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