Bioinformatics engineer working on Nextflow & nf-core
Hello — I'm Edmund Miller, a Bioinformatics Engineer at Seqera and nf-core core team member. I earned a PhD in Molecular and Cell Biology (functional genomics) at UT Dallas. I got into bioinformatics after realizing I didn't have golden hands at the bench during undergrad.
That taste of programming got me dabbling in writing smart contracts and web apps. Through my research experience I acquired a taste for processing data with reproducible, high-throughput workflows.
I saw the light in March 2020 when I found nf-core and tossed aside the reptilian workflow manager for Nextflow. I love a good crossover episode of technologies and I'm always trying to push the envelope.
Start here
If you're here for bioinformatics tooling, reproducible workflows, or Emacs-shaped developer ergonomics, these are the best next steps.
Posts
Richard Hamming on choosing important problems, doing first-class work, and making the most of the one life we have.
How I turned a Jupyter notebook into a full-fledged Python package for UpSet plots
nf-core containers automation: how it'll all work behind the curtain
What Seqera Containers is and why we want to move to it.
Install Pixi with conda-forge and Bioconda, add Nextflow, define tasks, and import an existing environment.yml on a cluster or local machine.
Wire snakefmt into Doom Emacs Apheleia (set-formatter!), plus a Nix package for snakefmt when it is missing from nixpkgs.
How I hack on Nextflow scripts using Emacs
Privacy-friendly personal-site analytics: GoatCounter vs Umami vs Plausible vs Fathom — self-hostable options without creepy tracking.
Astro in Doom Emacs with astro-ts-mode, Tree-sitter, lsp-mode, Apheleia + Prettier, and Tailwind CSS IntelliSense — without broken template formatting.
Set up age.el and rage in Doom Emacs, configure SSH key paths, and save org-journal entries as encrypted .org.age files when EasyPG hangs.