Not sure if this addresses your problem, but generally you transfer files and do the work in the same command. So:
$ ls my_files | parallel --sshlogin foo --transfer my_job {}
will both transfer my_files and run my_job on them.
Not sure if this addresses your problem, but generally you transfer files and do the work in the same command. So:
$ ls my_files | parallel --sshlogin foo --transfer my_job {}
will both transfer my_files and run my_job on them.