Is there any good reason that a module which takes a VCF shouldn’t optionally take an index file? I guess it potentially adds some staging overhead, but I feel that some tools silently accept VCFs without an index but then just generate one themselves if it doesn’t exist - or perhaps worse fall back to unindexed access. Is there logic in doing a sweep of modules for those which take a VCF without also allowing an index?

Myself and @Louis Le Nézet did a similar exercise for everything samtools a while back, so I don't see any issues

For most modules it makes sense to add it. I think one of the exceptions here might be sorting modules?