Snakemake Language Support

Provides basic language support for Snakemake files (Snakefile, *.smk). Feedback, suggestions, and contributions are very welcome!

This project has been started by Peter Alping, and can be considered a fork of this repository.

Features

• Syntax definitions based on Python, with added Snakemake keywords
• Language rules based on Python
• Snippets

Example

Example taken from Snakemake documentation.

Supported Syntax

[Keywords and Functions](src/keywords.yaml)

• Configurations

  • these keywords specified in the format <keyword>: <values> within a snakefile.
  • for example:

    configfile: "config.yaml"
    
    onsuccess:
        print("All jobs finished successfully.")
    
    include: "workflow/report.smk"

• Rules and Modules

  • rule <rulename>: defines a rule with its parameters, followed by an indented body
  • [checkpoint <rulename>:] is a special type of rule that allows dynamic determination of workflow steps based on its output.
  • module <modulename>: declares a module repository from which rules can be imported
  • subworkflow is now deprecated

• Rule Parameters

  • Used in rule and checkpoint blocks to define inputs, outputs, and other settings.
  • You can re- used rule <rulename> as <newrulename> ... with different parameters, but you cannot change the way it runs, including:
    • run
    • shell
    • script
    • notebook
    • wrapper
    • template_engine
    • cwl

• Module Parameters:

  • Define where and how to import rules when using the module directive.
  • Example:

    module remote:
        snakefile: "local.smk"
        config: {**config, "remote": True}
        replace_prefix: "local/"
        prefix: "remote/"
    
    use rule * from remote as remote_*

• Global Variables:

  • The following classes are available without explicit import from the snakemake module:
    • Path
    • WorkflowError
  • Important variables used across workflows include:
    • snakemake
    • rules: reference rules via rules.<rulename>
    • workflow
    • checkpoints: access outputs of checkpoint rules
    • storage
    • access
    • scatter and gather

• Job Parameters:

  • These parameters are only available during job execution and should be used within run or shell blocks
    • input
    • output
    • params
    • wildcards
    • threads
    • resources
    • log
  • config is a dict that contains the configuration values and can be accessed everywhere

• Functions:

  • Various built-in helper functions are available for use without needing to import them

TODO

• recognize files provided as string after include:, conda, snakefile, and allow quickly jumping to them
• add bash-color to docstring in shell: block
• Indentation rules (really tricky for some reason)
• Recognize wildcard constraints inside string substitutions: "{sample,[A-Za-z0-9]+}"

Snakemake Support for other Editors

• Vim