Refurbish germline processing with ONT data

[holtgrewe]

Is your feature request related to a problem? Please describe. We have some code for processing of ONT long-read data.

Describe the solution you'd like Make the code paths functional again and ensure that the code is up to standard with tests.

Describe alternatives you've considered N/A

Additional context N/A

[holtgrewe]

Implementation Steps

• [ ] ngs_mapping
  • [ ] minimap2
  • [ ] other step parts for QC
• [ ] variant_calling
  • [ ] clair3
  • [ ] other step parts for QC
• [ ] wgs_sv_calling
  • [ ] sniffles2
• [ ] varfish_export
  • [ ] mehari, will probably need a patch