Hi @musfira ,
the tool used for the mapping step has recently been updated and I think this is not yet reflected in the tutorial. The long story is that the tool now accepts only collection input, not two separate datasets anymore, but for the purpose of following the tutorial you can just switch back to an older version of the tool as explained here: Bowtie2 on galaxy europe platform does not work - #5 by wm75 . You should then be able to proceed just as described.