Search code examples
workflowsnakemakemodularization

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

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?

Solution

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