Enable multiple assembler runs by default and compare results

[Daniel-VM]

Description of feature

Description

Update the pipeline to allow running multiple assemblers in parallel (e.g., Flye, MEGAHIT, Trycycler) followed by polishing, so users can compare results using tools like QUAST and BUSCO.

Goal

• Add a config setting (e.g., --run_multiple_assemblers)
• Ensure assemblies go through polishing stages
• Summarize results in QUAST and BUSCO reports for comparison
• Provide documentation

Note: This depends on having more than one assembler for each short, long, and hybrid assembly mode.