Snakemake update

[johnne]

This pull request makes several improvements and cleanups to the Snakemake tutorial documentation and example workflow. The main changes include removing unnecessary instructional print statements, updating URLs for sample downloads, cleaning up and reorganizing rule definitions for clarity and consistency, and improving formatting and explanations throughout the tutorial.

Key changes:

Documentation and instructional cleanups:

• Removed suggestions to add print statements for debugging wildcards and the corresponding instructions to remove them later, streamlining the tutorial flow. [1] [2] [3]
• Removed certain callout boxes to reduce clutter and make the tutorial more concise.

Workflow and code improvements:

• Updated sample download URLs from figshare.scilifelab.se to ndownloader.figshare.com for consistency and reliability, both in the Snakefile and configuration file. [1] [2]
• Removed unnecessary docstrings from rule definitions and reorganized the placement of input, output, and log directives for better readability and consistency across rules. [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17]
• Modified shell commands in rules to remove unnecessary user-agent flags from curl and to use updated parameter passing. [1] [2] [3]

Formatting and explanatory improvements:

• Improved line wrapping and paragraph formatting for better readability, especially in explanations of Snakemake features like shadow directories and wildcard expansion. [1] [2] [3]

These changes collectively make the tutorial more concise, up-to-date, and easier to follow for new users.