[User Story] Consistent naming of pipeline subworkflows

[fellen31]

Need

As a developer, I want consistent naming of pipeline subworkflows, because it makes developing easier.

Suggested approach

• All subworkflows, their files and configs are called the same
• Subworkflows of same character is named similarly, e.g. all that does calling starts with call and all that annotates starts with annotate

Can be closed when

•  Rename short_variant_calling to call_snvs
• Rename snv_annotation to annotate_snvs
• Rename assembly_variant_calling to call_assembly_variants
• Rename cnv to call_cnvs
• Rename ASSEMBLY/genome_assembly to assemble_genome?
• Rename methylation to methylation_analysis ?
• Rename phasing ?
• Rename prepare_genome to prepare_references (?)
• Rename structural_variant_calling to call_svs

Blockers

No response

Anything else?

No response