tophat2_sample_template.vtf: changed the naming convention used for bed files (copy target) to <rpt>.<type>.bed (e.g. 12345_2#13.deletions.bed). This should now match the convention expected by the iRODS archiver in data_handling.
vtfp.pl: when multiple instances of a subst_param use the same name in a hash map, the repeated instances now have their attribute names recorded in walk()