And then my new best friend also compiled this list of subworkflows that may not meet the complexity to be called a subworkflow: https://github.com/nf-core/modules/issues/11075 this also requires humans to double check. Context, for those not in the maintainers call: we have subworkflows that are relatively thin wrappers around modules. This causes that each time some brave soul (@Matthias De Smet) is updating samtools or some other core module, that not only 35 modules need updating but also 20 subworkflows. We therefore want to review if all these subworkflows still meet the criteria to be a subworkflow or if some of these may need to be retired. Rough rule of thumb 3 tools or have reasonably complex channel operations. Functions that can be repurposed could possibly also moved to a plugin and not live on in a shared subworkflow

I think we could go ahead and let claude open the PRs to deprecate most all of them and probably add the align + qc sbwf?