Now have automatic updating of read lengths and reference panel depending on analysis mode
Can find the correct smk pipeline to run automatically
Have made the cns pipeline more modular, so should be on the way to slotting in post-read trimming
Challenge
Best way to mask the correct locations for primer sites depending on protocol, without messing up alignment
Tried to soft mask the sites at the start and end of the mapping alignment for VP1, and to do that 30 bases in from start and end of alignment for WG- but this mangled the alignment for some reason, and gave rise to weird variant results.
Challenge