How to use the command snakefmt (with examples)
Snakefmt is a command line tool that allows users to format Snakemake files, which are used for creating and managing data workflows. This tool helps to ensure that Snakemake files are properly formatted and easy to read and understand.
Use case 1: Format a specific Snakefile
Code:
snakefmt path/to/snakefile
Motivation: This use case is useful when you want to format a specific Snakemake file without affecting other files in the directory. This can help improve code readability and maintainability.
Explanation:
snakefmt: The command to format Snakemake files.path/to/snakefile: The path to the specific Snakefile that you want to format.
Example output:
10: rule all:
11: input:
12: "output.txt"
Use case 2: Format all Snakefiles recursively in a specific directory
Code:
snakefmt path/to/directory
Motivation: This use case is useful when you have multiple Snakemake files in a directory, and you want to format all of them at once. This can help ensure consistency in code formatting across multiple files.
Explanation:
snakefmt: The command to format Snakemake files.path/to/directory: The path to the directory containing the Snakemake files. The command will recursively search for Snakemake files in this directory and format them.
Example output:
Formatting file: path/to/directory/Snakefile1
Formatting file: path/to/directory/Snakefile2
Formatting file: path/to/directory/subdir/Snakefile3
Use case 3: Format a file using a specific configuration file
Code:
snakefmt --config path/to/config.toml path/to/snakefile
Motivation: This use case is useful when you want to format a Snakemake file using a specific configuration file. Configuration files can specify formatting rules and options, allowing you to customize the formatting according to your needs.
Explanation:
snakefmt: The command to format Snakemake files.--config path/to/config.toml: Specifies the path to the configuration file that contains the formatting rules and options.path/to/snakefile: The path to the Snakemake file that you want to format.
Example output:
Formatting file: path/to/snakefile
Using configuration file: path/to/config.toml
Use case 4: Format a file using a specific maximum line length
Code:
snakefmt --line-length 100 path/to/snakefile
Motivation: This use case is useful when you want to specify a maximum line length for the formatted Snakemake file. This can help ensure that lines in the file do not exceed a certain length, making the code more readable.
Explanation:
snakefmt: The command to format Snakemake files.--line-length 100: Specifies the maximum line length for the formatted Snakemake file (in this example, 100 characters).path/to/snakefile: The path to the Snakemake file that you want to format.
Example output:
Formatting file: path/to/snakefile
Using maximum line length: 100
Use case 5: Display the changes that would be performed without performing them (dry-run)
Code:
snakefmt --diff path/to/snakefile
Motivation: This use case is useful when you want to see the changes that would be made to a Snakemake file without actually modifying the file. This can help you understand the formatting changes that would be applied.
Explanation:
snakefmt: The command to format Snakemake files.--diff: Specifies that the command should only display the formatting changes without actually modifying the file.path/to/snakefile: The path to the Snakemake file that you want to format.
Example output:
--- path/to/snakefile
+++ path/to/snakefile.formatted
@@ -10,3 +10,4 @@
input:
"input.txt"
+ "output.txt"
Conclusion:
Snakefmt is a powerful tool for formatting Snakemake files. With its various options, you can easily format individual files, multiple files in a directory, and even customize the formatting using configuration files. It also provides a dry-run option to preview the formatting changes before applying them. By using snakefmt, you can ensure that your Snakemake files are consistently formatted and easy to read and understand.
