The options for blast and lulu should probably be off by default, rather than on. Thus, instead of skipping blast on --skip-blast, we blast on the existence of a --blast-db option and instead of skipping on --skip-lulu, we'll do lulu on --lulu.
I think that --skip-primer-match is still probably appropriate since it's an edge case, but maybe we'll change the name to --no-pcr or something.
The options for blast and lulu should probably be off by default, rather than on. Thus, instead of skipping blast on
--skip-blast, we blast on the existence of a--blast-dboption and instead of skipping on--skip-lulu, we'll do lulu on--lulu.I think that
--skip-primer-matchis still probably appropriate since it's an edge case, but maybe we'll change the name to--no-pcror something.