Pandemics (2023 Oct)

Learning Nextflow using Single-Cell RNA-Sequencing Data

By Sebastian Kreisel, Lucas Florin & Jordan Lay (Published on May 24, 2024)

The aim of this project was to explore Nextflow [1], a commonly used bioinformatics tool. Nextflow orchestrates various other bioinformatics tools and produces repeatable workflows that may include containerized programs, cloud resources and caching. It is widely used in bioinformatics to build pipelines for analyzing sequencing data. The main application of Nextflow is the analysis of sequence data. We limited our exploration to RNA sequence data.

Our team came to this project with different backgrounds and skill sets. Sebastian and Lucas have a background in software engineering, data analysis and machine learning, Jordan has a biology background.In the first four weeks our project cohort worked through the Nextflow basic training program. This tutorial included building a very simple RNA sequencing pipeline with Nextflow. In the following two weeks Sebastian, Lucas and Jordan worked together on setting up and running a single-cell RNA-sequencing (scRNA-seq) pipeline for data collected from COVID-19 patients and published in Science Immunology [2].

We hope that the experience we gained through this project will be helpful in our academic career or for job applications in biotech industry, ultimately working towards biosecurity as a long-term career goal. To give an example, at the time of writing Ginkgo Bioworks [3] has an open position with experience in Nextflow as a requirement.

You can read the full project submission here.


  1. Paolo Di Tommaso et al. “Nextflow enables reproducible computational workflows”. In: Nature biotechnology 35.4 (2017), pp. 316–319.

  2. Jeong Seok Lee et al. “Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19”. In: Science immunology 5.49 (2020), eabd1554.

  3. Open Position – Ginkgo Bioworks – Bioinformatics Engineer III. listings/?gh_jid=4116226007. Accessed: 2024-02-17.

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