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claude-codescience

Babysitter nextflow-pipeline-executor

Nextflow workflow management skill for reproducible bioinformatics pipelines

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 "$T/library/specializations/domains/science/bioinformatics/skills/nextflow-pipeline-executor" ~/.claude/skills/a5c-ai-babysitter-nextflow-pipeline-executor && rm -rf "$T"
manifest: library/specializations/domains/science/bioinformatics/skills/nextflow-pipeline-executor/SKILL.md
tags
#workflow#nextflow#bioinformatics#reproducibility#containerization
source content

Nextflow Pipeline Executor Skill

Purpose

Provide Nextflow workflow management for reproducible bioinformatics pipelines.

Capabilities

  • DSL2 workflow execution
  • Container integration (Docker/Singularity)
  • Cloud execution (AWS, GCP, Azure)
  • Pipeline parameterization
  • Resume and caching
  • Execution reports and timelines

Usage Guidelines

  • Use DSL2 for modular pipelines
  • Containerize processes for reproducibility
  • Configure for target execution environment
  • Enable resume for fault tolerance
  • Generate execution reports
  • Document pipeline versions

Dependencies

  • Nextflow
  • nf-core
  • Snakemake

Process Integration

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