I am working on number 5 (HV DRM) as I think there's a need for a non-consensus based HIV DRM pipeline and number 1 (isolate denovo; which I call targeted viral denovo).

I think that HIV DRM with de novo is something that you could also integrate in the viralrecon pipeline, unless you need to have your own for some reason

The HIV DRM pipeline would theoretically touch both arms of viralrecon, denovo and mapping. There's a bunch of preprocessing steps that need to be performed before that as well. Also I think due to the public health importance of HIV and the impact of calling DRM, it should be it's own dedicated pipeline. I would make the same argument for wasterwater pipeline, frejya has recently been updated to support more organisms and on top of this there are other tools for wastewater analysis (each software has it's own pros/cons which necessitates their incorporation.

I think that if the pipeline is maintained and the tools are reliable, there's no need to have specific pipeline because it's important for public health... In Spain we have been solving public health outbreaks since 2020 using viralrecon. If there's enough support and validation with HIV DRM, I don't see the problem of having all together. For a bioinformatics unit that performs analysis of SARS, Flu, MPXV, Hanta, HIV, Crimea, Measles, Rabies and a bunch of viruses more, for public health outbreak response, having a all-in-one pipeline that can be tuned with params is much more easier... As I said, if the community prefers to keep viralrecon simple and generic, I don't have any problem of doing this all-in-one in our fork.

That's fair enough, I think if the community prefers the current setup then it settles it.