Port local modules to nf-core/modules

[georgiakes]

Description of feature

• bcftools/reheader
• bcftools/rename
• bgzip/tabix
• sort_bed -> gnu/sort
• subtract_vcf -> bcftools/isec (SV analyser output is not a VCF file )
• variant_extractor -> new module: VARIANT-EXTRACTOR modules#9996
• reformat_header -> nf-core/gawk
• vcf_to_csv -> gatk4/variantstotable
• publish_processed_vcfs -> ideally deleted (TBD)

[kubranarci]

bcftools/reheader, bcftools/rename, bgzip_tabix are part of #267

[georgiakes]

sort_bed and reformat_header in #268

[Gab-23]

Ciao! It's the guys from Istituto Europeo di Oncologia!
We will start working on this issue during the Hack-a-thon!

[kubranarci]

fix FIX_VCF_PREFIX for #287

[sbreuch]

variant_extractor module has been merged into nf-core/modules via nf-core/modules#10894 (closes nf-core/modules#9996).