NeatSeq-Flow’s Module and Workflow Repository

Documentation Status

This repository contains modules and workflows for use with NeatSeq-Flow. To install, follow the instructions in installation section bellow.

See also the main NeatSeq-Flow website.

Installing and using the modules

NeatSeq-Flow is available for download on github.


In order to include these modules in your workflow, please:

  1. download the repository:

    curl -LO
  2. Alternatively, clone the repository:

    git clone
  3. add the following line in the Global_params section of your workflow parameter file:

    module_path: /path/to/location/of/modules/repository

See more about definition of workflow parameter files in the NeatSeq-Flow User Manual at the Parameter file definition section.


Some of the modules in this package are included in the main NeatSeq-Flow repository. These are indicated below with a *.


NeatSeq-Flow enables users to program their own modules and workflows. You are encouraged to share your modules with the public by adding it to this repository. In order to do so, please fork the repository on github, upload your new module or workflow and open a pull request.