NeatSeq-Flow’s Module and Workflow Repository

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Documentation Status

NeatSeq-Flow is a lightweight software for efficient execution of high throughput sequencing workflows. See the NeatSeq-Flow documentation at

NeatSeq-Flow is available for download on github.

Following is a list of modules included in this repository.


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

  1. download the repository:

  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 documentation for the main NeatSeq-Flow package at


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.


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