This is part of a series of workflows to annotate a genome, tagged with `TSI-annotation`. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows. The workflows can be run in this order: * Repeat masking * RNAseq QC and read trimming * Find transcripts * Combine transcripts * Extract transcripts * Convert formats * Fgenesh annotation **** About this workflow: * Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta * Runs many steps to convert outputs into the formats required for Fgenesh - .pro, .dat and .cdna