if I remove the `assembly/` output directory, shouldn't eelpond rerun everything after that too?

[ctb]

right now if you remove the assembly directory, and then run default, eelpond shrugs and does nothing because all of its targets are available. this seems wrong overall.

[bluegenes]

Hmm. Agreed, not intended functionality.

During the refactor, I started splitting rules into include and targets categories to simplify the dag, as snakemake back-calculates previous targets as needed. I think this issue is an argument for going back to calculating explicit targets for all rules.

[ctb]

sure, let's explore reasons. want to understand whole thing before more wholesale changes, and maybe get some more tests in there!