Given the limited BDBV diversity, viralrecon might be the better choice here as you don’t necessarily need an untargeted approach. The NGS part of viralrecon and viralmetagenome overlap quite largely actually, the difference comes with viralrecon adding support for tools like nextstrain for quick lineage classification. If you believe that a single reference genome isn’t sufficient because of for instance recombination events, then yeah #C0905QCFTPE will be what you need. But given that the team is already using it, that will likely not be the case. I believe if for viralrecon if you have a good decontamination dataset (kraken2 based) as well as

--nextclade_dataset_name nextstrain/ebola/bdbv

--fasta NC_014373.1.fasta

.... you know where to get everything. Might be interesting to set up real a config like we have for other viruses to make it easier as well for ur collaborators. https://github.com/nf-core/configs/blob/master/conf/pipeline/viralrecon/genomes.config