I was doing a general review on the docs motivated by recent issues https://github.com/nf-core/mag/issues/983, https://github.com/nf-core/mag/issues/985 and found out that

spades_downstreaminput

right now is a dead parameter. Its functionality got removed in the big refactor to add read only assembly: https://github.com/nf-core/mag/pull/718. Should we add this back or drop the parameter? I personally has never used contigs to do the binning, I always use the scaffolds, so not sure how big is the impact, but I guess the safest option is to add back the functionality. Opinions?

@James Fellows Yates wrote this PR: https://github.com/nf-core/mag/pull/979 Not sure why we didn't merge it?

Oh, I didn't see that PR, my bad 😅

Because I completely forgot that you reviewed it! Sorry @Jim Downie!