Update Snakemake from v6 to newer v8

[jaamarks]

Current version in GwasQcPipeline

$ snakemake --version
6.15.5

Latest version: v8.20.5

Migration

• https://snakemake.readthedocs.io/en/stable/getting_started/migration.html
• https://snakemake.readthedocs.io/en/v7.0.0/

Note that upgrading has some breaking changes, for example support for the subworkflow directive has been removed. So we will need to keep this in mind.

Reasons to keep Snakemake up-to-date

Keeping Snakemake up-to-date is important for several reasons:

• Bug Fixes: Avoid issues and ensure a smoother workflow.
• Compatibility: Maintain compatibility with other tools and libraries.
• Security: Protect your system from vulnerabilities.
• Performance Improvements: Experience faster and more efficient workflows.
• Community Support: Access the latest resources and support.
• New Features: Benefit from the latest enhancements and functionality.

In our case, since we are using Snakemake version 6.15.5 and the latest version is 8.20.5, it would be beneficial to review the release notes for the newer version to understand the changes and improvements made, and consider upgrading to take advantage of those enhancements.

[rajwanir]

I second this migration. Quite a bit of new syntax functions I see in the newer v8 that would make developmental work easier. However, I didn't realize that subworkflow support was retired in favour of modules.