Add genome rotation step to start chromosomes at dnaA

[Daniel-VM]

Description of feature

Description

Add a post-assembly step to rotate circular bacterial chromosomes so that they start at the dnaA gene. This is useful for consistent genome comparisons and annotations.

Goal

• Choose between dnaapler or circlator fixstart for rotation
• Integrate the rotation step after polishing
• Apply only to circular assemblies (check with gfastats or assembler metadata)
• Add test data and document output changes

Depends on: #204 & #211

[mlarjim]

Circlator is not supported anymore, so dnaapler is the most suitable app
By default, Unicycler and Dragonflye rotate the assembly