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

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system

https://dib-lab.github.io/elvers/

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if I remove the `assembly/` output directory, shouldn't eelpond rerun everything after that too? #77

Open ctb opened 5 years ago

ctb commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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