Add outputs and adjust split size

[scanon]

This adds several missing outputs from the structural annotation portion
of the pipeline (crt, genemark, prodigal, trnascan, rfam). These
outputs were being used in the full outputs but the individual GFF files
weren't being propagated as outputs.

This also adjusts the split size to 100M. Testing found that the memory
requirements and run-times are still pretty reasonable at this split
size. This significantly improves throughput since most of the steps
run in the same amount of time for the larger split size.

[aclum]

@scanon okay if I close this PR as obsolete? The block size of 100 is already in the master branch and reconciling missing output files was addressed in December 2022.