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SNAKEMAKE

Linters

Linter Additional
snakemake
SNAKEMAKE_LINT
GitHub stars
snakefmt
SNAKEMAKE_SNAKEFMT
GitHub stars formatter

Linted files

  • File extensions:
    • .smk
  • File names:
    • Snakefile

Configuration in MegaLinter

Variable Description Default value
SNAKEMAKE_PRE_COMMANDS List of bash commands to run before the linters None
SNAKEMAKE_POST_COMMANDS List of bash commands to run after the linters None
SNAKEMAKE_FILTER_REGEX_INCLUDE Custom regex including filter
SNAKEMAKE_FILTER_REGEX_EXCLUDE Custom regex excluding filter