API vs. CLI stability

Hey all,
I’m a bioinformatician at a systems biology lab and I’m writing a QIIME2-based code for one of the students.
I’ve started about a year ago (q2-2017.9) and have ported the code to q2-2018.8 since there were some changes between versions.

I prefer using the API, but I stick to bash and CLI since I’m operating under the assumption that the high-level CLI is more robust than the API and therefore will perform better in terms of back-compatibility; am I right?


Hi there @omera.WIS!

No, q2cli and the Artifact API are both just interfaces to the same framework and plugins ---- the goal of QIIME 2 is to allow for multiple interfaces to provide interaction to common plugins.

What exactly are you doing, are you developing a plugin? Or maybe this is a workflow of some kind? We can provide some more guidance if we have a little more context. But, to answer your question, no, there is no difference between the two interfaces in terms of backwards compatibility or support, they are just two different “views” of the same system.

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