Are you sure this is necessary? biocontainers should have added a trimmomatic executable to the $PATH, as that's what they usually do. It should be unneeded to invoke the full path here.

I was trying to work out access to the executable, but without cd'ing to the exact directory I wasn't able to get it to work

That's likely because it's being called with java. There is a utility wrapper script at /usr/local/bin/trimmomatic that provides the functionality and is on PATH. So you should be able to swap java -jar trimmomatic.jar with trimmomatic and remove the directory change.

Thank you @adthrasher! Hadn't noticed that distinction