Version Compatibility

Reference examples tested with: Snakemake 8.0+, Python 3.11+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Note: Snakemake 8 (Jan 2024) removed --cluster, --drmaa, and the *RemoteProvider classes from core and moved them to pip-installable EXECUTOR plugins (--executor slurm, package snakemake-executor-plugin-slurm) and STORAGE plugins (storage.s3(...), snakemake-storage-plugin-s3). --use-conda/--use-singularity became --software-deployment-method / --sdm conda apptainer. A Snakemake 7 command line does not run unchanged on 8/9. Run snakemake --version FIRST and branch all execution guidance on 7 vs 8/9.

Snakemake Workflows

"Build a reproducible bioinformatics pipeline with Snakemake" -> Declare each step as a rule that says "a file matching THIS output pattern is produced FROM those inputs", let the engine resolve the DAG backward from requested targets, fan out over samples with wildcards, and pin the software environment so the result reproduces next year.

• Python: Snakefile rule/checkpoint blocks with expand(), wildcards, config, resources, and conda:/container: (Snakemake)

The governing principle: Snakemake is pull/goal-oriented - it builds a STATIC DAG backward from requested target files