support the execution of a bunch of notebooks upon completion

dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system

https://dib-lab.github.io/elvers/

Other

28 stars 3 forks source link

support the execution of a bunch of notebooks upon completion #52

Open ctb opened 5 years ago

ctb commented 5 years ago

it would be great to have both standard and customized execution of notebooks after a run!

not sure how to make 'em conditional on the workflow run, but that can be a detail we figure out later.

I think Jupyter Notebooks and RMarkdown notebooks would be the primary things to support here. Would need to parameterize the notebooks e.g. via papermill.

ctb commented 5 years ago

would also be nice to develop some notebooks to summarize and/or compare two or more runs. think a la mmetsp gigascience paper

ctb commented 5 years ago

brainstorming a bit more --

provide default summary notebooks that get executed at the end of each step
have goal be HTML output
link those into a master 'run list of notebooks' in the top level directory, or something
also supply meta notebooks that take in a bunch of runs & maybe associated config files => do summarization/comparison

I'll be developing some of these for my GGG 201(b) course this term, so we'll see how that goes!