Consolidate tasks+workflows definitions where reasonable

[johnmaruska]

As of this writing, almost all WDLs are just ports from CWL as close to 1:1 as possible. WDL lets us combine tasks into single files.

We'd like to consolidate pieces to group like pieces, group pieces that all rely on the same tool (e.g. samtools or picard), and we'd also like to combine common tasks for optimization reasons wherever reasonable. Identify places this can be done, do them as needed. This is probably an ongoing effort and not a single task.