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Edmund Miller

Formatting Snakemake using snakefmt in Emacs using Apheleia

/ 3 min read

Dooms Emacs recently switched to using Apheleia as it’s default formatter, thanks to a huge effort from Ellis Kenyő to refactor the format module.

I’ve been writing a bit of Snakemake for the Applied Genomics Course that I teach in the Summer. The last time that I wrote much Snakemake(circa 2020), snakefmt didn’t exist yet. It follows the design and specifications of Black.

Aside: Packaging up snakefmt with Nix

I’ve chosen the path less traveled, and use NixOS. Meaning I’ve sworn off using Conda, global pip installs, and other small conviences in the already narrow path that is using linux as a desktop environment.

While Snakemake itself is packaged up in nixpkgs, snakefmt hasn’t made it to the most magical repo on GitHub yet.

Recently though I found a handy tool for quickly generating package derivations, nix-init.

Terminal window
nix run github:nix-community/nix-init -- --url

It pulls in the version and the dependencies, ✨Automagically✨.

python3.pkgs.buildPythonApplication rec {
pname = "snakefmt";
version = "0.10.2";
pyproject = true;
src = fetchFromGitHub {
owner = "snakemake";
repo = "snakefmt";
rev = "v${version}";
hash = "sha256-Sp48yedUiL8NCF7WF9QdvaOGocPXIBZ5bXXj7r4RVIM=";
nativeBuildInputs = [
propagatedBuildInputs = with python3.pkgs; [
pythonImportsCheck = ["snakefmt"];
meta = with lib; {
description = "The uncompromising Snakemake code formatter";
homepage = "";
changelog = "${src.rev}/";
license =;
maintainers = with maintainers; [edmundmiller];
mainProgram = "snakefmt";


There are tons of code formatters out there. There’s usually multiple for popular languages. Everyone’s got an opinion on what style to use.

Apheleia aims to remove specific Emacs packages for formatters. It’s goal is to have one interface to run all of your formatters from Emacs.

running a code formatter on save suffers from the following two problems:

  1. It takes some time (e.g. around 200ms for Black on an empty file), which makes the editor feel less responsive.
  2. It invariably moves your cursor (point) somewhere unexpected if the changes made by the code formatter are too close to point’s position.

Apheleia is an Emacs package which solves both of these problems comprehensively for all languages, allowing you to say goodbye to language-specific packages such as Blacken and prettier-js.

The main opinion everyone shares is that a good code formatter should be fast, and therefore you should be able to forget about it.

It’s really simple to configure formatters in Doom Emacs.

(set-formatter! 'snakefmt '("snakefmt" "-") :modes '(snakemake-mode))

The set-formatter! macro takes:

  1. The name you want to give the formatter snakefmt
  2. The command you want ran (--quiet is used here often) snakefmt -
  3. The modes you want associated with the formatter snakemake-mode

Another example for Alejandra for Nix.

;;; :lang nix
(set-formatter! 'alejandra '("alejandra" "--quiet") :modes '(nix-mode))

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