snakefmt

Format Snakefile

$ snakefmt [Snakefile]

$ snakefmt --check [Snakefile]

$ snakefmt [workflow/]

$ snakefmt --diff [Snakefile]

$ snakefmt -l [100] [Snakefile]

$ cat [Snakefile] | snakefmt -

$ snakefmt -v [Snakefile]

snakefmt [--check] [--diff] [-l length] [options] files

snakefmt is an opinionated code formatter for Snakemake workflow files. It enforces a consistent style across Snakefiles and associated rules files, handling both standard Python syntax and Snakemake-specific extensions like rule, checkpoint, and module blocks.
The formatter is built on top of Python's black formatter, using the same default line length of 88 characters and similar formatting philosophy. It understands Snakemake's domain-specific syntax, correctly formatting rule parameters like input, output, params, and shell while preserving semantic meaning.
Check mode (--check) verifies formatting without modifying files, returning a non-zero exit code if changes are needed, which is useful for CI pipelines. Diff mode (--diff) previews the exact changes that would be made before committing to them.

--check

Check only, no changes.

Show changes.

Max line length.

Verbose output.

Include pattern.

Exclude pattern.

Read from stdin.

Snakemake-specific. May need adjustment for complex rules. Black-based formatting style.

snakefmt was created for the Snakemake workflow management system. It brings consistent formatting to bioinformatics pipelines.

snakemake(1), black(1), python(1)