How to identify genes from a genome assembly of C. Elegans?
You don't want BLAST here, or at least not regular BLASTn. A better method would be to use tBLASTn to map the known C. Elegans proteins to the translated genome. However, I would recommend using a slightly more sophisticated approach:

Collect fasta sequences of all known C. Elegans proteins (amino acid sequences, not nucleotide). This should be easy enough to do on WormBase. For example, the protein sequences for C. elegans strain VC2010, assembly PRJEB28388, can be found here: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/species/c_elegans/PRJEB28388/c_elegans.PRJEB28388.WS279.protein.fa.gz

Use a tool that can model introns and exons to map a protein into a genome. I haven't worked in this field in more than 10 years now, so it is very likely that there are other programs around today, but back in the day, I would do this using either exonerate or genewise. With exonerate, the command would be:
exonerate -m protein2genome -n 1 -t assembly.fasta -q allproteins.pep &gt; out



That will give you a list of best-hits for each of your input proteins and should accurately map the protein to the genome. Once you have that, you can extract the matches and start comparing.