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Snakemake 8+ workflow development with Slurm executor plugin for HPC clusters. Covers profiles, resource directives, job debugging, NFS gotchas, and multiple software environment approaches.
Verified all skill elements by running 11 independent test workflows on a real Slurm cluster (Snakemake 9.17.3, executor plugin 2.5.4). Fixes: - Remove `runtime` from profile examples — does not propagate to Slurm's --time flag via default-resources/set-resources (only works when set directly in rule resources: blocks) Additions: - Automatic Partition Selection via partitions.yaml — recommended approach that also avoids numeric partition summing bug in group jobs - Intermediate File Cleanup section (temp(), protected()) — critical for shared HPC storage management - Shadow Rules section — isolated execution with automatic cleanup - Partition summing bug warning in Grouping Jobs section - New entries in failure patterns table and Critical Rules
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Summary
slurm-snakemakeplugin for Snakemake 8+ workflow development on Slurm HPC clusters--cluster), profiles, resource directives, job debugging, NFS latency handling, job groupingTest plan
claude --plugin-dir ./plugins/slurm-snakemake/slurm-snakemake:slurm-snakemakePR Review Checklist
Per https://github.com/whitehead/claude-plugins#pr-review-checklist: