TMB module based on vembrane output

This PR adds a TMB calculation module based on the TSV output from vembrane.

Features

Using the parameter bedfile, a path to a BED file can be provided. The BED file should contain three columns without a header covering the chromosome, the start and the end position (as genomic position) to ensure compability with bcftools and PyRanges.
The check_bedfiles controls the structure of the BED file for compability and generates three output files (bed_stats_structure.txt, bed_stats_eligibility.txt and bed_stats_size.txt). The two latter ones are only created, if the BED file covers more than 1 MBp of genetic regions. The generation of these files as optional outputs sets the conditional logic for other modules (e.g. prefiltering of regions using bcftools and TMB calculation) in Nextflow.
If a BED file was provided and the bed_stats_eligibility.txt file exists, TMB calculation will be performed after vembrane TSV output was generated if so desired.

TMB calculation will be performed if the option --calculate_tmb true is provided and the bed_stats_eligibility.txt file exists.
TMB calculation will be performed based on provided thresholds min_af, max_af, min_cov and max_popfreq. Furthermore, a filtering for InDels can be performed by setting the parameter filter_indels to "true".
TMB values will be generated as a .txt file per VCF based on the provided filtering thresholds.
A .png per input file will be created which plots the distribution of variants based on consequence and allele frequency. The .png is not interactive.

Improve the calculcation based on input BAM files, accounting for variants on locally amplified or lost copy-number segments as further QC for allele frequencies of variants, influencing the filtering thresholds.
Generate an alternative VCF-based calculcation module to circumvent TMB underestimation due to filtered variants in the TSV output (e.g. filter_vep), which would be otherwise eligible.
Improve visualization of variant distribution by making the plot interactive.
Collect TMB values per input VCF in a single output file.
Implement results from TMB calculation into the HTML report.
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