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snakemake-workflows

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Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.

When to use

• Authoring reproducible bioinformatics pipelines
• Wiring rules by output-file pattern
• Using wildcards and expand() for sample fan-out
• Adding checkpoints for runtime-unknown outputs
• Escalating memory on retry for OOM-killed jobs
• Porting Snakemake 7 commands to Snakemake 8+ executor plugins
• Deciding between Snakemake and Nextflow
• Diagnosing job reruns under mtime-plus-provenance triggers

When not to use

• Nextflow channel/dataflow authoring
• Imperative order rule wiring

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