Qiita Plugins

The Qiita plugins allow to extend the functionality of Qiita by adding new data formats or new processing pipelines. The list of officially supported plugins can be found in the Qiita Spots GitHub organization.

Overview of Qiita’s plugin system

Qiita’s plugin system has been designed to increase Qiita’s flexibility to process -omics datasets, while allowing plugin developers to create plugins using the programming language that they are more comfortable with.

In order to achieve this flexibility, Qiita represents the different -omics datasets using Artifacts where an Artifact is a file or set of files that conceptually represents a dataset. Note that Qiita is not Artifact or Pipeline aware, thus it is up to the Qiita Plugins to define what an Artifact is and which methods can be applied to it. With the goal of reducing community development effort, there are two different types of plugins: Qiita Type Plugins and Qiita Plugins.

The Qiita Type Plugins define new artifact types. These plugins must define two operations: Validate and Generate HTML summary.

Given the artifact type, the prep information (see, Prepare information files) and the user-uploaded files, the Validate operation decides if the user-uploaded files conform Artifact of the new type. If the files do not create a valid artifact, the plugin should try to fix the files using the given information, but only if the files can be deterministically fixed and not generate ambiguous results.

The Generate HTML summary generates a single HTML file with an overview of the contents of the artifact. Note that the summary HTML is a single file and should contain all information about all the files attached to that Artifact.

The Qiita Plugins define pipelines and methods that can be applied to the Artifacts. They don’t need to import directly from the Qiita Type Plugins that is defining the Artifact type, but they will need such plugin to be present in the system, otherwise Qiita will not accept Artifacts of the given type. There are no limitation on the Qiita Plugin methods: they can take one or more input artifacts and generate one or more output Artifacts. Besides defining individual methods, the Qiita Plugins also have the ability to define default workflows, where a workflow is a set of methods connected by their input/outputs to perform a bigger task over one or a set of artifacts.

Plugins run in independent software environments from Qiita (i.e. different PATH and PYTHONPATH environment variables, among others), allowing them to have any dependency stack as well as being able to be written in any language. Qiita only needs a single script to start the plugin, which should conform with this call:


The plugin will then use QIITA’s REST API to gather the needed information to run the given job JOB_ID and to send back the results of the job.

Developing a Qiita Plugin

To facilitate the development of Qiita Plugins, we have created a library that simplifies the usage of Qiita’s REST api: Qiita Client. This library encapsulates the authentication of the plugin when using Qiita’s REST api, as well as providing convenient functions to retrieve the job information, update the job status and complete the job. This library should not require any further development from the plugin developer and it should be ready to use.

We have also created two Cookiecutter templates to create plugins:

These templates are designed to set up new Qiita Type Plugins and Qiita Plugins, respectively. They take care of the initial repository layout, the initial plugin set up and the initial communication with Qiita. Please, refer to the README file in each of the templates for instructions on how to fill these templates to implement your plugins.