# My Troubles with nf-core

A blog post about my frustrations and experiences working with the popular nf-core framework in bioinformatics.

## Introduction

As a biologist who has worked extensively with different software tools for analyzing biological data, I have always been impressed by the power and flexibility of the nf-core platform. However, after several years of using and contributing to this excellent toolset, I have come to realize that there are some fundamental issues with the way nf-core is currently structured and maintained.

## Background

NF-core (short for Next-Generation Sequencing Core) is an open-source framework developed by the Broad Institute of MIT and Harvard that provides a comprehensive set of tools for analyzing high-throughput sequencing data. The platform has been widely adopted in the scientific community due to its ease of use, scalability, and flexibility.

## My Experience with nf-core

As a bioinformatician, I have worked extensively with various pipelines built on top of nf-core, including the popular SNEAK pipeline for variant discovery. While nf-core has provided me with a reliable platform for analyzing large datasets, I have consistently encountered issues with its organization, documentation, and community support.

## Issues with Organization

One of my biggest frustrations with nf-core is the lack of clear organization within its repository. The project’s main directory contains an overwhelming number of subdirectories, each representing a different tool or pipeline. This makes it difficult to navigate the codebase and understand how the various tools interact with each other.

## Documentation and Community Support

NF-core has excellent documentation, but in my experience, this documentation is often incomplete or outdated. I have encountered several instances where I was unable to find relevant information about a particular tool or pipeline, leading me to waste hours of time searching for answers online.

Moreover, the nf-core community has historically been relatively inactive, with few developers actively contributing to the project over the years. This lack of support and resources makes it challenging to address issues or implement new features.

## Impact on Bioinformaticians

Despite my personal frustrations with nf-core, I firmly believe that this platform remains an essential tool for bioinformaticians around the world. The benefits of using nf-core include its scalability, flexibility, and ease of use. However, I strongly advocate for a renewed focus on addressing the issues mentioned above to ensure that this platform continues to meet the evolving needs of the scientific community.

## Conclusion

As someone who has dedicated their career to bioinformatics, it pains me to see a project like nf-core hindered by its own structure and lack of support. While I will continue to contribute to and use nf-core in my work, I hope that this article will serve as a catalyst for the developers and community leaders involved in maintaining this platform to prioritize much-needed changes.

## Recommendations

To address the issues I have raised above, I recommend the following steps:

- Reorganize the repository structure to make it more logical and easier to navigate.
- Update and expand the documentation to include comprehensive information on all tools and pipelines within nf-core.
- Foster a more active community by engaging with bioinformaticians through regular forums, workshops, or online events.

By addressing these issues, I am confident that nf-core can continue to thrive as a powerful tool for analyzing high-throughput sequencing data.