snakefmt

snakefmt documentation

Version in Mega-Linter: 0.4.4
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See How to configure snakefmt rules
- If custom .snakefmt.toml config file is not found, .snakefmt.toml will be used

Configuration in Mega-Linter

Enable snakefmt by adding SNAKEMAKE_SNAKEFMT in ENABLE_LINTERS variable
Disable snakefmt by adding SNAKEMAKE_SNAKEFMT in DISABLE_LINTERS variable

Enable auto-fixes by adding SNAKEMAKE_SNAKEFMT in APPLY_FIXES variable

Variable	Description	Default value
SNAKEMAKE_SNAKEFMT_ARGUMENTS	User custom arguments to add in linter CLI call Ex: `-s --foo "bar"`
SNAKEMAKE_SNAKEFMT_FILTER_REGEX_INCLUDE	Custom regex including filter Ex: `(src\\|lib)`	Include every file
SNAKEMAKE_SNAKEFMT_FILTER_REGEX_EXCLUDE	Custom regex excluding filter Ex: `(test\\|examples)`	Exclude no file
SNAKEMAKE_SNAKEFMT_CLI_LINT_MODE	Override default CLI lint mode - `file`: Calls the linter for each file - `list_of_files`: Call the linter with the list of files as argument - `project`: Call the linter from the root of the project	`{linter.cli_lint_mode}`
SNAKEMAKE_SNAKEFMT_FILE_EXTENSIONS	Allowed file extensions. `"*"` matches any extension, `""` matches empty extension. Empty list excludes all files Ex: `[".py", ""]`	`[".smk"]`
SNAKEMAKE_SNAKEFMT_FILE_NAMES_REGEX	File name regex filters. Regular expression list for filtering files by their base names using regex full match. Empty list includes all files Ex: `["Dockerfile(-.+)?", "Jenkinsfile"]`	`["Snakefile"]`
SNAKEMAKE_SNAKEFMT_PRE_COMMANDS	List of bash commands to run before the linter	None
SNAKEMAKE_SNAKEFMT_POST_COMMANDS	List of bash commands to run after the linter	None
SNAKEMAKE_SNAKEFMT_CONFIG_FILE	snakefmt configuration file name Use `LINTER_DEFAULT` to let the linter find it	`.snakefmt.toml`
SNAKEMAKE_SNAKEFMT_RULES_PATH	Path where to find linter configuration file	Workspace folder, then Mega-Linter default rules
SNAKEMAKE_SNAKEFMT_DISABLE_ERRORS	Run linter but consider errors as warnings	`true`
SNAKEMAKE_SNAKEFMT_DISABLE_ERRORS_IF_LESS_THAN	Maximum number of errors allowed	`0`

Mega-Linter Flavours

This linter is available in the following flavours

Flavor	Description	Embedded linters
all	Default Mega-Linter Flavor	94
dart	Optimized for DART based projects	41
documentation	Mega-Linter for documentation projects	40
dotnet	Optimized for C, C++, C# or VB based projects	47
go	Optimized for GO based projects	42
java	Optimized for JAVA based projects	42
javascript	Optimized for JAVASCRIPT or TYPESCRIPT based projects	49
php	Optimized for PHP based projects	44
python	Optimized for PYTHON based projects	49
ruby	Optimized for RUBY based projects	41
rust	Optimized for RUST based projects	41
salesforce	Optimized for Salesforce based projects	43
scala	Optimized for SCALA based projects	41
swift	Optimized for SWIFT based projects	41
terraform	Optimized for TERRAFORM based projects	45

Behind the scenes

How are identified applicable files

File extensions: .smk
File names (regex): Snakefile

How the linting is performed

snakefmt is called one time by identified file

Example calls

snakefmt --check --compact-diff Snakefile

snakefmt --check --compact-diff --config .snakefmt.toml Snakefile

snakefmt --config .snakefmt.toml Snakefile

Help content

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 logger.

Installation on mega-linter Docker image

PIP packages (Python):
- snakefmt

Example success log

Results of snakefmt linter (version 0.2.4)
See documentation on https://nvuillam.github.io/mega-linter/descriptors/snakemake_snakefmt/
-----------------------------------------------

[SUCCESS] .automation/test/snakemake/snakemake_good_1.smk
    =====> Diff for .automation/test/snakemake/snakemake_good_1.smk <=====


    [INFO] All 1 file(s) would be left unchanged 🎉

Example error log

Results of snakefmt linter (version 0.2.4)
See documentation on https://nvuillam.github.io/mega-linter/descriptors/snakemake_snakefmt/
-----------------------------------------------

[ERROR] .automation/test/snakemake/snakemake_bad_1.smk
    =====> Diff for .automation/test/snakemake/snakemake_bad_1.smk <=====

    --- original
    +++ new
    @@ -1,10 +1,11 @@
     rule all:
         input:
    -        file1='result.txt',
    +        file1="result.txt",
    +

     rule simulation:
         output:
    -        file1="result.txt"
    +        file1="result.txt",
         shell:
             """
             touch {output}

    [INFO] 1 file(s) would be changed 😬