Hey, people at our site need to update the versions on all samtools subcommands, given there are 30 subcommands, they wanted to do it in one PR. I think this will mess up the CI checks right, and maybe be more complicated that a PR for each module. What is the best practice?

way ahead of you https://github.com/nf-core/modules/pull/10654

Great! Glad it works like that in one :)