Sorry this PR looks really messy because I reorganized a few things. This adds evaluation and annotation steps:
"map" the reads back to the final transcriptome with salmon
predict orfs & run busco using dammit. Dammit does more than just transdecoder by itself, and produces a cleaner set of files (along with CDS and amino acids, all with nice names). Because of this, I also removed transdecoder steps.
Sorry this PR looks really messy because I reorganized a few things. This adds evaluation and annotation steps: