In Snakemake, workflows are specified as Snakefiles. Inspired by GNU Make, a Snakefile contains rules that denote how to create output files from input files. Dependencies between rules are handled implicitly, by matching filenames of input files against output files. Thereby wildcards can be used to write general rules.
The Snakefile syntax obeys the following grammar, given in extended Backus-Naur form (EBNF)
snakemake = statement | rule | include | workdir rule = "rule" (identifier | "") ":" ruleparams include = "include:" stringliteral workdir = "workdir:" stringliteral ni = NEWLINE INDENT ruleparams = [ni input] [ni output] [ni params] [ni message] [ni threads] [ni (run | shell)] NEWLINE snakemake input = "input" ":" parameter_list output = "output" ":" parameter_list params = "params" ":" parameter_list log = "log" ":" parameter_list benchmark = "benchmark" ":" statement cache = "cache" ":" bool message = "message" ":" stringliteral threads = "threads" ":" integer resources = "resources" ":" parameter_list version = "version" ":" statement run = "run" ":" ni statement shell = "shell" ":" stringliteral
while all not defined non-terminals map to their Python equivalents.
Depend on a Minimum Snakemake Version¶
From Snakemake 3.2 on, if your workflow depends on a minimum Snakemake version, you can easily ensure that at least this version is installed via
from snakemake.utils import min_version min_version("3.2")
given that your minimum required version of Snakemake is 3.2. The statement will raise a WorkflowError (and therefore abort the workflow execution) if the version is not met.
Snakemake (>=5.11) comes with a code quality checker (a so called linter), that analyzes your workflow and highlights issues that should be solved in order to follow best practices, achieve maximum readability, and reproducibility. The linter can be invoked with
given that a
workflow/Snakefile is accessible from your working directory.
It is highly recommended to run the linter before publishing any workflow, asking questions on Stack Overflow or filing issues on Github.