Ali Khan

Great! I have a basic set of recipes in order to get the snakebids conda package built, just need to revisit it: https://github.com/akhanf/conda-snakebids-builds And it looks like all our other...

closing this since the particular use case is fixed now in pybids (ie ignoring .zarr directories)

I haven't tried it out, but there is now built-in jinja templating with snakemake: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#template-rendering-integration So the rule-based option would be pretty trivial. I agree having this in the cookiecutter...

That's a great idea! Yes we can put something together for the bids app repo, I am thinking one that just replicates what the existing bids app example does would...

Took an initial stab at it here: https://github.com/akhanf/example-snakebids Let me know what you guys think, and PRs are welcome of course

I updated the example app again, @tkkuehn @kaitj @pvandyken please have a look when you can. FYI I also made the simpler example (not bids app) workflow we talked about,...

That would be super, thanks Remi! Actually the PRs on that repo are merged so you can still work to your strengths and add any issues there! 😉

I like that approach, would fit nicely with the way I am running apps right now. To be clear, it could be used to rerun an app that has since...

With readthedocs it just builds from the docs requirements.

That's the tradeoff with easy development of workflow scripts in snakemake -- instead of trying to make the snakemake scripts callable from outside, I think the better approach for established...