Can a process resource limits somehow be changed to increase by the number of inputs?

It depends what you mean. Imagine a process that takes one or more VCF files and you have the input channel

tuple val(meta), path(vcf)

you should be able to do:

cpu = { vcf instanceof List ? vcf.size() * 2 : 2 }

And this would give you 2 CPUs per input vcf

Formulated differently, it can be calculated (because closures are supported) from things known at process submission time.

ohhh that is amazing, thank you both.