OpenSkillIndex← back to search
claude-codescience

Babysitter snakemake-workflow-manager

Snakemake workflow management skill for rule-based pipeline execution

install
source · Clone the upstream repo
git clone https://github.com/a5c-ai/babysitter
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/bioinformatics/skills/snakemake-workflow-manager" ~/.claude/skills/a5c-ai-babysitter-snakemake-workflow-manager && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/snakemake-workflow-manager/SKILL.md
tags
#workflow#snakemake#reproducibility#bioinformatics#pipeline#automation
source content

Snakemake Workflow Manager Skill

Purpose

Enable Snakemake workflow management for rule-based pipeline execution.

Capabilities

  • DAG-based workflow execution
  • Cluster/cloud execution
  • Conda environment management
  • Checkpointing and resume
  • Benchmark collection
  • Report generation

Usage Guidelines

  • Define rules with clear inputs/outputs
  • Use Conda for environment management
  • Configure for cluster execution
  • Enable checkpointing for large workflows
  • Collect benchmarks for optimization
  • Generate workflow reports

Dependencies

  • Snakemake
  • Conda
  • Bioconda

Process Integration

  • Reproducible Research Workflow (reproducible-research)
  • Analysis Pipeline Validation (pipeline-validation)