I've been thinking about that! @Ammar Aziz @Sam Wilkinson. nf-core/bacass contains several

<software>_args

params github.com/nf-core/bacass/blob/…/nextflow.config#… that can be use through CLI. If it makes viralrecon easier for the community I can think about the most important and customizable softwares through the pipeline and expose their params in a more general way, along with the already defined specific ones (min_depth, min_allele_frequency...). I'll try to think about a good way to do it and discuss it in the next viralrecon development meeting!

That's a good solution without having to expose 100 params for each tool. But I think some params are critical and should be exposed to the user.

#C0905QCFTPE does the same thing, key params that are used across multiple tools, are through a ‘global’ param in addition to having software specific params

I'll have a look at viralmetagenome too then! Thanks!