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  <updated>2025-03-27T15:19:13-05:00</updated>

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  <title>My Troubles with nf-core</title>
  <published>2024-09-01T00:00:00&#43;00:00</published>
  <updated>2024-09-01T00:00:00&#43;00:00</updated>
  <author>
      <name>Thomas A. Christensen II</name>
      <uri>http://localhost:1313/people/thomas-a.-christensen-ii/</uri>
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  <category term="bioinformatics" />
  <category term="nf-core" />
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  <summary type="text">
       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.

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    &lt;!-- raw HTML omitted --&gt;&#xA;&lt;!-- raw HTML omitted --&gt;&#xA;&lt;h1 id=&#34;my-troubles-with-nf-core&#34;&gt;My Troubles with nf-core&lt;/h1&gt;&#xA;&lt;p&gt;A blog post about my frustrations and experiences working with the popular&#xA;nf-core framework in bioinformatics.&lt;/p&gt;&#xA;&lt;h2 id=&#34;introduction&#34;&gt;Introduction&lt;/h2&gt;&#xA;&lt;p&gt;As a biologist who has worked extensively with different software tools for&#xA;analyzing biological data, I have always been impressed by the power and&#xA;flexibility of the nf-core platform. However, after several years of using and&#xA;contributing to this excellent toolset, I have come to realize that there are&#xA;some fundamental issues with the way nf-core is currently structured and&#xA;maintained.&lt;/p&gt;&#xA;&lt;h2 id=&#34;background&#34;&gt;Background&lt;/h2&gt;&#xA;&lt;p&gt;NF-core (short for Next-Generation Sequencing Core) is an open-source framework&#xA;developed by the Broad Institute of MIT and Harvard that provides a&#xA;comprehensive set of tools for analyzing high-throughput sequencing data. The&#xA;platform has been widely adopted in the scientific community due to its ease of&#xA;use, scalability, and flexibility.&lt;/p&gt;&#xA;&lt;h2 id=&#34;my-experience-with-nf-core&#34;&gt;My Experience with nf-core&lt;/h2&gt;&#xA;&lt;p&gt;As a bioinformatician, I have worked extensively with various pipelines built on&#xA;top of nf-core, including the popular&#xA;&lt;a&#xA;  href=&#34;https://github.com/broadinstitute/SNEAK&#34;&gt;SNEAK&lt;/a&gt; pipeline for variant discovery.&#xA;While nf-core has provided me with a reliable platform for analyzing large&#xA;datasets, I have consistently encountered issues with its organization,&#xA;documentation, and community support.&lt;/p&gt;&#xA;&lt;h2 id=&#34;issues-with-organization&#34;&gt;Issues with Organization&lt;/h2&gt;&#xA;&lt;p&gt;One of my biggest frustrations with nf-core is the lack of clear organization&#xA;within its repository. The project&amp;rsquo;s main directory contains an overwhelming&#xA;number of subdirectories, each representing a different tool or pipeline. This&#xA;makes it difficult to navigate the codebase and understand how the various tools&#xA;interact with each other.&lt;/p&gt;&#xA;&lt;h2 id=&#34;documentation-and-community-support&#34;&gt;Documentation and Community Support&lt;/h2&gt;&#xA;&lt;p&gt;NF-core has excellent documentation, but in my experience, this documentation is&#xA;often incomplete or outdated. I have encountered several instances where I was&#xA;unable to find relevant information about a particular tool or pipeline, leading&#xA;me to waste hours of time searching for answers online.&lt;/p&gt;&#xA;&lt;p&gt;Moreover, the nf-core community has historically been relatively inactive, with&#xA;few developers actively contributing to the project over the years. This lack of&#xA;support and resources makes it challenging to address issues or implement new&#xA;features.&lt;/p&gt;&#xA;&lt;h2 id=&#34;impact-on-bioinformaticians&#34;&gt;Impact on Bioinformaticians&lt;/h2&gt;&#xA;&lt;p&gt;Despite my personal frustrations with nf-core, I firmly believe that this&#xA;platform remains an essential tool for bioinformaticians around the world. The&#xA;benefits of using nf-core include its scalability, flexibility, and ease of use.&#xA;However, I strongly advocate for a renewed focus on addressing the issues&#xA;mentioned above to ensure that this platform continues to meet the evolving&#xA;needs of the scientific community.&lt;/p&gt;&#xA;&lt;h2 id=&#34;conclusion&#34;&gt;Conclusion&lt;/h2&gt;&#xA;&lt;p&gt;As someone who has dedicated their career to bioinformatics, it pains me to see&#xA;a project like nf-core hindered by its own structure and lack of support. While&#xA;I will continue to contribute to and use nf-core in my work, I hope that this&#xA;article will serve as a catalyst for the developers and community leaders&#xA;involved in maintaining this platform to prioritize much-needed changes.&lt;/p&gt;&#xA;&lt;h2 id=&#34;recommendations&#34;&gt;Recommendations&lt;/h2&gt;&#xA;&lt;p&gt;To address the issues I have raised above, I recommend the following steps:&lt;/p&gt;&#xA;&lt;ul&gt;&#xA;&lt;li&gt;Reorganize the repository structure to make it more logical and easier to&#xA;navigate.&lt;/li&gt;&#xA;&lt;li&gt;Update and expand the documentation to include comprehensive information on&#xA;all tools and pipelines within nf-core.&lt;/li&gt;&#xA;&lt;li&gt;Foster a more active community by engaging with bioinformaticians through&#xA;regular forums, workshops, or online events.&lt;/li&gt;&#xA;&lt;/ul&gt;&#xA;&lt;p&gt;By addressing these issues, I am confident that nf-core can continue to thrive&#xA;as a powerful tool for analyzing high-throughput sequencing data.&lt;/p&gt;&#xA;
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