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Quansight-Labs / nextstrain.org

The Nextstrain website
https://nextstrain.org
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Write "customizing a build" doc page and contribute it back #1

Open rgommers opened 4 years ago

rgommers commented 4 years ago

https://nextstrain.org/docs/bioinformatics/customizing-a-build

jerowe commented 4 years ago

We will need to coordinate with NextStrain on this somewhat.

Right now they have a very particular build system that relies on docker and snakemake.

From what I can tell the nextstrain build looks at a Snakefile (snakemake workflow definition), possibly spins up a docker container, and I think snakemake also acts as a wrapper around conda as well. I've used it quite a bit in the past, but not recently.

My feeling is that the next strain will want to maintain that. It IS probably a nice idea to allow for groups to contribute workflows as Snakefiles.

But we could still contribute plenty of docs on how to modify an analysis by modifying the Zika Tutorial and adding in variables for the different files. I'll find someone who can point me towards an actual COVID19 set and we can write up some docs for that.