running diffexp on examples/nema.yaml doesn't do anything?

[ctb]

I first ran:

./run_eelpond examples/nema.yaml

which completed successfully, and then ran:

./run_eelpond examples/nema.yaml diffexp

which did... nothing?

The output did include

        deseq2: /mnt/research/ged/ctb/eelpond/nema_out/diffexp
                     for explanation of this step, see: https://dib-lab.github.i
o/eelpond/deseq2

but that directory doesn't exist.

[ctb]

I tried

./run_eelpond examples/nema.yaml quantify diffexp

and it yelled at me about missing input files, so then I tried

./run_eelpond examples/nema.yaml assemble quantify diffexp

which seems to be appropriately making use of the preexisting assembly. Yay!

[ctb]

I think the desired behavior is to produce better error messages and suggestions. Doing this in a modular way is key - I don't think run_eelpond should have this error checking in it directly! Maybe we could put in something that when a particular rule file is included, it has some high level checks that it runs, or maybe that should be connected in some way to the higher level workflows mentioned in pipeline_defaults.yaml?

[ctb]

assemble quantify diffexp worked!