Recommendations:

• Use threads and resources properly
• Avoid huge single jobs
• Break workflows into modular rules
• Use conda or containers
• Use –dry-run before submitting large workflows
• Store configuration in YAML files

Common HPC Pitfalls with Workflow Managers

Examples:

• Requesting too many cores per rule
• Forgetting to specify memory
• Submitting thousands of tiny jobs
• Running Snakemake or Nextflow themselves on a login node

Key Takeaways with Workflow Managers

Snakemake & Nextflow provide:

• Reproducible pipelines
• Automatic dependency tracking
• Scalable HPC execution
• Environment management
• Workflow portability