[FEATURE REQUEST] Full pipeline execution

[valentynbez]

Problem
Assuming the end goal of tool usage is to cluster sequences, the user must call 3 separate commands, which produce intermediate files. For user convenience purposes, it would be great to have a single command that leads to a final goal, similar to MMseqs2 workflows.

Proposed solution
Create i.e. cluster-sequences command, that executes necessary steps and produces a file with clusters.