This repository provides formatting for Snakemake files. It follows the design and specifications of Black.

⚠️WARNING⚠️: snakefmt modifies files in-place by default, thus we strongly recommend ensuring your files are under version control before doing any formatting. You can also pipe the file in from stdin, which will print it to the screen, or use the --diff or --check options. See Usage for more details.

• Install
  • PyPi
  • Conda
  • Containers
  • Local
• Example File
• Usage
  • Basic Usage
  • Full Usage
• Configuration
• Integration
  • Editor Integration
  • Version Control Integration
  • Github Actions
• Plug Us
• Changes
• Contributing
• Cite

pip install snakefmt

conda install -c bioconda snakefmt

As snakefmt has a Conda recipe, there is a matching image built for each version by Biocontainers.

In the following examples, all tags (<tag>) can be found here.

$ docker run -it "quay.io/biocontainers/snakefmt:<tag>" snakefmt --help

$ singularity exec"docker://quay.io/biocontainers/snakefmt:<tag>" snakefmt --help

These instructions include installing uv.

# install uv curl -LsSf https://astral.sh/uv/install.sh | sh git clone https://github.com/snakemake/snakefmt &&cd snakefmt # install snakefmt in a new environment make install # you can now run snakefmt with uv run snakefmt --help

Input

fromsnakemake.utilsimportmin_versionmin_version("5.14.0") configfile: "config.yaml"# snakemake keywords are treated like classes i.e. 2 newlinesSAMPLES= ['s1', 's2'] # strings are normalisedCONDITIONS= ["a", "b", "longlonglonglonglonglonglonglonglonglonglonglonglonglonglonglong"] # long lines are wrappedinclude: "rules/foo.smk"# 2 newlinesruleall: input: "data/results.txt"# newlines after keywords enforced and trailing commarulegets_separated_by_two_newlines: input: files=expand("long/string/to/data/files/gets_broken_by_black/{sample}.{condition}",sample=SAMPLES, condition=CONDITIONS) ifTrue: rulecan_be_inside_python_code: input: "parameters", "get_indented"threads: 4# Numeric params stay unindentedparams: key_val="PEP8_formatted"run: print("weirdly_spaced_string_gets_respaced")

Output

fromsnakemake.utilsimportmin_versionmin_version("5.14.0") configfile: "config.yaml"# snakemake keywords are treated like classes i.e. 2 newlinesSAMPLES= ["s1", "s2"] # strings are normalisedCONDITIONS= [ "a", "b", "longlonglonglonglonglonglonglonglonglonglonglonglonglonglonglong", ] # long lines are wrappedinclude: "rules/foo.smk"# 2 newlinesruleall: input: "data/results.txt", # newlines after keywords enforced and trailing commarulegets_separated_by_two_newlines: input: files=expand( "long/string/to/data/files/gets_broken_by_black/{sample}.{condition}", sample=SAMPLES, condition=CONDITIONS, ), ifTrue: rulecan_be_inside_python_code: input: "parameters", "get_indented", threads: 4# Numeric params stay unindentedparams: key_val="PEP8_formatted", run: print("weirdly_spaced_string_gets_respaced")

Format a single Snakefile.

snakefmt Snakefile

Format all Snakefiles within a directory.

snakefmt workflows/

Format a file but write the output to stdout.

snakefmt - < Snakefile

$ snakefmt --help Usage: snakefmt [OPTIONS] [SRC]... The uncompromising Snakemake code formatter. SRC specifies directories and files to format. Directories will be searched for file names that conform to the include/exclude patterns provided. Files are modified in-place by default; use diff, check, or `snakefmt - < Snakefile` to avoid this. Options: -l, --line-length INT Lines longer than INT will be wrapped. [default: 88] --check Don't write the files back, just return the status. Return code 0 means nothing would change. Return code 1 means some files would be reformatted. Return code 123 means there was an error. -d, --diff Don't write the files back, just output a diff for each file to stdout. --compact-diff Same as --diff but only shows lines that would change plus a few lines of context. --include PATTERN A regular expression that matches files and directories that should be included on recursive searches. An empty value means all files are included regardless of the name. Use forward slashes for directories on all platforms (Windows, too). Exclusions are calculated first, inclusions later. [default: (\.smk$|^Snakefile)] --exclude PATTERN A regular expression that matches files and directories that should be excluded on recursive searches. An empty value means no paths are excluded. Use forward slashes for directories on all platforms (Windows, too). Exclusions are calculated first, inclusions later. [default: (\.snakemake|\.eg gs|\.git|\.hg|\.mypy_cache|\.nox|\.tox|\.venv|\.svn|_ build|buck-out|build|dist)] -c, --config PATH Read configuration from PATH. By default, will try to read from `./pyproject.toml` -h, --help Show this message and exit. -V, --version Show the version and exit. -v, --verbose Turns on debug-level logging. 

snakefmt is able to read project-specific default values for its command line options from a pyproject.toml file. In addition, it will also load any black configurations you have in the same file.

