Giving pVACseq output files unique names

[evelyn-schmidt]

Making sure that all output file names from pVACseq contain identifiers that make them unique from one another would be really helpful during the review process. At the moment if these files are being viewed at the same time or uploaded they require manual renaming to make their distinctions separate.

So instead of
.../pVACseq/mhc_i/5120_19_Tumor_FF.all_epitopes.aggregated.tsv .../pVACseq/mhc_ii/5120_19_Tumor_FF.all_epitopes.aggregated.tsv

It would be
.../pVACseq/mhc_i/5120_19_Tumor_FF.all_epitopes.aggregated.classI.tsv .../pVACseq/mhc_ii/5120_19_Tumor_FF.all_epitopes.aggregated.classII.tsv

A further enhancement would be to make sure that all output files have the case name in them to make sure they are distinct from other runs/cases.