Update default reference path (alt-aware reference) in template config

[tnyamaguchi]

          @yashpatel6 @j2salmingo I suggest that we work on this task before implementing #234 as it's relatively straightforward and it will provide important insights on /scratch usage. Also, unrelated but we might want to create a new release soon after we update the default reference path (alt-aware reference) in the template config.

Originally posted by @tyamaguchi-ucla in #278 (comment)

[yashpatel6]

Agreed, I'm also updating the default in the metapipeline template config as that's separate from the align-DNA template. @j2salmingo can handle it here