Finer-grained control over analysis regions

[fellen31]

Description of feature

Currently, there's one --bed input parameter that controls SNV-calling regions, mosdepth QC, methylation pileups and that filters SV-calls. But there are cases where someone would for example like to use --bed to remove variants on unplaced contigs, while still doing QC over all regions of the genome (using mosdepth's --by 1000 parameter and not --by bedfile.bed).

The filtering should be done as early as possible in most cases, but for CG in Stockholm we also need to be able to keep all variants to the end, before making a final filtering (clinical set of variants) that is output together with all the other (research set) variants.

Suggest we could have individual parameters for the different uses of a BED-file, that are default set to params.bed but can be overwritten, e.g.:

params.bed                        = null
params.qc_regions                 = params.bed ? params.bed : null
params.snv_calling_regions        = params.bed ? params.bed : null
params.methylation_pilups_regions = params.bed ? params.bed : null

etc.