Official docs suggest .smk as file extension of modules. Editors recognize only 'Snakefile 'and '.smk' for formatting. Suggest changing current file: simulation.snake, n_t.snake, and dfe.snake to simulation.smk, n_t.smk, and dfe.smk.
"In addition to the central Snakefile, rules can be stored in a modular way, using the optional subfolder workflow/rules. Such modules should end with .smk, the recommended file extension of Snakemake."
https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html
Official docs suggest .smk as file extension of modules. Editors recognize only 'Snakefile 'and '.smk' for formatting. Suggest changing current file: simulation.snake, n_t.snake, and dfe.snake to simulation.smk, n_t.smk, and dfe.smk.
"In addition to the central Snakefile, rules can be stored in a modular way, using the optional subfolder workflow/rules. Such modules should end with .smk, the recommended file extension of Snakemake."
https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html