Update output to use type dir

[mirpedrol]

We should probably try to do this systematically for all modules 🤔 In this case it was already annotated in the meta yaml:

https://github.com/nf-core/modules/blob/a25abe62ccf3fe3767d2449d8322a35ab62844e0/modules/nf-core/sratools/prefetch/meta.yml#L44

Originally posted by @ewels in https://github.com/nf-core/modules/issues/6645#issuecomment-2352128611