Sorry, I can't really point you toward any online courses for learning bioinformatics... I kind of learned it on the job. I know they exist, though. But, there are some threads here, and also some at Biostars (in the "
tutorial" category) that reference various online resources.
As for adapters.fa, you can either copy it to the same directory, or set the absolute or relative path as the argument for "ref=".