Keeping up with Snakemake changes

[tbooth]

From @jdblischak

Snakemake 7.8 introduced a few big changes. Your tutorial is based on version 5.32.2. You have a box in the episode "How Snakemake plans what jobs to run" that notes these changes in behavior. However, given that Snakemake 7.8 was released in May 2022, at some point it will make more sense for the episode to describe the 7.8+ behavior, and then only mention the <7.8 behavior in a box.

Another cool Snakemake feature that I really like is the ability to freeze the conda environments used in each rule. This would be worth mentioning in the lesson on conda integration

[tbooth]

Agreed, but as noted elsewhere the (#36) the 7.8 behaviour has some issues and may change again.

I'm hoping I can get the lesson approved for inclusion in the Lab in the current format before chasing the newest Snakemake, as the upgrade will entail re-testing everything and updating a lot of sample outputs where errors and wording have changed.

[tbooth]

The current version of the lesson now uses Snakemake 8.5.3. This is a major update to Snakemake itself, refactoring a bunch of features into optional modules. Hopefully it represents the Snakemake core, which is what this material mostly covers, becoming more stable over time. This will reduce the burden of maintenance to "chase" new Snakemake features in this material.