This has been my solution as well. There’s little that feels as good as running `make -B report` and watching the whole thing be rebuilt from scratch.
How do you manage encapsulating each step, and passing data between them?
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I don't do it well. See
https://github.com/4kbt/ReplicableAnalysis
and
https://github.com/4kbt/PlateWash
as examples. The former is smaller/less complicated. The latter was my thesis work -- more complicated and (unfortunately) abuses recursive calls to Make.
Would that be easier with rake than with make?