[User Story] Update local modules to nf-core

[fellen31]

Description of feature

As a pipeline developer, I want to update all possible local modules to nf-core modules, since local modules are harder to maintain, test and keep up to date.

Tracked issues:

• Remove or replace bcftools/fillfromfasta with nf-core module #161
• Remove or replace bcftools/filltags with nf-core module #341
• Remove bcftools/view_regions.nf #299
• Remove or replace build_intervals with nf-core module
• Remove or replace echtvar/anno with nf-core module #286
• Remove or replace echtvar/encode with nf-core module #287
• Remove or replace hiphase with nf-core module #193
• Remove or replace modkit/pileup with nf-core module #165
• Remove or replace pacbio/hificnv with nf-core module #199
• Remove or replace split_bed_chunks with nf-core module
• Remove or replace whatshap/haplotag with nf-core module #285
• Remove or replace whatshap/phase with nf-core module #194
• Remove or replace whatshap/stats with nf-core module #284
• Remove CONVERT_ONT_READNAMES #237
• Remove or replace cramino with nf-core module #288
• Remove or replace dipcall with nf-core module #187
• Remove or replace fqcrs with nf-core module #338
• Replace TRGT with another caller #139
• Remove or replace yak with nf-core module #289