Hisat2 : which option should mention for strand specific library read
--fr/--rf/--ff should rarely be set, since they refer to the relative orientation of reads and basically everything these days is --fr. Mate-pairs were --rf, but you don't see those much any more.

--rna-strandedness is a very different option, since it sets how reads are expected to align against genes. Most stranded protocols in use these days follow the dUTP-method, where read #2 in a pair has the same orientation as the transcript from which it arose. So either R or RF would typically be appropriate, unless the library is unstranded. In practice, I expect this is more useful if you plan to run stringTie downstream, since then the XS auxiliary tag is set appropriately.