must include PED, and annotation TSV files             │
│                                    [default: None]                                                                                │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --strip-family-regex                        TEXT             Regular expression to process family name with [default: ^FAM_]      │
│ --case-name-suffix                          TEXT             Suffix to append to case name                                        │
│ --force-fresh           --no-force-fresh                     Force using fresh case import even if old draft found                │
│                                                              [default: no-force-fresh]                                            │
│ --resubmit              --no-resubmit                        Force resubmission of cases in submit state [default: no-resubmit]   │
│ --genomebuild                               [GRCh37|GRCh38]  The genome build (GRCh37/GRCh38) of this case, defaults to GRCh37.   │
│                                                              [default: GRCh37]                                                    │
│ --help                                                       Show this message and exit.                                          │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