Simple nextflow example?

janzheng commented 7 months ago

This is so cool, and makes it possible for citizen scientists to run their own bioinformatics (without access to clusters!)

Could you show a couple of examples of running a vanilla hello world Nextflow pipelines?

hgbrian commented 7 months ago

Hey Jan, I don't use nextflow so i'd have to think about this. Part of the reason I like modal is to avoid the extra dependency of workflow managers!

There are two ways it could work:

modal run a python script that calls nextflow (all nextflow steps in one container) This is just e.g., run("nextflow run minimap2.nf") in a modal function
replace the shell commands in nextflow with modal run... This is just e.g., replacing "minimap2 a.fna b.fna" with "modal run modal_minimap2.py a.fna b.fna" in minimap2.nf (plus making sure the files appear in the right place.)

I think either could make sense but it depends on what the goal is I guess?

hgbrian commented 4 days ago

Hey Jan, I added modal_nextflow_example.py at last.

Hope that helps!

hgbrian / biomodals