NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows.

Additional NeatSeq-Flow modules

This repository includes modules that extend the functionality of NeatSeq-Flow to additional programs.

Over time, additional modules will be added to the repo to extend NeatSeq-Flow to new and existing programs not yet included.

Installing and executing NeatSeq-Flow

Please follow the instructions in the main NeatSeq-Flow repo.

Using the additional modules repo

1. Download and unzip this repo to a location of your choice.
2. Create a pipeline parameter file using the directions specified here.
3. Add the path to the module_path global parameter. (If you have more than one path, you can pass several to the module_path as a YAML list).
4. Execute NeatSeq-Flow as described here. Don't forget to pass your pipeline parameter file with the -p option.

Adding your own modules to NeatSeq-Flow

You can easily write your own modules, to include currently unsupported programs in NeatSeq-Flow. Adding these modules is done by adding the local path to the module_path line in the parameter file.

Alternatively, you can add your program without creating a module, using the Generic module. This enables quickly adding steps to your pipeline without needing to create modules. However, you will need to define the input and output locations in the parameter file. See the documentation for the generic module.

Contact

Please contact Menachem Sklarz at: sklarz@bgu.ac.il

Citation

When using NeatSeq-Flow, please cite as follows:

Sklarz, M.Y., et al. (2017) NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows. bioRxiv doi: 10.1101/173005