customize conditional deletions for specific competing pipeline flags

[afrendeiro]

I was running two pipelines in the same directory/sample and when one finished, it noticed the flag of the other (even though it is named diferently) and did not clean its conditional files. Is this the intended behavior - shouldn't a pipeline only care about its inputs/outputs/flags? Sorry if this is indeed a bug and was fixed in a later version (running 0.6.0 now), but couldn't find a previous issue or docs on this.

[nsheff]

actually this is intended behavior...

I did it this way because two different pipelines could in theory use some of the same intermediate files. If one is still running, you don't want to clean intermediate files from the other.

you just need to run looper clean I guess in this scenario; there's no way for it to just know whether two pipelines do or do not use intermediate files from one another...

[nsheff]

probably this would be better to put as an option to PipelineManager so the author could state which pipelines to consider, or whether to consider none at all, when deciding whether to auto-clean...