Snakemake: referencing output beyond parent in recursive sub-workflow scenario

Question

I have a workflow with three layers of subworkflows, where wfA is a subworkflow of wfB is a subworkflow of wfC.

When executing wfC, both wfA and wfB get executed correctly if needed.

In wfC I can do wfB("some/output"), but I can't do wfA("some/output"), since it would give a "name 'wfA' is not defined" error.

Is this something that's supported? Any other way around it?

score 2 · Accepted Answer · answered Aug 17 '17 at 07:47

2

Currently, this is not supported and I see no way around except flattening the hierarchy.

answered Aug 17 '17 at 07:47

Johannes Köster

Right, yes, I have a sort of "hybrid" hierarchy. Not ideal (since one needs to manually enforce the execution order) but it works. – Tomas Di Domenico Aug 18 '17 at 09:21

1 Answers1