Jonathan Manning
Senior Bioinformatics Engineer
Bearsden, Scotland, United Kingdom
Summary
🤩
Rockstar🎓
Top SchoolJonathan Manning is a Senior Bioinformatics Engineer with over a decade of hands-on experience building reproducible, scalable genomics workflows across HPC and cloud platforms. At Seqera he helps customers deploy Nextflow-based pipelines and drives adoption through training, demos and community engagement, while also contributing core enhancements to Nextflow's Kubernetes integration. His background spans academic and commercial roles (EMBL-EBI, Healx, Edinburgh Genomics) where he developed pipelines for RNA‑seq, single-cell, methylation, ATAC and variant calling and introduced SOPs and CI-driven practices. An active nf-core maintainer, he leads the Differential Abundance workflow and contributes modules and tooling used widely by the community. He pairs practical infrastructure-as-code skills (Terraform, Kubernetes, AWS/GCP/OpenStack) with user-facing work such as R Shiny apps to make complex analyses accessible. Based in Bearsden, Scotland, he blends deep domain knowledge with a focus on sustainability and reproducibility in bioinformatics engineering.
10 years of coding experience
21 years of employment as a software developer
PhD Bioinformatics, PhD Bioinformatics at University of DundeeMRes Bioinformatics, MRes Bioinformatics at University of Leeds
Github Skills (29)
go-modules10
kubernetes10
docker10
package-management10
groovy10
dsl10
testing10
r10
bash10
conda10
workflow-engine10
kernel-module10
dockers10
nextflow10
pipeline-framework10
Programming languages (15)
Github contributions (5)
nf-core/modules
Oct 2022 - Jan 2023
Repository to host tool-specific module files for the Nextflow DSL2 community!
Role in this project:
Full-stack Developer
Full-stack DeveloperContributions:422 reviews, 29 commits, 291 PRs in 3 months
Contributions summary:Jonathan made significant contributions to the `nf-core/modules` repository, focused on creating and enhancing Nextflow DSL2 modules. Their work involved the addition of new modules, such as `gtf2featureannotation`, `deseq2`, and components for `shinyngs`, demonstrating a focus on bioinformatics pipeline development. The commits also included code improvements like linting fixes, documentation updates, and handling various input file formats (CSV/TSV), solidifying their involvement in module functionality and maintainability. Additionally, the user addressed versioning and containerization for the modules.
nf-corehostnextflow-dsl2nextflowdsl2
bioconda/bioconda-recipes
Aug 2018 - Jan 2023
Conda recipes for the bioconda channel.
Role in this project:Automation Engineer
Automation EngineerContributions:120 reviews, 102 commits, 213 PRs in 4 years 5 months
Contributions summary:Jonathan primarily focused on automating and scripting the build and testing processes within the Bioconda recipes repository. Their contributions include adding and modifying build scripts (build.sh files) for various bioinformatics tools and wrapper scripts. A significant portion of their work involves integrating testing frameworks like Bats and making modifications to existing scripts.
recipescondabiocondabioinformaticspackage-management
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