Gaius-Augustus/BRAKER4 ? reverse-engineered prompt

Build me a Snakemake workflow for genome annotation that works like BRAKER4.

I want to give it a genome plus evidence files in a simple samples.csv, then run one command and have it do the whole gene prediction pipeline for me. It should support multiple genomes in one run, restart cleanly if something fails, and work with Singularity containers so I do not have to install the bioinformatics tools myself.

Please include the main modes for RNA Seq, protein evidence, both together, genome only, and IsoSeq if the data is there. If the genome is not already masked, have it handle repeat masking automatically. If transcript evidence is available, add UTR decoration and basic ncRNA prediction as an optional setting. I also want the workflow to produce the usual output files, some QC like BUSCO style checks, and be easy to run locally or on SLURM.

If anything is unclear, look up the current tool docs online and make sensible defaults.