fix variant_filtering subworkflow

[kubranarci]

Description of the bug

• params.exclude_expression != null | params.include_expression != null
• fix indexing
• add a way to filter out SV variants when performing small variant benchmarking

Command used and terminal output

Relevant files

No response

System information

No response

[kubranarci]

include_expression = '(ILEN >= -5 && ILEN <= 5)' is an example on how to limit variant sizes in small variant benchmarking. bcftools filter will be used as well