By default, snakefmt will search in the parent directories of the formatted file(s) for a file called pyproject.toml and use any configuration there. If your configuration file is located somewhere else or called something different, specify it using --config.

Any options you pass on the command line will take precedence over default values in the configuration file.

pyproject.toml

[tool.snakefmt] line_length = 90include = '\.smk$|^Snakefile|\.py$'# snakefmt passes these options on to black [tool.black] skip_string_normalization = true

In this example we increase the --line-length value and also include python (*.py) files for formatting - this effectively runs black on them. snakefmt will also pass on the [tool.black] settings, internally, to black.

For instructions on how to integrate snakefmt into your editor of choice, refer to docs/editor_integration.md

snakefmt supports pre-commit, a framework for managing git pre-commit hooks. Using this framework you can run snakefmt whenever you commit a Snakefile or *.smk file. Pre-commit automatically creates an isolated virtual environment with snakefmt and will stop the commit if snakefmt would modify the file. You then review, stage, and re-commit these changes. Pre-commit is especially useful if you don't have access to a CI/CD system like GitHub actions.

To do so, create the file .pre-commit-config.yaml in the root of your project directory with the following:

repos: - repo: https://github.com/snakemake/snakefmtrev: v0.10.2 # Replace by any tag/version ≥v0.6.0 : https://github.com/snakemake/snakefmt/releaseshooks: - id: snakefmt

Then install pre-commit and initialize the pre-commit hooks by running pre-commit install (Note you need to run this step once per clone of your repository). Additional pre-commit hooks can be found here.

GitHub Actions in combination with super-linter allows you to automatically run snakefmt on all Snakefiles in your repository e.g. whenever you push a new commit.

To do so, create the file .github/workflows/linter.yml in your repository:

--- name: Linton: # yamllint disable-line rule:truthypush: nullpull_request: nullpermissions: {}jobs: build: name: Lintruns-on: ubuntu-latestpermissions: contents: readpackages: read# To report GitHub Actions status checksstatuses: writesteps: - name: Checkout codeuses: actions/checkout@v5with: # super-linter needs the full git history to get the# list of files that changed across commitsfetch-depth: 0persist-credentials: false - name: Lint Code Baseuses: super-linter/[email protected]env: VALIDATE_ALL_CODEBASE: falseDEFAULT_BRANCH: mainGITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }}VALIDATE_SNAKEMAKE_SNAKEFMT: true

Additional configuration parameters can be specified by creating .github/linters/.snakefmt.toml:

[tool.black] skip_string_normalization = true

For more information check the super-linter readme.

If you can't get enough of badges, then feel free to show others you're using snakefmt in your project.

[![Code style: snakefmt](https://img.shields.io/badge/code%20style-snakefmt-000000.svg)](https://github.com/snakemake/snakefmt)

.. image:: https://img.shields.io/badge/code%20style-snakefmt-000000.svg:target:https://github.com/snakemake/snakefmt

See CHANGELOG.md.

See CONTRIBUTING.md.

@article{snakemake2021, doi = {10.12688/f1000research.29032.2}, url = {https://doi.org/10.12688/f1000research.29032.2}, year = {2021}, month = apr, publisher = {F1000 Research Ltd}, volume = {10}, pages = {33}, author = {Felix M\"{o}lder and Kim Philipp Jablonski and Brice Letcher and Michael B. Hall and Christopher H. Tomkins-Tinch and Vanessa Sochat and Jan Forster and Soohyun Lee and Sven O. Twardziok and Alexander Kanitz and Andreas Wilm and Manuel Holtgrewe and Sven Rahmann and Sven Nahnsen and Johannes K\"{o}ster}, title = {Sustainable data analysis with Snakemake}, journal = {F1000Research} }